METHODS OF IDENTIFYING RISK OF BEVACIZUMAB-INDUCED PROTEINURIA AND HYPERTENSION

Information

  • Patent Application
  • 20210395833
  • Publication Number
    20210395833
  • Date Filed
    May 06, 2021
    3 years ago
  • Date Published
    December 23, 2021
    2 years ago
Abstract
The disclosure relates to methods of identifying subjects at risk of developing bevacizumab-induced toxicities such as proteinuria and/or hypertension involving measuring nucleic acid or gene mutations in a sample obtained from the subject.
Description
FIELD

The present disclosure relates to methods of identifying patients at risk of developing bevacizumab-induced toxicities. In particular, the disclosure relates methods of identifying patients at risk of developing bevacizumab-induced proteinuria and/or hypertension involving measuring nucleic acid mutations in a sample obtained from the patient.


BACKGROUND

Bevacizumab is a recombinant humanized monoclonal antibody that targets vascular endothelial growth factor (VEGF), inhibiting its binding to its receptors VEGFR1 and VEGFR2. It was approved by the U.S. Food and Drug Administration (FDA) in 2004 and by the European Medicines Agency in 2005 for the treatment of metastatic colorectal cancer. The FDA has also approved its use for the treatment of advanced non-squamous lung cancer, metastatic renal cell carcinoma, recurrent glioblastoma, advanced cervical cancer and platinum-resistant ovarian cancer.1 Bevacizumab antitumor efficacy relies on its inhibition of the VEGF-signaling pathway involved in endothelial survival, vascular permeability and therefore angiogenesis.2


Despite the demonstrated efficacy of bevacizumab in combination with other therapies, patients frequently experience toxicity that limits the duration of therapy with bevacizumab and the efficacy of the regimen. The most frequent toxicities are hypertension and proteinuria, with a prevalence that varies in different studies (proteinuria 21%-41%, hypertension 3%-43).3-5 Although hypertension and proteinuria are usually asymptomatic, they can be occasionally life threatening.4,5


The underlying mechanisms of how bevacizumab induces hypertension and proteinuria are not well understood, but they are postulated to involve nitric oxide (NO) inhibition and increases in peripheral vascular resistance, renal dysfunction and glomerular damage by inhibition of VEGF produced by podocytes. It is not clear whether the occurrence of proteinuria shares the same mechanism responsible for hypertension, or whether the kidney damage is a secondary effect.6


Currently, there are no validated biomarkers to predict bevacizumab-induced hypertension or proteinuria. Previous genetic studies of bevacizumab-induced hypertension focused on a few single-nucleotide polymorphisms (SNPs) in genes of the VEGF pathway.7-14


Despite the reported associations, none of the studies generated robust enough evidence to use these markers in the clinic, mostly because the biomarker signal was not concordant across multiple studies.16 Accordingly, what is needed are robust biomarkers and methods of identifying patients at risk of bevacizumab-induced hypertension and/or proteinuria that can be reproduced in different studies.


SUMMARY

Provided herein are methods for determining risk and/or treating a subject.


In one aspect, provided herein is a method including detecting a mutation in one or more nucleic acids in a sample obtained from a subject who is undergoing therapy or is a candidate for therapy with a VEGF-pathway inhibitor.


In another aspect, provided herein is a method of predicting the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in a subject, including detecting a mutation in one or more nucleic acids in a sample obtained from the subject who is undergoing therapy or is a candidate for therapy with a VEGF-pathway inhibitor, and determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject based upon the presence or absence of the mutation in the one or more nucleic acids in the sample.


In another aspect, provided herein is a method of treating a subject, comprising detecting a mutation in one or more nucleic acids in a sample obtained from a subject who is undergoing therapy or is a candidate for therapy with a VEGF-pathway inhibitor; determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject based upon the presence or absence of the mutation in the one or more nucleic acids in the sample; and modulating therapy with a VEGF-pathway inhibitor and/or providing the subject with one or more supportive therapies based upon the determined risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject.


In another aspect, provided herein is a method for treating or preventing a VEGF pathway inhibitor-induced toxicity in a subject in need of treatment with a VEGF-pathway inhibitor, the method comprising identifying the subject as having a genetic mutation that confers a risk of developing the VEGF pathway inhibitor-induced toxicity, and treating the subject with a supportive and/or prophylactic therapy for the toxicity in addition to the VEGF-pathway inhibitor.


In another aspect, provided herein is a method for treating a subject having a disease or disorder, wherein the disease or disorder is indicated for treatment with a VEGF pathway inhibitor, the method comprising identifying the subject as having a genetic mutation that confers a risk of developing a VEGF pathway inhibitor-induced toxicity, treating the subject with a supportive and/or prophylactic therapy to prevent or reduce the toxicity, and treating the subject with the VEGF-pathway inhibitor.


In embodiments, the mutation is in a gene selected from the group consisting of KCNAB1, DNAH5, TRIO, RIPK4, IL17F, ASPH, TTMA, EPB41L3 and SLC25A24. In embodiments, the genetic mutation is a SNP. In embodiments, the genetic mutation is a mutation that lowers expression of KCNAB1 relative to wild type.


In embodiments, the SNP is selected from the group consisting of rs339947, rs12482855, rs13135230, rs2350620, rs11662763, rs6770663, rs408130, rs418173, rs12482855, rs444904, and rs427554. In embodiments, the base identified at rs339947 is an adenine, the base identified at rs12482855 is an adenine, the base identified at rs11662763 is an adenine, the base identified at rs408130 is an adenine, the base identified at rs418173 is an adenine, the base identified at rs12482855 is an adenine, the base identified at rs13135230 is an adenine, the base identified at rs11662763 is an adenine, the base identified at rs6770663 is a guanine, the base identified at rs444904 is an adenine, the base identified at rs427554 is an adenine, the base identified at rs2350620 is a guanine, or the base identified at rs11662763 is an adenine. In embodiments, the toxicity comprises hypertension and the SNP is rs677063, wherein the base identified at rs6770663 is a guanine.


In embodiments, the toxicity comprises hypertension, proteinuria, or both. In embodiments, the methods provided herein comprise administering a prophylactic and/or supportive therapy to prevent or reduce the toxicity. In embodiments, the prophylactic and/or supportive therapy is administered to the patient prior to and/or concurrently with administration of the VEGF pathway inhibitor. In embodiments, the methods comprise delaying the initiation of treatment with the VEGF pathway inhibitor until the prophylactic and/or supportive therapy has been administered to the subject for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more days, and/or until the subject's hypertension or proteinuria or other condition associated with the toxicity is reduced and/or resolved and/or under control. In embodiments, the methods comprise adding one or more prophylactic and/or supportive therapy to the subject's treatment regimen; switching the subject to a different prophylactic and/or supportive therapy; and/or increasing the dose and/or frequency of dosing of an anti-hypertensive agent relative to the dose administered to the subject prior to treatment with the VEGF pathway inhibitor. For example, in embodiments, a subject may have already been undergoing a treatment regimen with a prophylactic and/or supportive therapy for the condition associated with the toxicity risk. In such situations, the methods may comprise adding one or more additional prophylactic and/or supportive therapy, switching to a different class of drug for the prophylactic and/or supportive therapy, switching to a different drug within the same class for the prophylactic and/or supportive therapy, and/or increasing the dose and/or frequency of dosing with the prophylactic and/or supportive therapy, when the subject is identified as being at risk of developing the toxicity upon treatment with a VEGF pathway inhibitor.


In embodiments, the methods provided herein comprise modulating the dose of the VEGF pathway inhibitor. For example, in embodiments, the methods comprise reducing the total dosing amount, mg/kg dosing amount, or frequency of dosing of the VEGF pathway inhibitor. In embodiments, modulating the dose of the VEGF pathway inhibitor comprises starting at a dose lower than the recommended starting dose and maintaining the low dose or increasing the dose as appropriate with close monitoring for signs of the toxicity. In embodiments, the dose modulation is for the duration of treatment of the VEGF pathway inhibitor. In embodiments, the dose modulation is for a portion of the treatment with the VEGF pathway inhibitor, for example while symptoms of the toxicity persist. In embodiments, the methods comprise monitoring the subject for signs and symptoms of the toxicity or for worsening severity of the toxicity.


In embodiments, the toxicity comprises hypertension. In embodiments, the methods comprise monitoring the blood pressure of the subject, and/or monitoring the blood pressure of the subject more frequently than the blood pressure would be monitored in a patient who does not have the risk factor for the toxicity as provided herein. In embodiments, the toxicity comprises proteinuria. In embodiments, the toxicity comprises monitoring for proteinuria. In embodiments, monitoring for proteinuria comprises a urine dipstick and sulfosalicyclic acid test, a 24 hour urine collection test assay, or a spot albumin or protein-to-creatinine ratio test. In embodiments, the prophylactic and/or supportive therapy is an anti-hypertensive agent and/or an agent that treats or prevents proteinuria (e.g., a proteinuria medication). In embodiments, the anti-hypertensive agent or proteinuria medication is selected from the group consisting of loop diuretics, thiazide diuretics, thiazide-like diuretics, potassium-sparing diuretics, calcium channel blockers, ACE inhibitors, angiotensin II receptor antagonists, adrenergic receptor antagonists, vasodilators, renin inhibitors, aldosterone receptor antagonists, alpha-2 adrenergic receptor agonists, and endothelium receptor blockers.


In embodiments, the VEGF pathway inhibitor is any drug or therapeutic agent that inhibits, interferes with, or alters the VEGF pathway. For example, the VEGF pathway inhibitor may be an antibody, an antibody-like molecule, a small molecule, a soluble protein, a peptide, or the like that interferes with the VEGF-VEGFR interaction. In embodiments, the VEGF pathway inhibitor is selected from the group consisting of bevacizumab, bevacizumab-awwb, bevacizumab-bvzr, ranibizumab, aflibercept, ziv-aflibercept, lenalidomide, lenvatinib, ramucirumab, cabozantinib, pazopanib, sunitinib malate, regorafenib, axitinib, tipiracil and trifluridine, ponatinib, vandetanib, sorafenib, everolimus, thalidomide, temsirolimus, interferon alfa, interferon alfa-2B, interferon alfa-N3, peginterferon alfa-2B, peginterferon alfa-2A, rhEndostatin, cediranib, semaxanib, pomalidomide, alitretinoin, imiquimod, sinecatechins, vismodegib, sonidegib, pegaptanib sodium, dexamethasone intravitreal implant, fluocinolone acetonide, conbercept, brolucizumab-dbll, selpercatinib, nintedanib, apatinib, and motesanib. In embodiments, the VEGF pathway inhibitor is any biosimilar, generic, salt, ester, ether, isomer, mixture of isomers, complex, prodrug, or derivative of any VEGF pathway inhibitor provided herein or otherwise known in the art.


In embodiments, treating the subject with the VEGF pathway inhibitor comprises reducing exposure of the subject to the VEGF pathway inhibitor relative to the exposure of a subject treated as provided on prescribing information (e.g., the package insert or label) for the VEGF pathway inhibitor. For example, in embodiments, the methods provided herein comprise delaying initiation of treatment with the VEGF inhibitor, reducing the dose of the VEGF inhibitor, reducing the total number of doses of the VEGF inhibitor, reducing the dosing frequency of the VEGF inhibitor, and/or selecting a different VEGF pathway inhibitor (e.g., a VEGF pathway inhibitor that is less likely to be associated with the toxicity) or a non-VEGF pathway inhibitor therapy in the method of treating the subject, wherein the subject has been identified as being at risk of developing the toxicity. In embodiments, reducing the dose of the VEGF inhibitor comprises reducing the dose by about 5%, about 10%, about 25%, about 33%, about 50%, about 75%, or more relative to a reference dose, wherein the reference dose is the dose provided in prescribing information for the VEGF inhibitor. In embodiments, reducing the total number of doses of the VEGF inhibitor comprises reducing the total number of doses by about 5%, about 10%, about 25%, about 33%, about 50%, about 75%, or more relative to a reference total number of doses, wherein the reference total number of doses are total number of doses provided in prescribing information for the VEGF inhibitor. In embodiments, the methods comprise starting the subject on a lower dose and/or dosing frequency than the starting dose and/or dosing frequency recommended on the package insert for the VEGF pathway inhibitor, and titrating the dose upward to the dose and/or dosing frequency recommended on the package insert. In embodiments, such dosing comprising upward titrating is performed in combination with close monitoring of the subject for the toxicity. In embodiments, reducing the dosing frequency of the VEGF inhibitor comprises reducing the dosing frequency to about one third, about half, or about three quarters as often as the dosing frequency provided in prescribing information for the VEGF inhibitor.


Definitions

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. In case of conflict, the present document, including definitions, will control. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the present disclosure. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting.


The terms “comprise(s),” “include(s),” “having,” “has,” “can,” “contain(s),” and variants thereof, as used herein, are intended to be open-ended transitional phrases, terms, or words that do not preclude the possibility of additional acts or structures. The singular forms “a,” “and” and “the” include plural references unless the context clearly dictates otherwise. The present disclosure also contemplates other embodiments “comprising,” “consisting of and “consisting essentially of,” the embodiments or elements presented herein, whether explicitly set forth or not.


For the recitation of numeric ranges herein, each intervening number there between with the same degree of precision is explicitly contemplated. For example, for the range of 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the number 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 are explicitly contemplated. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise-Indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if a concentration range is stated as 1% to 50%, it is intended that values such as 2% to 40%, 10% to 30%, or 1% to 3%, etc., are expressly enumerated in this specification. These are only examples of what is specifically intended, and all possible combinations of numerical values between and including the lowest value and the highest value enumerated are to be considered to be expressly stated in this disclosure.


The term “single nucleotide polymorphism” or “SNP” as used interchangeably herein refer to a DNA sequence variation occurring when a single nucleotide (adenine (A), thymine (T), cytosine (C), or guanine (G)) in the genome differs between members of a species. Single nucleotides may be changed (substitution), removed (deletions) or added (insertion) to a polynucleotide sequence. Single nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions between genes. SNPs within a coding sequence may not necessarily change the amino acid sequence of the protein that is produced, due to degeneracy of the genetic code.


“Subject” and “patient” as used herein interchangeably refers to any vertebrate, including, but not limited to, a mammal (e.g., cow, pig, camel, llama, horse, goat, rabbit, sheep, hamsters, guinea pig, cat, dog, rat, and mouse, a non-human primate (e.g., a monkey, such as a cynomolgus or rhesus monkey, chimpanzee, etc.) and a human). In some embodiments, the subject may be a human or a non-human. In one embodiment, the subject is a human. The subject or patient may be undergoing various forms of treatment, such as with a VEGF-pathway inhibitor. The subject may be male or female. The subject may be of any ancestry. In some embodiments, the subject is of European ancestry.


“Treat,” “treating” or “treatment” are each used interchangeably herein to describe reversing, alleviating, or inhibiting the progress of a disease and/or injury, or one or more symptoms of such disease, to which such term applies. Depending on the condition of the subject, the term also refers to preventing a disease, and includes preventing the onset of a disease, or preventing the symptoms associated with a disease. A treatment may be either performed in an acute or chronic way. The term also refers to reducing the severity of a disease or symptoms associated with such disease prior to affliction with the disease. Such prevention or reduction of the severity of a disease prior to affliction refers to administration of a treatment to a subject that is not at the time of administration afflicted with the disease. “Preventing” also refers to preventing the recurrence of a disease or of one or more symptoms associated with such disease.


“Therapy” and/or “therapy regimen” generally refer to the clinical intervention made in response to a disease, disorder or physiological condition manifested by a patient or to which a patient may be susceptible. The aim of treatment includes the alleviation or prevention of symptoms, slowing or stopping the progression or worsening of a disease, disorder, or condition and/or the remission of the disease, disorder or condition. The term “providing” or “administering” as used herein with relation to a therapy (e.g. a VEGF-pathway inhibitor or a supportive therapy) may refer to providing to the subject the therapy or modulating the dose of a therapy currently being provided to the patient. For example, providing a supportive therapy may refer to increasing the dose of a supportive therapy currently being administered to the subject. The term “supportive therapies” and the like may be used interchangeably herein with “prophylactic therapies” and the like and refers to a therapy other than the therapy with the VEGF pathway inhibitor that prevents or controls (e.g., reduces the severity of or resolves) an adverse event such as hypertension or proteinuria. For example, the supportive therapy may be an anti-hypertensive agent.





DESCRIPTION OF THE DRAWINGS

These and other features, aspects, and advantages of the present disclosure will become better understood with regard to the following drawings:



FIG. 1 shows CONSORT and quality control flowchart for CALGB 80303, 40503, 90401, and 40502. MAF minor allele frequency, HWE Hardy-Weinberg Equilibrium.



FIG. 2 shows Manhattan plots (left) and quantile-quantile (Q-Q) plots (right) from the SNP-based association results for proteinuria, hypertension, and composite toxicity grade≥2. Composite toxicity is defined as the occurrence of either proteinuria or hypertension or both.



FIG. 3 shows effect of genotypes of rs339947 and rs12482855 associated with proteinuria grade≥2, rs13135230 and rs2350620 associated with hypertension grade≥2, and rs11662763 associated with composite toxicity grade≥2. Composite toxicity is defined as the occurrence of either proteinuria or hypertension or both.



FIG. 4A-4C shows LocusZoom plots using 400 kb window left and right from the variant limits associated with bevacizumab-induced grade≥2 proteinuria (FIG. 4A, top panel and FIG. 4C., top panel), composite toxicity (FIG. 4A, bottom panel), and hypertension (FIGS. 4B and 4C., bottom panel) in SNP-based analysis. Each circle represents the p-value for one SNP, with the top SNP shown in purple and the SNPs in the region colored depending on their degree of linkage disequilibrium (LD) (R2). X-axis denotes the position of the SNP in the region on chromosome; Y-axis denotes the p-value of the association.



FIG. 5 shows Manhattan plots (left) and quantile-quantile (Q-Q) plots (right) from the SNP-based association results for proteinuria, hypertension, and composite toxicity grade≥3. Composite toxicity is defined as the occurrence of either proteinuria or hypertension or both.



FIG. 6 shows LocusZoom plots using 400 kb window left and right from the variant limits associated with bevacizumab-induced grade≥3 proteinuria, hypertension, and composite toxicity in SNP-based analysis. Each circle represents the p-value for one SNP, with the top SNP shown in purple and the SNPs in the region colored depending on their degree of linkage disequilibrium (LD) (R2). X-axis denotes the position of the SNP in the region on chromosome; Y-axis denotes the p-value of the association.



FIG. 7 shows quantile-quantile (Q-Q) plot from gene-based association results for grade≥3 proteinuria, hypertension, and composite toxicity. Composite toxicity is defined as the occurrence of either proteinuria or hypertension or both.



FIG. 8 shows LocusZoom plots using 400 kb window left and right from the IL17F and SLC25A24 limits associated with bevacizumab-induced proteinuria and composite toxicity, respectively, in gene-based analysis of grade≥3. Each circle represents the p-value for one SNP, with the top SNP shown in purple and the SNPs in the region colored depending on their degree of linkage disequilibrium (LD) (R2). X-axis denotes the position of the SNP in the region on chromosome; Y-axis denotes the p-value of the association. Composite toxicity is defined as the occurrence of either proteinuria or hypertension or both.



FIG. 9A provides a quality control flowchart for the TARGET study. Abbreviations: IBS: identical by state, MAF: minor allele frequency, HWE: Hardy-Weinberg Equilibrium, QC: quality control, SNP: single nucleotide polymorphism.



FIG. 9B is a bar graph showing the frequency of rs444904 AA, GA, and GG genotypes associated with sorafenib-induced hypertension.



FIG. 10 shows the effect of genotypes of rs427554 associated with bevacizumab-induced hypertension.



FIG. 11 is a graphic showing the mechanism of action of sorafenib and bevacizumab65.



FIG. 12 is a graphic showing the function of the SP1 transcription factor.67 DNMT: DNA methyl transferase.



FIG. 13 shows the cumulative incidence of grade≥2 hypertension for rs2350620 and rs6770663.





DETAILED DESCRIPTION

Provided herein are methods of predicting risk and/or treating a subject. In some embodiments, the methods comprise detecting one or more mutations in one or more nucleic acids in a sample obtained from the subject. In some aspects, the methods comprise detecting one or more mutations in one or more genes in a sample obtained from the subject.


In one aspect, provided herein is a method comprising detecting one or more mutations (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 mutations) in one or more nucleic acids or genes in a sample obtained from a subject. In some embodiments, the method further comprises determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject based upon the presence or absence of one or more mutations in the one or more nucleic acids or genes in the sample.


In another aspect, provided herein is a method of predicting the risk of developing one or more toxicities induced by a therapeutic agent (e.g., a VEGF-pathway inhibitor) in a subject. The method comprises detecting one or more mutations (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 mutations) in one or more nucleic acids or genes in a sample obtained from the subject, and determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject based upon the presence or absence of the mutation in the one or more nucleic acids or genes in the sample.


In another aspect, provided herein is a method of treating a subject comprising detecting one or more mutations in one or more nucleic acids or genes in a sample obtained from a subject, determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject based upon the presence or absence of one or more mutations in the one or more nucleic acids or genes in the sample, and modulating therapy with a VEGF-pathway inhibitor based upon the determined risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject. Modulating the therapy may include, for example, monitoring the subject for improvement or worsening of the toxicity, administering a supportive therapy to the subject, and/or adjusting the dose of the VEGF-pathway inhibitor. For example, in embodiments, the present disclosure provides methods of treating a subject comprising detecting one or more mutations in one or more nucleic acids or genes in a sample obtained from a subject, determining the risk of hypertension or severe hypertensive crisis in the subject based upon the presence or absence of one or more mutations in the one or more nucleic acids or genes in the sample, and administering to the subject an anti-hypertensive agent prior to or concurrently with administration of the VEGF-pathway inhibitor.


In another aspect, provided herein is a method of treating a subject, comprising determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject based upon the presence or absence of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more mutations) in one or more nucleic acids or genes in a sample obtained from a subject, and modulating therapy with a VEGF-pathway inhibitor based upon the determined risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject. In some aspects, the method of treating a subject may be performed by one party. In other aspects, the method of treating a subject may be performed by two or more parties. For example, the presence or absence of one or more mutations in one or more nucleic acids in a sample may be measured by one party and a different party could modulate therapy with a VEGF-pathway inhibitor. For example, one party could analyze the sample to detect one or more mutations in nucleic acids or genes and provide information regarding these mutations to enable a second party to determine the risk in the subject and modulate therapy with the VEGF-pathway inhibitor based upon the determined risk. Alternatively, one party could analyze the sample to detect one or more mutations in nucleic acids or genes and determine the risk of developing one or more VEGF-pathway inhibitor-induced toxicities based upon the analysis, and a second party (e.g. a physician) could then modulate therapy with a VEGF-pathway inhibitor based upon the risk determination provided by the first party.


In an aspect, provided herein is a method for treating a subject having a disease or disorder associated with neovascularization or angiogenesis, the method comprising identifying the subject as having a mutation in the gene KCNAB1; treating the subject with an anti-hypertensive agent; and treating the subject with an angiogenesis inhibitor (e.g., a VEGF pathway inhibitor). In embodiments, the mutation is an SNP. In embodiments, the SNP is rs6770663. In embodiments, the base identified at rs6770663 is a guanine. In embodiments, provided herein is a method for treating a population of patients with a VEGF-pathway inhibitor, the method comprising providing a first population of patients who have a disease or disorder indicated for treatment with a VEGF-pathway inhibitor; separating patients who have the SNP rs6770663 into a second population of patients; and treating the second population of patients with an anti-hypertensive agent prior to or concurrently with administering the VEGF pathway inhibitor to the subject.


In accordance with any of the aspects and embodiments described herein, the subject may be a mammal. In particular embodiments, the subject is a human. The subject may be undergoing treatment or a candidate for treatment with a VEGF-pathway inhibitor.


Detecting a mutation in one or more nucleic acids in the sample may comprise detecting one or more single-nucleotide polymorphisms (SNPs) in the one or more nucleic acids in the sample, one or more deletions, insertions, copy number variations, inversions, or dislocations; and/or deletion of an entire gene of interest; and/or one or more mutations in one or more genes that affect the expression or function of a gene of interest. In some embodiments, the method comprises detecting a single SNP. In some embodiments, the method comprises detecting two SNPs. In yet other embodiments, the method comprises detecting three SNPs. In other embodiments, the method comprises detecting four SNPs, etc. In some embodiments, one or more SNPs is located in one or more genes provided in Table 8 or Table 9. In embodiments, the mutations provided herein that are associated with the risk of developing a VEGF-pathway-inhibitor-induced toxicity are present in one or more genes selected from the group consisting of KCNAB1 and ASPH.


KCNAB1 encodes the K+ voltage activated channel subfamily 1 subunit β1 (Kvβ1.1-1.3) and it is highly expressed in arteries (aorta, coronary, tibial), and endothelial cells. Variant rs6770663 is located in a region of H3K4me1 enhancers in the aorta (see Table 14).


In embodiments, the present disclosure provides mutations that predispose for lower expression of KCNAB1. For example, the present disclosure provides methods for treating patients with rs6770663 with a VEGF pathway inhibitor (e.g., bevacizumab), wherein the method comprises modifying the VEGF pathway inhibitor treatment by including monitoring for hypertension, prophylactically treating to prevent hypertension, and/or reducing the dosing level or dosing regimen for the VEGF pathway inhibitor in view of the patient's increased risk of hypertension. Variant rs6770663 has a frequency of about 10% in Europeans and a global frequency of 30%.


ASPH (aspartate β-hydroxylase) encodes the junction protein which is expressed in arteries and in endothelial cells.


In some embodiments, the SNP is selected from the SNPs provided in Table 4, Table 5, Table 6, Table 7, Table 10, Table 11, Table 12, Table 13, rs444904, rs427554, or any combinations thereof. For example, one or more SNPs may be selected from the group consisting of rs339947, rs12482855, rs13135230, rs2350620, rs11662763, rs6770663, rs408130, rs418173, rs12482855, rs444904, and rs427554, or any combinations thereof. In some embodiments, a single mutation may be detected. In embodiments, more than one mutation (e.g., 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more mutations) may be detected. For example, multiple SNPs may be evaluated for mutations in the subject. In embodiments, SNP rs6770663 confers susceptibility to VEGF-pathway inhibitor-induced hypertension.


The present disclosure provides data and validation of the mutations (e.g. SNPs) provided herein as clinically relevant biomarkers of VEGF pathway inhibitor toxicities. For example, the present disclosure demonstrates that mutations provided herein are biomarkers for hypertension and/or proteinuria elicited by more than one different type of VEGF pathway inhibitor. The skilled person will understand that the results provided herein apply to any angiogenesis inhibitor, e.g., any VEGF pathway inhibitor.


The methods described herein may involve determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject. Any suitable toxicity may be evaluated. VEGF inhibitor-induced toxicities include, for example, fatigue, asthenia, weight loss, pain, depression, pyrexia, chills, myalgia, neurologic-sensory neuropathy, gastrointestinal toxicities (e.g. anorexia, decreased appetite, dry mouth, stomatitis, mucositis, nausea, vomiting, diarrhea, constipation, GI perforation), skin toxicities (e.g. HFS, rash, alopecia, depigmentation, pruritus, dry skin, wound healing complications), cardiovascular toxicities (e.g. hypertension, CHF, cardiac ischemia, cerebrovascular ischemia, embolism/thrombosis, bleeding, dyspnea, cough, pneumonitis, dysphonia), myelotoxicities (e.g. anemia, hemoglobin elevation, leukopenia, neutropenia, thrombocytopenia, lymphopenia), metabolic abnormalities (e.g. bilirubin, ALT, AST, gamma-GT abnormalities, INR abnormalities, PTT abnormalities, increased alkaline phosphatase, hypoalbuminemia, lipase elevation, amylase elevation, creatinine increase, increased uric acid, proteinuria, hypophosphatemia, hypothyroidism, increased triglycerides, increased cholesterol, hyperglycemia, hypoglycemia, hypercalcemia, hypocalcemia, hyponatremia), and the like.


In particular embodiments, VEGF-pathway inhibitor-induced toxicities are selected from proteinuria, hypertension, or both. For example, determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities may comprise diagnosing the subject as having a high risk of developing proteinuria. In particular embodiments, the subject is diagnosed as having a high risk of developing proteinuria when the base identified at rs339947 is an adenine, the base identified at rs12482855 is an adenine, the base identified at rs11662763 is an adenine, the base identified at rs408130 is an adenine, the base identified at rs418173 is an adenine, or the base identified at rs12482855 is an adenine.


As another example, determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities may comprise diagnosing the subject as having a high risk of developing hypertension. In particular embodiments, the subject is diagnosed as having a high risk of developing hypertension when the base identified at rs13135230 is an adenine, the base identified at rs11662763 is an adenine, the base identified at rs6770663 is a guanine, the base identified at rs444904 is an adenine, or the base identified at rs427554 is an adenine. In embodiments, the subject is determined to be of high risk of developing hypertension when the base identified at rs6770663 is a guanine.


In some embodiments, determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities comprises diagnosing the subject as having a low risk of developing hypertension. For example, the subject may be diagnosed as having a low risk of developing hypertension when the base identified at rs2350620 is a guanine.


In some embodiments, determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities comprises diagnosing the subject as having a high risk of developing either proteinuria, or hypertension, or both (e.g. composite toxicity). For example, the subject may be diagnosed as having a high risk of developing proteinuria or hypertension or both when the base identified at rs11662763 is an adenine.


In some embodiments, the methods described herein further comprise modulating therapy with a VEGF-pathway inhibitor based upon the risk determined in the subject. For example, the method may comprise providing the subject with a VEGF-pathway inhibitor or increasing the therapeutic dose of the VEGF pathway inhibitor when the subject is determined to have a low risk of developing one or more VEGF-pathway inhibitor toxicities. For example, the method may comprise providing the subject with a VEGF-pathway inhibitor or increasing the therapeutic dose of the VEGF pathway inhibitor when the subject is diagnosed as having a low risk of developing proteinuria, hypertension, or both. In some embodiments, the method may comprise lowering the dose of a VEGF-pathway inhibitor or ceasing treatment with the VEGF-pathway inhibitor when the subject is determined to have a high risk of developing one or more VEGF-pathway inhibitor toxicities, such as a high risk of developing proteinuria, hypertension, or both. In embodiments, the method may comprise starting the subject who is determined to have a high risk of developing one or more VEGF pathway inhibitor toxicities, such as the high risk of developing proteinuria, hypertension, or both, at a lower dose and/or lower dosing frequency compared to the dose and/or regimen that is recommended on the package insert for the VEGF pathway inhibitor, monitoring the subject for the one or more toxicities, and titrating the dose and/or dosing frequency upwards, if appropriate based on the monitoring for the toxicity.


In some embodiments, the methods described herein further comprise modulating therapy with or providing the subject with one or more supportive therapies. The term “supportive therapies” refers to a therapy other than the therapy with an anti-cancer agent (e.g. a VEGF pathway inhibitor or other anti-cancer agent). For example, the supportive therapy may be an anti-hypertensive agent and/or a proteinuria medication. Suitable anti-hypertensive agents and/or proteinuria medications include, for example, diuretics, beta blockers, alpha and beta blockers, calcium channel blockers, angiotensin-converting enzyme (ACE) inhibitors, angiotensin II receptor antagonists (ARBs), adrenergic receptor antagonists, vasodilators (e.g. direct vasodilators), renin inhibitors, aldosterone receptor antagonists, alpha-2 adrenergic receptor agonists, central alpha-2 agonists and other centrally acting drugs, endothelin receptor blockers, and the like.


In embodiments, if the subject is determined to be at risk of developing one or more VEGF-pathway inhibitor toxicities, the methods provided herein comprise adding a supportive therapy to the subject's treatment regimen, increasing the dose and/or dosing frequency of a supportive therapy that is already a part of the subject's treatment regimen, and/or adding one, two, three, or more additional supportive therapies to the subject's treatment regimen. In embodiments, the added one, two, three or more additional supportive therapies may be different drugs in the same class as one another and/or as a supportive therapy that was already a part of the subject's treatment regimen; or the one, two, three, or more additional supportive therapies may be drugs in a different class as one another and/or as a supportive therapy that was already part of the subject's treatment regimen. Classes of supportive therapies are known in the art and exemplified herein, such as, for example, diuretics, beta blockers, ACE inhibitors, angiotensin II receptor antagonists, calcium channel blockers, direct renin inhibitors, alpha-2 adrenergic receptor agonists, central alpha-2 agonists, and vasodilators.


Exemplary diuretics may be thiazide or thiazide-type diuretics. For example, the diuretic may be chlorthalidone, hydrochlorothiazide, indapamide, or metolazone. Chlorthalidone or hydrochlorothiazide may be administered, for example, at a dose of about 12.5 to about 50 mg/day, once daily. Indapamide may be administered, for example at a dose of about 1.25 to about 2.5 mg/day, once daily. Metolazone may be administered, for example, at a dose of about 2.5 to about 5 mg/day, once daily. Exemplary diuretics may also be loop diuretics, such as bumetanide, furosemide, or torsemide. Bumetanide may be administered, for example, twice daily at a dose of about 0.5 to about 2 mg/day. Furosemide may be administered, for example, twice daily at a dose of about 20 to about 80 mg/day. Torsemide may be administered, for example, once daily at a dose of about 5 to about 10 mg/day. Exemplary diuretics may also be potassium sparing diuretics, such as amiloride or triamterene. Amiloride may be administered, for example, once or twice daily at a dose of about 5 to about 10 mg/day. Triamterene may be administered, for example, once or twice daily at a dose of about 50 to about 100 mg/day. Exemplary diuretics may also be aldosterone antagonists, such as eplerenone or spironolactone. Eplerenone may be administered, for example, once or twice daily at a dose of about 50 to about 100 mg/day. Spironolactone may be administered, for example, twice daily at a dose of about 25 to about 100 mg/day. Exemplary diuretics may also include thiazide/potassium-sparing combination diuretics, such as hydrochlorothiazide/triamterene. Hydrochlorothiazide/triamterene may be administered once daily, for example, at a dose of about 25 mg/about 37.5 mg to about 50 mg/about 75 mg.


Exemplary beta blockers may be cardioselective (e.g., atenolol, betaxolol, bisoprolol, metoprolol (tartate), or metoprolol (succinate) extended release), noncardioselective (e.g., nadolol, propranolol, or long-acting propranolol), cardioselective and vasodilatory (e.g., nebivolol), or intrinsic and sympathomimetic activity beta-blockers (e.g., acebutolol, penbutolol, and pindolol). Atenolol may be administered, for example, once or twice daily at a dose of about 25 to about 100 mg/day. Betaxolol may be administered, for example, once daily at a dose of about 5 to about 20 mg/day. Bisoprolol may be administered, for example, once daily at a dose of about 2.5 mg to about 20 mg/day. Metoprolol (tartate) may be administered once or twice daily at a dose of about 50 to about 200 mg/day. Metoprolol (succinate) extended release may be administered, for example, once daily at a dose of about 50 to about 200 mg/day. Nadolol may be administered, for example, once daily at a dose of about 40 to about 120 mg/day. Propanolol may be administered, for example, twice daily at a dose of about 40 to about 160 mg/day. Long-acting propranolol may be administered, for example, once daily at a dose of about 60 to about 180 mg/day. Nebivolol may be administered, for example, once daily at a dose of about 5 to about 40 mg/day. Acebutolol may be administered, for example, twice daily at a dose of about 200 to about 800 mg/day. Penbutolol may be administered, for example, once daily at a dose of about 10 to about 40 mg/day. Pindolol may be administered, for example, twice daily at a dose of about 10 to about 60 mg/day. Exemplary combined alpha and beta blockers include carvedilol, carvedilol phosphate, and labetalol. Carvedilol may be administered, for example, twice daily at a dose of about 12.5 to about 50 mg/day. Carvedilol phosphate may be administered, for example, once daily at a dose of about 20 to about 80 mg/day. Labetalol may be administered, for example, twice daily at a dose of about 100 mg to about 400 mg/day.


Exemplary ACE inhibitors include benazepril, captopril, enalapril, fosinopril, lisinopril, moexipril, perindopril, quinapril, ramipril, and trandolapril. Benazepril may be administered, for example, once or twice daily at a dose of about 10 to about 40 mg/day. Captopril may be administered, for example, twice or three times daily at a dose of about 12.5 to about 150 mg/day. Enalapril may be administered, for example, once or twice daily at a dose of about 5 to about 40 mg/day. Fosinopril may be administered, for example, once daily at a dose of about 10 to about 40 mg/day. Lisinopril may be administered, for example, once daily at a dose of about 5 mg to about 40 mg/day. Moexipril may be administered, for example, once or twice daily at a dose of about 7.5 mg to about 30 mg/day. Perindopril may be administered, for example, once daily at a dose of about 2 to about 16 mg/day. Quinapril may be administered, for example, once or twice daily at a dose of about 10 to about 80 mg/day Ramipril may be administered, for example, once or twice daily at a dose of about 2.5 to about 20 mg/day. Trandolapril may be administered, for example, once daily at a dose of about 1 to about 4 mg/day.


Exemplary angiotensin II receptor antagonists include candesartan, eprosartan, irbesartan, losartan, olmesartan, telmisartan, valsartan, and azilsartan. Candesartan may be administered, for example, once daily at a dose of about 8 to about 32 mg/day. Eprosartan may be administered, for example, once or twice daily at a dose of about 400 to about 800 mg/day. Irbesartan may be administered, for example, once daily at a dose of about 150 to about 300 mg/day. Losartan may be administered, for example, once daily at a dose of about 25 to about 100 mg/day. Olmesartan may be administered, for example, once daily at a dose of about 20 about 40 mg/day. Telmisartan may be administered, for example, once daily at a dose of about 20 to about 80 mg/day. Valsartan may be administered, for example, once or twice daily at a dose of about 80 to about 320 mg/day. Azilsartan may be administered, for example, once daily at a dose of about 40 to about 80 mg/day.


Exemplary calcium channel blockers may be dihydropyridines (e.g., amlodipine, felodipine, nifedipine long-acting, nisoldipine, isradipine, and nicardipine SR) or nondihydropyridines (e.g., diltiazem ER, verapamil IR, verapamil SR, and verapamil-delayed onset ER). Amlodipine may be administered, for example, once daily at a dose of about 2.5 to about 10 mg/day. Felodipine may be administered, for example, once daily at a dose of about 2.5 to about 20 mg/day. Nifedipine long acting may be administered, for example, once daily at a dose of about 30 to about 90 mg/day. Nisoldipine may be administered, for example, once daily at a dose of about 10 to about 40 mg/day. Isradipine may be administered, for example, twice daily at a dose of about 5 to about 10 mg/day. Nicardipine SR may be administered, for example, twice daily at a dose of about 60 to about 120 mg/day. Diltiazem may be administered, for example, once daily at a dose of about 120 to about 360 mg/day. Verapamil IR may be administered, for example, three times daily at a dose of about 120 to about 360 mg/day. Verapamil SR maybe administered, for example, once or twice daily at a dose of about 120 to about 360 mg/day. Verapamil-delayed onset ER may be administered, for example, once daily in the evening at a dose of about 100 to about 300 mg/day.


An exemplary direct renin inhibitor is aliskiren. Aliskiren may be administered, for example, once daily at a dose of about 150 to about 300 mg/day. Exemplary alpha-1 blockers include doxazosin, prazosin, and terazosin. Doxazosin may be administered, for example, once daily at a dose of about 1 to about 16 mg/day. Prazosin may be administered, for example, two or three times daily at a dose of about 2 to about 20 mg/day. Terazosin may be administered, for example, once or twice daily at a dose of about 1 to about 20 mg/day. Exemplary central alpha2-agonists and other centrally acting drugs include, for example, clonidine oral, clonidine patch, methyldopa, and guanfacine. Clonidine oral may be administered, for example, twice daily at a dose of about 0.1 to about 0.8 mg/day. Clonidine patch may be administered, for example, once weekly at a dose of 0.1 to about 0.3 mg. Methyldopa maybe administered, for example, twice daily at a dose of about 250 to about 1000 mg/day. Guanfacine may be administered, for example, once daily at a dose of about 0.5 to about 2 mg/day. Exemplary direct vasodilators include hydralazine and minoxidil. Hydralazine may be administered, for example, two or three times daily at a dose of about 100 to about 200 mg/day. Minoxidil may be administered, for example once, twice, or three times daily at a dose of about 5 to about 100 mg/day.


In embodiments, any two or more supportive therapies may be used in combination. The skilled person will recognize that the decision of which agents to combine should be based on the complementarity of mechanism of action, evidence of better antihypertensive effect of the combination than either individual agent, and favorable tolerability of the combination. For example, the following combinations of supportive therapies may be used in the methods provided herein: calcium antagonist and ACE inhibitor; calcium antagonist and angiotensin receptor antagonist; calcium antagonist (dihydropiridine) and beta-blocker; calcium antagonist and thiazide diuretic; thiazide diuretic and ACE inhibitor; and thiazide diuretic and angiotensin receptor antagonist.


In embodiments, a newly added supportive therapy and/or an increased dose of a supportive therapy may be administered prior to treatment with the VEGF-pathway inhibitor. For example, a subject may be identified as having a high risk of developing one or more VEGF-pathway inhibitor toxicities as provided herein, and may be administered a new supportive therapy, and additional supportive therapy, an increased dose of supportive therapy, and/or an increased frequency of dosing of a supportive therapy, for at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, or more days before initiation of treatment with the VEGF-pathway inhibitor. In embodiments, the subject is monitored for evidence that the risk of developing one or more VEGF-pathway inhibitor toxicities, or that the likely severity of any such VEGF-pathway inhibitor toxicity, has been reduced prior to initiating therapy with the VEGF-pathway inhibitor. For example, in embodiments, the subject's blood pressure is monitored and the VEGF-pathway inhibitor is withheld until the subject has been determined to be in a safe range for blood pressure.


In embodiments, a subject has been identified as being at risk of developing one or more VEGF pathway inhibitor toxicities, wherein the subject's blood pressure monitoring is increased prior to, during, or following initiation of therapy with a VEGF pathway inhibitor. In embodiments, increasing blood pressure monitoring may mean increasing the intensity of monitoring. For example, increasing blood pressure monitoring may comprise increasing the frequency of monitoring. For subjects who were not currently monitoring blood pressure regularly, increasing blood pressure monitoring may mean initiating ambulatory blood pressure monitoring, and/or monitoring blood pressure more than once daily, once daily, once every 2, 3, 4, 5, or 6, days, or once weekly. For subjects who were monitoring blood pressure regularly at home, increasing blood pressure monitoring may mean initiating ambulatory blood pressure monitoring where the subject previously only periodically measured blood pressure; or may mean periodic blood pressure monitoring that is performed more often, for example, twice as often. Blood pressure monitoring may be conducted at home by the subject, using single blood pressure measurement devices and/or ambulatory blood pressure monitoring, and/or may be conducted in a hospital or clinic. Ambulatory blood pressure monitoring is blood pressure monitoring using a device that records blood pressure automatically and periodically over a period of time, for example, of 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, or longer.


In some embodiments, therapy with a VEGF-pathway inhibitor may be modulated and one or more supportive therapies may be provided to the subject based upon the determined risk. For example, the method may comprise lowering the dose of a VEGF-pathway inhibitor and providing a supportive therapy to the subject when the subject is determined to have a high risk of developing one or more VEGF-pathway inhibitor-induced toxicities. In embodiments, lowering the dose of the VEGF pathway inhibitor may comprise starting the subject at a lower dose and/or lower dosing frequency compared to the recommended dose on the package insert for the VEGF pathway inhibitor, and may further comprise monitoring the subject for the toxicity and/or providing a supportive therapy for the toxicity, and titrating the dose and/or dosing frequency upwards as appropriate. In embodiments, the method may comprise lowering the dose of the VEGF-pathway inhibitor and providing an anti-hypertensive agent or increasing the dose of an anti-hypertensive agent provided to the subject when the subject is determined to have a high risk of developing VEGF-pathway inhibitor-induced hypertension. As another example, the method may comprise lowering the dose of the VEGF-pathway inhibitor and providing a proteinuria medication or increasing the dose of a proteinuria medication provided to the subject when the subject is determined to have a high risk of developing VEGF-pathway inhibitor-induced proteinuria.


VEGF-pathway inhibitors may be any suitable agent, such as an antibody or a small molecule. VEGF-pathway inhibitors include agents that inhibit any part of the VEGF pathway, including antibodies that bind to VEGF or a VEGF receptor (VEGFR), soluble proteins that bind to or otherwise block interaction of VEGF and VEGFR, small molecule drugs that interfere with the VEGF/VEGFR interaction, and kinase inhibitors. Exemplary VEGF-pathway inhibitors include, without limitation, bevacizumab, bevacizumab-awwb, bevacizumab-bvzr, ranibizumab, aflibercept, ziv-aflibercept, lenalidomide, lenvatinib, ramucirumab, cabozantinib, pazopanib, sunitinib malate, regorafenib, axitinib, tipiracil and trifluridine, ponatinib, vandetanib, sorafenib, everolimus, thalidomide, temsirolimus, interferon alfa, interferon alfa-2B, interferon alfa-N3, peginterferon alfa-2B, peginterferon alfa-2A, rhEndostatin, cediranib, semaxanib, pomalidomide, alitretinoin, imiquimod, sinecatechins, vismodegib, sonidegib, pegaptanib sodium, dexamethasone intravitreal implant, fluocinolone acetonide, conbercept, brolucizumab-dbll, selpercatinib, nintedanib, apatinib, and motesanib. VEGF-pathway inhibitors encompassed by the disclosure also include any biosimilar, generic, salt, ester, ether, isomer, mixture of isomers, complex, prodrug, or derivative of a VEGF-pathway inhibitor. The skilled person will understand how to obtain prescribing information (e.g., information from the product insert or approved label) for VEGF pathway inhibitors; exemplary prescribing information is also provided herein.


In embodiments, the VEGF-pathway inhibitor is bevacizumab (AVASTIN) or bevacizumab-awwb (MVASI) or bevacizumab-bvzr (ZIRABEV). Bevacizumab is a vascular endothelial growth factor inhibitor indicated for the treatment of metastatic colorectal cancer, in combination with intravenous fluorouracil based chemotherapy for first- or second-line treatment; metastatic colorectal cancer, in combination with fluoropyrimidine-irinotecan- or fluoropyrimidine-oxaliplatin-based chemotherapy for second-line treatment in patients who have progressed on a first-line bevacizumab-containing regimen; unresectable, locally advanced, recurrent or metastatic non-squamous non-small cell lung cancer, in combination with carboplatin and paclitaxel for first-line treatment; recurrent glioblastoma in adults; metastatic renal cell carcinoma in combination with interferon alfa; persistent, recurrent, or metastatic cervical cancer, in combination with paclitaxel and cisplatin, or paclitaxel and topotecan; and epithelial ovarian, fallopian tube, or primary peritoneal cancer (i) in combination with carboplatin and paclitaxel, followed by bevacizumab as a single agent, for stage III or IV disease following initial surgical resection, (ii) in combination with paclitaxel, pegylated liposomal doxorubicin, or topotecan for platinum-resistant recurrent disease who received no more than 2 prior chemotherapy regimens, and (iii) in combination with carboplatin and paclitaxel or carboplatin and gemcitabine, followed by bevacizumab as a single agent, for platinum sensitive recurrent disease. Bevacizumab is administered intravenously and is provided in dosage forms of 100 mg/4 mL (25 mg/mL) or 400 mg/16 mL (25 mg/mL) in a single-dose vial.


For metastatic colorectal cancer, bevacizumab is administered at a dose of 5 mg/kg every 2 weeks with bolus-IFL (irinotecan 125 mg/m2, fluorouracil 500 mg/m2, and leucovorin 20 mg/m2 given once weekly for 4 weeks every 6 weeks); 10 mg/kg every 2 weeks with FOLFOX4; or 5 mg/kg every 2 weeks or 7.5 mg/kg every 3 weeks with fluoropyrimidine-irinotecan- or fluoropyrimidine-oxaliplatin-based chemotherapy after progression on a first-line bevacizumab containing regimen. For first-line non-squamous non-small cell lung cancer, bevacizumab is administered at a dose of 15 mg/kg every 3 weeks with carboplatin and paclitaxel. For recurrent glioblastoma, bevacizumab is administered at a dose of 10 mg/kg every 2 weeks. For metastatic renal cell carcinoma, bevacizumab is administered at a dose of 10 mg/kg every 2 weeks with interferon alfa. For persistent, recurrent, or metastatic cervical cancer, bevacizumab is administered at a dose of 15 mg/kg every 3 weeks with paclitaxel and cisplatin, or paclitaxel and topotecan. For stage III or IV epithelial ovarian, fallopian tube or primary peritoneal cancer following initial surgical resection, bevacizumab is administered at a dose of 15 mg/kg every 3 weeks with carboplatin and paclitaxel for up to 6 cycles, followed by 15 mg/kg every 3 weeks as a single agent, for a total of up to 22 cycles. For platinum-resistant recurrent epithelial ovarian, fallopian tube or primary peritoneal cancer, bevacizumab is administered at a dose of 10 mg/kg every 2 weeks with paclitaxel, pegylated liposomal doxorubicin, or topotecan given every week, or 15 mg/kg every 3 weeks with topotecan given every 3 weeks. For platinum-sensitive recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer, bevacizumab is administered at a dose of 15 mg/kg every 3 weeks with carboplatin and paclitaxel for 6-8 cycles, followed by 15 mg/kg every 3 weeks as a single agent; or 15 mg/kg every 3 weeks with carboplatin and gemcitabine for 6-10 cycles, followed by 15 mg/kg every 3 weeks as a single agent.


Arterial thromboembolic events, venous thromboembolic events, hypertension, and proteinuria are among the adverse reactions that can occur in patients administered bevacizumab. For hypertension, blood pressure may be monitored and patients may be treated for the hypertension, e.g., with an anti-hypertensive agent; bevacizumab may be withheld if hypertension is not medically controlled. Bevacizumab can be resumed once controlled, but should be discontinued for hypertensive crisis or hypertensive encephalopathy. For renal injury and proteinuria, doctors are instructed to monitor urine protein and to discontinue bevacizumab for nephrotic syndrome, and withhold until less than 2 grams of protein are detectable in urine. Presently, there is no known method for identifying patients at risk of hypertension and/or proteinuria prior to treatment with bevacizumab.


In embodiments, the VEGF-pathway inhibitor is ranibizumab. Ranibizumab (LUCENTIS) is a vascular endothelial growth factor (VEGF) inhibitor, indicated for the treatment of patients with neovascular (wet) Age-Related Macular Degeneration (AMD), macular edema following retinal vein occlusion (RVO), diabetic macular edema (DME), diabetic retinopathy (DR), and myopic choroidal neovascularization (mCNV). Ranibizumab is for ophthalmic intravitreal injection. For wet AMD, 0.5 mg (0.05 mL) is recommended to be administered by intravitreal injection once a month (approximately 28 days). Although not as effective, patients may be treated with 3 monthly doses followed by less frequent dosing, or may be treated with one dose every 3 months after 4 monthly doses, with regular assessment. For macular edema following RVO, 0.5 mg (0.05 mL) is recommended to be administered by intravitreal injection once a month (approximately 28 days). For DME and DR, 0.3 mg (0.05 mL) is recommended to be administered by intravitreal injection once a month (approximately 28 days). For mCNV, 0.5 mg (0.05 mL) is recommended to be initially administered by intravitreal injection once a month (approximately 28 days) for up to three months. Patients may be retreated if needed. The dosage forms provided for ranibizumab are single-use prefilled syringe or glass vials containing 10 mg/mL solutions designed to provide 0.05 mL for intravitreal injections; or containing 6 mg/mL solution (0.3 mg). There is a potential risk of arterial thromboembolic events following intravitreal use of VEGF inhibitors.


In embodiments, the VEGF-pathway inhibitor is aflibercept. Aflibercept (EYLEA) is a vascular endothelial growth factor (VEGF) inhibitor indicated for the treatment of patients with wet AMD, macular edema following RVO, DME, and DR. For wet AMD, the recommended dose is 2 mg (0.05 mL) administered by intravitreal injection every 4 weeks (approximately every 28 days, monthly) for the first 3 months, followed by 2 mg (0.05 mL) via intravitreal injection once every 8 weeks (2 months). Some patients may need every 4 week (monthly) dosing after the first 12 weeks (3 months). Although not as effective as the recommended every 8 week dosing regimen, patients may also be treated with one dose every 12 weeks after one year of effective therapy. For macular edema following RVO, the recommended dose is 2 mg (0.05 mL) administered by intravitreal injection once every 4 weeks (approximately every 25 days, monthly). For DME and DR, the recommended dose is 2 mg (0.05 mL) administered by intravitreal injection every 4 weeks (approximately every 28 days, monthly) for the first 5 injections followed by 2 mg (0.05 mL) via intravitreal injection once every 8 weeks (2 months). Some patients may need every 4 week (monthly) dosing after the first 20 weeks (5 months). Aflibercept is provided in dosage forms for injection of 2 mg/0.05 mL solution in a single-dose pre-filled syringe or a single-dose vial. As with ranibizumab, there is a potential risk of arterial thromboembolic events following intravitreal use of aflibercept.


In embodiments, the VEGF-pathway inhibitor is ziv-aflibercept. Ziv-aflibercept (ZALTRAP) is indicated for the treatment of patients with metastatic colorectal cancer that is resistant to or has progressed following an oxaliplatin-containing regimen, a vascular endothelial growth factor inhibitor, in combination with fluorouracil, leucovorin, irinotecan (FOLFIRI). Ziv-aflibercept is administered 4 mg/kg as an intravenous infusion over 1 hour every 2 weeks in combination with FOLFIRI until disease progression or unacceptable toxicity. Ziv-aflibercept is to be administered prior to any component of the FOLFIRI regimen on the day of treatment. Arterial thromboembolic events, hypertension, and proteinuria are among the adverse effects that may be induced by zif-aflibercept administration. For hypertension, doctors may monitor blood pressure and treat hypertension; may temporarily suspend ziv-aflibercept if hypertension is not controlled (and upon resumption, permanently reduce to 2 mg/kg); and may discontinue it if hypertensive crisis develops. For proteinuria, doctors may monitor urine protein; may suspend ziv-aflibercept for proteinuria of 2 grams per 24 hours or more (to be resumed when proteinuria is less than 2 grams per 24 hours, and then permanently reduce to 2 mg/kg for recurrent proteinuria); and may discontinue it if nephrotic syndrome or thrombotic microangiopathy (TMA) develops. The provided dosage forms of ziv-aflibercept are a 100 mg/4 mL (25 mg/mL) and a 200 mg/8 mL (25 mg/mL) solution in a single-dose vial for injection.


In embodiments, the VEGF-pathway inhibitor is lenalidomide. Lenalidomide (REVLIMID) is a thalidomide analogue indicated for the treatment of adult patients with multiple myeloma (MM), in combination with dexamethasone (25 mg once daily orally on Days 1-21 of repeated 28-day cycles in combination with dexamethasone); MM, as maintenance following autologous hematopoietic stem cell transplantation (auto-HSCT) (initiated after therapy after adequate hematologic recovery (ANC at least 1000/mcL and/or platelet counts at least 75,000/mcL, recommended starting dose of 10 mg once daily continuously (Days 1-28 of repeated 28-day cycles) until disease progression or unacceptable toxicity, and after 3 cycles of maintenance therapy, the dose can be increased to 15 mg once daily if tolerated); transfusion-dependent anemia due to low- or intermediate-1-risk myelodysplastic syndromes (MDS) associated with a deletion 5q abnormality with or without additional cytogenetic abnormalities (10 mg once daily); mantle cell lymphoma (MCL) whose disease has relapsed or progressed after two prior therapies, one of which included bortezomib (25 mg once daily orally on Days 1-21 of repeated 28-day cycles); previously treated follicular lymphoma (FL), in combination with a rituximab product (20 mg once daily orally on Days 1-21 of repeated 28-day cycles for up to 12 cycles in combination with a rituximab-product); and previously treated marginal zone lymphoma (MZL), in combination with a rituximab product (20 mg once daily orally on Days 1-21 of repeated 28-day cycles for up to 12 cycles in combination with a rituximab-product). Lenalidomide is provided as 2.5 mg, 5 mg, 10 mg, 15 mg, 20 mg, and 25 mg capsules. There is significantly increased risk of deep vein thrombosis an pulmonary embolism as well as risk of myocardial infarction and stroke in patients receiving REVLIMID with dexamethasone; anti-thrombotic prophylaxis is recommended.


In embodiments, the VEGF-pathway inhibitor is lenvatinib (LENVIMA). Lenvatinib is a kinase inhibitor that is indicated for the treatment of patients with locally recurrent or metastatic, progressive, radioactive iodine-refractory differentiated thyroid cancer (DTC); combination with everolimus, for the treatment of patients with advanced renal cell carcinoma (RCC) following one prior antiangiogenic therapy; for the first-line treatment of patients with unresectable hepatocellular carcinoma (HCC); and in combination with pembrolizumab, for the treatment of patients with advanced endometrial carcinoma that is not microsatellite instability-high (MSI-H) or mismatch repair deficient (dMMR), who have disease progression following prior systemic therapy and are not candidates for curative surgery or radiation. Lenvatinib is available as 4 mg and 10 mg capsules. Lenvatinib is taken daily at a recommended dosage of 24 mg orally (for DTC), 18 mg orally with 5 mg everolimus (for RTC), and 20 mg orally with 200 mg i.v. pembrolizumab (for endometrial carcinoma). For HCC, the recommended dosage is based on body weight:12 mg orally once daily for patients greater than or equal to 60 kg and 8 mg orally once daily for patients less than 60 kg. Doses are modified for adverse reactions as follows. For DTC, the first reduction is to 20 mg once daily, the second is to 14 mg once daily, the third is to 10 mg once daily. For RCC and endometrial carcinoma, the first reduction is to 14 mg once daily, the second is to 10 mg once daily, the third is to 8 mg once daily. For HCC patients that weigh 60 kg or more, the first reduction is to 8 mg once daily, the second reduction is to 4 mg once daily, and the third reduction is to 4 mg every other day; and for HCC patients that weight less than 60 kg, the first reduction is to 4 mg once daily, the second reduction is to 4 mg every other day, and the third is to discontinue. Hypertension, cardiac dysfunction, arterial thromboembolic events, and proteinuria are adverse reactions that may occur. For hypertension, blood pressure is monitored during treatment and lenvatinib is withheld for grade 3 hypertension despite optimal antihypertensive therapy. The drug can be resumed at a reduced dose when hypertension is controlled at less than or equal to grade 2. Lenvatinib is discontinued for grade 4 hypertension, grade 4 cardiac dysfunction, an arterial thromboembolic event of any grade, and nephrotic syndrome.


In embodiments, the VEGF-pathway inhibitor is ramucirumab. Ramucirumab (CYRAMZA) is a VEGFR2 antagonist indicated as a single agent or in combination with paclitaxel, for treatment of advanced or metastatic gastric or gastro-esophageal junction adenocarcinoma with disease progression on or after prior fluoropyrimidine- or platinum-containing chemotherapy; in combination with docetaxel, for treatment of NSCLC with disease progression on or after platinum-based chemotherapy; in combination with FOLFIRI, for the treatment of metastatic colorectal cancer with disease progression on or after prior therapy with bevacizumab, oxaliplatin, and a fluoropyrimidine; and as a single agent, for the treatment of hepatocellular carcinoma in patients who have an alpha fetoprotein of ≥400 ng/mL and have been treated with sorafenib. Ramucirumab is for intravenous infusion (first infusion over 60 minutes and if tolerated, all subsequent infusions may be administered over 30 minutes) and is supplied as a mg/10 mL (10 mg/mL) or 500 mg/50 mL (10 mg/mL) solution in a single-dose vial. Patients are premedicated with an intravenous histamine-1 receptor antagonist (e.g., diphenhydramine hydrochloride) before each infusion; or, for patients who have experienced a Grade 1 or 2 IRR, premedicate with a histamine-1 receptor antagonist, dexamethasone (or equivalent), and acetaminophen prior to each infusion. For gastric cancer, 8 mg/kg is administered every 2 weeks as a single agent or in combination with weekly paclitaxel. For non-small cell lung cancer (NSCLC), 10 mg/kg is administered on Day 1 of a 21-day cycle prior to docetaxel. For colorectal cancer, 8 mg/kg is administered every 2 weeks prior to FOLFIRI. For hepatocellular carcinoma, 8 mg/kg is administered every 2 weeks. ATEs, proteinuria, and hypertension are among the adverse events that may be induced by ramucirumab administration. For the first occurrence of increased urine protein levels greater than or equal to 2 g per 24 hours, doctors may withhold ramucirumab until urine protein level is less than 2 g per 24 hours and resume at a reduced dose (reduce 8 mg dose to 6 mg, and 10 mg dose to 8 mg). Upon a recurrence of urine protein level greater than 2 g per 24 hours following initial dose reduction, doctors may withhold ramucirumab until urine protein level is less than 2 g per 24 hours and resume at a reduced dose (reduce 6 mg dose to 5 mg, and 8 mg dose to 6 mg). Ramucirumab is permanently discontinued for urine protein levels greater than 3 g per 24 hours or nephrotic syndrome. For hypertensive adverse events, blood pressure should be monitored and hypertension should be treated. Ramucirumab should be withheld for severe hypertension until it is controlled; and should be permanently discontinued if it cannot be controlled with antihypertensive therapy and for hypertensive crisis or hypertensive encephalopathy


In embodiments, the VEGF-pathway inhibitor is cabozantinib. Cabozantinib (CABOMETYX, COMETRIQ) is a kinase inhibitor. CABOMETYX is indicated for the treatment of advanced renal cell carcinoma (RCC) and patients with hepatocellular carcinoma (HCC) who have been previously treated with sorafenib CABOMETRYX is provided as 20 mg, 40 mg, and 60 mg tablets and is administered once daily at a dose of 60 mg orally. COMETRIQ® is indicated for the treatment of patients with progressive, metastatic medullary thyroid cancer (MTC). The recommended dose is 140 mg orally, once daily, and COMETRIQ is supplied as a 20 mg or 80 mg capsule.


For both CABOMETRYX and COMETRIZ, doses can be reduced if coadministered with strong CYP3A4 inhibitors (e.g., ketoconazole, ritonavir, clarithromycin), or if adverse reactions occur. For example, CABOMETRYX can be reduced from 60 mg daily to 40 mg daily, or from 40 mg daily to 20 mg daily, and if 20 mg daily is not tolerated, CABOMETRYX should be discontinued; and COMETRIZ daily administration can be reduced by 40 mg (e.g., from 140 to 100, or from 100 to 60). For coadministration with strong CYPA34 induces, CABOMETRYX should be increased by 20 mg daily (for example, from 60 mg to 80 mg daily or from 40 mg to 60 mg daily) as tolerated; and COMETRIQ should be increased by 40 mg (e.g., 140 mg to 180 mg daily or 100 mg to 140 mg daily) as tolerated. Patients are monitored for hypertension and proteinuria, and cabozantinib is interrupted for hypertension that is not adequately controlled with anti-hypertensive therapy; and is discontinued for hypertensive crisis or severe hypertension that cannot be controlled with anti-hypertensive therapy. Cabozantinib is discontinued for nephrotic syndrome.


In embodiments, the VEGF-pathway inhibitor is pazopanib. Pazopanib (VOTRIENT) is a kinase inhibitor indicated for the treatment of patients with advanced renal cell carcinoma (RCC) or advanced soft tissue sarcoma (STS) who have received prior chemotherapy. 800 mg is administered once daily. For RCC, the initial dose reduction should be 400 mg, and additional dose decrease or increase should be in 200-mg steps based on individual tolerability. For STS, a decrease or increase should be in 200-mg steps based on individual tolerability. The recommended dose for patients with moderate hepatic impairment is 200 mg orally once daily and pazopanib is not recommended in patients with severe hepatic impairment. Concomitant use with strong CYP3A4 inhibitors should be avoided; if it is warranted, the pazopanib dose should be reduced to 400 mg. VOTRIENT is provided in a dosage form of 200 mg tablets. Cardiac dysfunction, arterial thromboembolic events, venous thromboembolic events, hypertension including hypertensive crisis, and proteinuria are among the adverse events for which patients should be monitored. Blood pressure should be well controlled before initiating pazopanib.


In embodiments, the VEGF-pathway inhibitor is sunitinib. Sunitinib malate (SUTENT) is a kinase inhibitor indicated for treatment of gastrointestinal stromal tumor (GIST) after disease progression on or intolerance to imatinib mesylate, treatment of advanced RCC, adjuvant treatment of adult patients at high risk of recurrent ACC following nephrectomy, and treatment of progressive, well-differentiated pancreatic neuroendocrine tumors (pNET) in patients with unresectable locally advanced or metastatic disease. The dosage form of sunitinib malate is 12.5 mg, 25 mg, 37.5 mg, or 50 mg capsules. For GIST and advanced RCC, the treatment regimen is 50 mg orally once daily, 4 weeks on treatment followed by 2 weeks off. For adjuvant RCC, the treatment regimen is 50 mg orally once daily, 4 weeks on treatment followed by 2 weeks off for nine 6-week cycles. For pNET, the treatment regimen is 37.5 mg orally once daily, continuously without a scheduled off-treatment period. Strong CYP3A4 inhibitors such as ketoconazole may increase sunitinib plasma concentrations and coadministration should be avoided. A dose reduction for to a minimum of 37.5 mg (GIST and RCC) or 25 mg (pNET) daily should be considered if sunitinib must be co-administered with a strong CYP3A4 inhibitor. CYP3A4 inducers such as rifampin may decrease sunitinib plasma concentrations and coadministration should be avoided. A dose increase for to a maximum of 87.5 mg (GIST and RCC) or 62.5 mg (pNET) daily should be considered if sunitinib must be co-administered with a CYP3A4 inducer. Adverse events that may occur and should be monitored for include cardiovascular events, hypertension, and proteinuria.


In embodiments, the VEGF-pathway inhibitor is regorafenib. Regorafenib (STIVARGA) is a kinase inhibitor indicated for the treatment of patients with metastatic colorectal cancer (CRC) who have been previously treated with fluoropyrimidine-, oxaliplatin- and irinotecan-based chemotherapy, an antiVEGF therapy, and, if RAS wild-type, an anti-EGFR therapy; patients with locally advanced, unresectable or metastatic GIST who have been previously treated with imatinib mesylate and sunitinib malate; and HCC patients who have been previously treated with sorafenib. The dosage form is 40 mg tablets. The recommended dose is 160 mg orally, once daily for the first 21 days of each 28-day cycle. If dose modifications are required, the dose should be reduced in 40 mg (one tablet) increments; the lowest recommended daily dose of regorafenib is 80 mg daily. Regorafenib should be temporarily or permanently withheld for severe or uncontrolled hypertension. For cardiac ischemia and infarction, regorafenib should be withheld and resumed only after resolution of acute ischemic events.


In embodiments, the VEGF-pathway inhibitor is axitinib. Axitinib (INLYTA) is a kinase inhibitor indicated for the treatment of advanced RCC after failure of one prior systemic therapy. Axitinib is provided in a dosage form 1 mg and 5 mg tablets. The starting dose is 5 mg orally twice daily. Over the course of treatment, patients who tolerate axitinib for at least two consecutive weeks with no adverse reactions>Grade 2 (according to the CTCAE), are normotensive, and are not receiving anti-hypertension medication, may have their dose increased. When a dose increase from 5 mg twice daily is recommended, the axitinib dose may be increased to 7 mg twice daily, and further to 10 mg twice daily using the same criteria. Over the course of treatment, management of some adverse drug reactions may require temporary interruption or permanent discontinuation and/or dose reduction. If dose reduction from 5 mg twice daily is required, the recommended dose is 3 mg twice daily. If additional dose reduction is required, the recommended dose is 2 mg twice daily. If coadministration with strong CYPA4/5 inhibitors is required, the dose of axitinib should be decreased by approximately half. Blood pressure should be well-controlled prior to initiating axitinib therapy and patients should be monitored for hypertension and treated as needed. For persistent hypertension despite use of anti-hypertensive medications, the axitinib dose should be reduced. Patients should also be monitored for arterial and venous thromboembolic events, cardiac failure, and proteinuria. For moderate to severe proteinuria, the axitinib dose should be reduced or temporarily interrupted


In embodiments, the VEGF-pathway inhibitor is LONSURF. LONSURF is a combination of trifluridine, a nucleoside metabolic inhibitor, and tipiracil, a thymidine phosphorylase inhibitor, and is indicated for the treatment of adult patients with metastatic colorectal cancer who have been previously treated with fluoropyrimidine-, oxaliplatin- and irinotecan-based chemotherapy, an anti-VEGF biological therapy, and if RAS wild-type, an anti-EGFR therapy; or for the treatment of metastatic gastric or gastroesophageal junction adenocarcinoma previously treated with at least two prior lines of chemotherapy that included a fluoropyrimidine, a platinum, either a taxane or irinotecan, and if appropriate, HER2/neu-targeted therapy. The dosage form of LONSURF® is 15 mg trifluridine/6.14 mg tipiracil or 20 mg trifluridine/8.19 mg tipiracil. The recommended dosage is 35 mg/m2 up to a maximum of 80 mg per dose (based on the trifluridine component) orally twice daily with food on Days 1 through 5 and Days 8 through 12 of each 28-day cycle. Doses are rounded to the nearest 5 mg increment. Within a treatment cycle, LONSURF is withheld for any of the following: absolute neutrophil count (ANC) less than 500/mm3 or febrile neutropenia, platelets less than 50,000/mm3, Grade 3 or 4 non-hematologic adverse reaction. After recovery, LONSURF can be resumed after reducing the dose by 5 mg/m2/dose. A maximum of 3 dose reductions are permitted LONSURF dosage is not escalated after it has been reduced. LONSURF is discontinued in patients who are unable to tolerate a dose of 20 mg/m2 orally twice daily.


In embodiments, the VEGF-pathway inhibitor is ponatinib. Ponatinib (ICLUSIG) is a kinase inhibitor indicated for treatment of adult patients with chronic phase, accelerated phase, or blast phase chronic myeloid leukemia (CML) or Ph+ ALL for whom no other tyrosine kinase inhibitor (TKI) therapy is indicated; or for treatment of adult patients with T315I-positive CML (chronic phase, accelerated phase, or blast phase) or T315I-positive Philadelphia chromosome positive acute lymphoblastic leukemia (Ph+ ALL). The dosage form is 15 mg, 30 mg, and 45 mg tablets. The recommended starting dose is 45 mg taken orally once daily with or without food. Dose modifications may be made for neutropenia and thrombocytopenia that are unrelated to leukemia; or for hepatotoxicity or pancreatitis and elevation of lipase. The recommended dose is reduced to 30 mg once daily when administering ICLUSIG with strong CYP3A inhibitors. Arterial occlusion, venous thromboembolism, heart failure, hypertension, and cardiac arrhythmias are among the adverse events that can occur. Blood pressure should be monitored.


In embodiments, the VEGF-pathway inhibitor is vandetanib. Vandetanib (CAPRELSA) is a kinase inhibitor indicated for the treatment of symptomatic or progressive medullary thyroid cancer in patients with unresectable locally advanced or metastatic disease. The dosage form is 100 mg and 300 mg tablets, and the dosing regimen is 300 mg once daily. The dose can be reduced to 200 mg (two 100 mg tablets) and then to 100 mg for CTCAE Grade 3 or greater toxicities. Vandetanib should be discontinued or interrupted in the event of ischemic cerebrovascular events, hemorrhage, heart failure, diarrhea, hypertension, and/or reversible posterior leukoencephalopathy syndrome.


In embodiments, the VEGF-pathway inhibitor is sorafenib. Sorafenib (NEXAVAR) is a kinase inhibitor indicated for the treatment of unresectable HCC, advanced RCC, and locally recurrent or metastatic, progressive, differentiated thyroid carcinoma refractory to radioactive iodine treatment. The dosage form is 200 mg tablets. For dosing, 400 mg is administered orally twice daily at least 1 hour before or 2 hours after a meal. Treatment should continue until the patient is no longer clinically benefiting from therapy or until unacceptable toxicity occurs. When dose reduction is necessary, the dose may be reduced to 400 mg once daily. If additional dose reduction is required, vandetanib may be reduced to a single 400 mg dose every other day. Dermatologic toxicities, cardiovascular events, and hypertension should be monitored.


In embodiments, the VEGF-pathway inhibitor is everolimus. Everolimus is an inhibitor of mammalian target of rapamycin (mTOR) marketed as AFINITOR, AFINITOR DISPERZ, or ZORTRESS. AFFINITOR is indicated for treatment of postmenopausal women with advanced hormone receptor-positive, HER2-negative breast cancer in combination with exemestane after failure of treatment with letrozole or anastrozole; adults with progressive neuroendocrine tumors of pancreatic origin (PNET) and adults with progressive, well-differentiated, non-functional neuroendocrine tumors (NET) of gastrointestinal (GI) or lung origin that are unresectable, locally advanced or metastatic; adults with advanced RCC after failure of treatment with sunitinib or sorafenib; and adults with renal angiomyolipoma and tuberous sclerosis complex (TSC), not requiring immediate surgery. AFINITOR and AFINITOR DISPERZ are indicated for the treatment of adult and pediatric patients aged 1 year and older with TSC who have subependymal giant cell astrocytoma (SEGA) that requires therapeutic intervention but cannot be curatively resected. AFINITOR DISPERZ is also indicated for the adjunctive treatment of adult and pediatric patients aged 2 years and older with TSC associated partial-onset seizures. Zortess is indicated for prophlylaxis of kidney transplant rejection (in combination with basiliximab, cyclosporine, and corticosteroids) or liver transplant rejection (in combination with tacrolimus and corticosteroids). The dosage form of AFINITOR is 2.5 mg, 5 mg, 7.5 mg, and 10 mg tablets; the dosage form of AFINITOR DISPERZ is 2 mg, 3 mg, and 5 mg tablets; the dosage form of ZORTRESS is 0.25 mg, 0.5 mg, and 0.75 mg. For breast cancer, NET, RCC, and TSC-associated angiomyolipoma, the approved dosage is 10 mg orally once daily. For TSC-associated SEGA, the approved dosage is 4.5 mg/m2 orally once daily, with dose adjustments to attain trough concentrations of 5-15 mg/mL. For kidney transplantation, the starting dose is 0.75 mg orally twice daily starting as soon as possible after transplantation; for liver transplantation the starting dose is 1.0 mg twice daily starting 30 days after transplantation. Everolimus concentrations are monitored and maintenance doses are adjusted to achieve trough concentrations within 3-8 ng/mL target range using LC/MS/MS assay method. Patients taking concomitant angiotensin-converting enzyme (ACE) inhibitors may be at increased risk of angioedema and proteinuria.


In embodiments, the VEGF-pathway inhibitor is thalidomide. Thalidomide (THALOMID) is indicated for the treatment of patients with newly diagnosed multiple myeloma (MM) in combination with dexamethasone; treatment of acute treatment of the cutaneous manifestations of moderate to severe erythema nodosum leprosum (ENL); and as a maintenance therapy for prevention and suppression of the cutaneous manifestations of ENL recurrence. Thalidomide is provided in a dosage form of 50 mg, 100 mg, 150 mg, and 200 mg. For MM, patients are administered 200 mg orally once daily, and the recommended dose of dexamethasone is 40 mg/day on days 1-4, 9-12, and 17-20 every 28 days. For ENL, patients are administered 100 to 300 mg/day for an episode of cutaneous ENL and up to 400 mg/day for severe cutaneous ENL. Dosing is continued until signs and symptoms of active reaction have subsided, usually a period of at least 2 weeks. Patients should be monitored for venous thromboembolism and ischemic heart disease (including myocardial infarction) and stroke.


In embodiments, the VEGF-pathway inhibitor is temsirolimus. Temsirolimus (TORISEL) is a kinase inhibitor indicated for treatment of advanced RCC. The dosage form is a 25 mg/mL solution for injection. The recommended dose of TORISEL is 25 mg infused over a 30-60 minute period once a week, until disease progression or unacceptable toxicity. Antihistamine pre-treatment is recommended. Temsirolimus should be held for absolute neutrophil count (ANC)<1,000/mm{circumflex over ( )}3, platelet count<75,000/mm{circumflex over ( )}3, or NCI CTCAE grade 3 or greater adverse reactions. Once toxicities have resolved to grade 2 or less, it may be restarted with the dose reduced by 5 mg/week to a dose no lower than 15 mg/week. The concomitant use of strong CYP3A4 inhibitors should be avoided (e.g. ketoconazole, itraconazole, clarithromycin, atazanavir, indinavir, nefazodone, nelfinavir, ritonavir, saquinavir, telithromycin, and voriconazole). Grapefruit juice may also increase plasma concentrations of sirolimus (a major metabolite of temsirolimus) and should be avoided. If patients must be co-administered a strong CYP3A4 inhibitor, based on pharmacokinetic studies, a temsirolimus dose reduction to 12.5 mg/week should be considered. The use of concomitant strong CYP3A4 inducers should be avoided (e.g. dexamethasone, phenytoin, carbamazepine, rifampin, rifabutin, rifampacin, phenobarbital). If patients must be co-administered a strong CYP3A4 inducer, based on pharmacokinetic studies, a temsirolimus dose increase from 25 mg/week up to 50 mg/week should be considered. Patients should be monitored for proteinuria and nephrotic syndrome.


In embodiments, the VEGF-pathway inhibitor is interferon alfa. Interferon alfa (interferon alfa-2B, interferon alfa-N3, peginterferon alfa-2B, and peginterferon alfa-2A) is marketed as INTRON A, PEGASYS, PEGINTRON, ALFERON N, and SYLATRON.


INTRON A is indicated for treatment with hairy cell leukemia (2 million IU/m2 administered intramuscularly or subcutaneously 3 times per week for up to 6 months), malignant melanoma (20 million IU/m2 as an intravenous infusion 5 consecutive days per week, for 4 weeks, with maintenance of treatment of 10 million IU/m2 as a subcutaneous injection three times per week for 48 weeks), follicular lymphoma (5 million IU subcutaneously three times per week for up to 18 months in conjunction with anthracycline-containing chemotherapy regimen and following completion of the chemotherapy regimen), condylomata acuminate 1.0 million IU per lesion in a maximum of 5 lesions in a single course; lesions are injected three times weekly on alternate days for 3 weeks), AIDS-related Kaposi's sarcoma (30 million IU/m2/dose administered subcutaneously or intramuscularly three times per week until disease progression or maximal response has been achieved after 16 weeks of treatment), chronic hepatitis C (3 million IU three times per week subcutaneously or intramuscularly), and chronic hepatitis B (in adults, 30 to 35 million IU per week, administered subcutaneously or intramuscularly, either as 5 million IU daily or as 10 million IU three times per week for 16 weeks; and in pediatrics, 3 million IU/m2 three times per week for the first week followed by dose escalation to 6 million IU/m2 three times per week subcutaneously, for a total duration of 16 to 24 weeks). PEGASYS is indicated for chronic hepatitis (180 mcg per week or 1.5 mcg/kg/week in adults; and 180 mcg/1.73 m2×BSA per week or 60 mcg/m2 per week in pediatrics). Potential adverse events include cardiovascular disorders and ischemic and hemorrhagic cerebrovascular events.


In embodiments, the VEGF-pathway inhibitor is rhEndostatin. rhEndostatin (ENDOSTAR) is indicated for HCC, NSCLC (squamous or non-squamous), postoperative NSCLC, advanced NSCLC with EGFR mutations, solid tumors in pediatric patients, and metastatic melanoma. For HCC, dosing is 30 mg/d, from 5 days before radiotherapy, for 7 days, 21 per cycle, with concurrent standard radiotherapy for HCC. For squamous NSCLC, dosing is 15 mg/m{circumflex over ( )}2 for 5 days and 200 mg of pembrolizumab at day 1 in each cycle, repeating every 3 weeks till PD or unacceptable toxicities. Squamous NSCLC patients also receive carboplatin (5U/AUC) or cisplatin (75 mg/m2) and [nab]-paclitaxel (100 mg/m2) for the first 4 cycles. For non-squamous NSCLC, dosing is 15 mg/m2 for 5 days, 200 mg of pembrolizumab at day 1 and pemetrexed (500 mg/m2 day 1) are given in each cycle, repeating every 3 weeks till to PD or unacceptable toxicities. Squamous and non-squamous NSCLC also receive carboplatin (5U/AUC) or cisplatin (75 mg/m2) and [nab]-paclitaxel (100 mg/m2) (squamous) or pemetrexed (500 mg/m2 day 1) (non-squamous) for the first 4 cycles. For untreated stage IIIB/IV NSCLC, dosing is continuous intravenous infusion rh-endostatin at 7.5 mg/m2 for 14 days each cycle, 21 days as one cycle, 4 cycles in total, with docetaxel or pemetrexed. For advanced NSCLC with EGFR mutations, dosing is 15 mg CIV days 1-9, Q3W with icotinib. For postoperative NSCLC, dosing is rh-Endostatin 7.5 mg/m2 days 1-14; 21 d as a cycle with pemetrexed and cis-platinum or with docetaxel and cis-platinum. For phase III B/IV squamous lung cancer with GP, dosing is rh-Endostatin at 7.5 mg/m2, continuous intravenous infusion for 14 days each cycle, 21 days as one cycle, 4 cycles in total with gemcitabine, cisplatin. For advanced NSCLC with docetaxel, dosing is rh-endostatin at 7.5 mg/m2, IV on day 1-14 of each 21-28 day cycle with docetaxel. For metastatic melanoma, dosing is based on body surface area as 15 mg/m2 rh-endostatin with cisplatin and dacarbazine.


In embodiments, the VEGF-pathway inhibitor is cediranib. Cediranib (RECENTIN) is approved for use in cancer, including ovarian, breast, colorectal, metastatic colorectal, renal, lung, non-small cell lung cancer, sarcoma, glioblastoma, fallopian tube, peritoneal cancer, and triple-negative breast cancer. Dosing is as follows. For metastatic colorectal cancer: 20 mg cediranib once a day in combination with FOLFOX or XELOX chemotherapy. For recurrent glioblastoma: 30 mg as monotherapy once daily; 20 mg once daily in combination with lomustine (110 mg/m2) every 6 weeks. For recurrent, platinum chemotherapy-sensitive disease or ovarian cancer related to mutations in BRCA genes: 30 mg once a day with 200 mg olaparib twice a day. For recurrent ovarian, fallopian tube, peritoneal, or triple-negative breast cancer: (1) 20 mg daily and olaparib 100 mg twice daily (BID) (2) cediranib 20 mg daily, olaparib 200 mg BID; (3) cediranib 30 mg daily, olaparib 200 mg BID; (4) cediranib 30 mg daily, olaparib 400 mg BID. For advanced non-small cell lung cancer: cisplatin 80 mg/m2 on day 1 and gemcitabine 1250 mg/m2 on days 1 and 8 of a 3-week cycle, and daily oral cediranib at either 30 mg or 45 mg.


In embodiments, the VEGF-pathway inhibitor is semaxanib. Semaxanib is a tyrosine kinase inhibitor indicated for colorectal cancer, solid tumors, brain tumors, kidney cancer, melanoma, head and neck cancer, hematologic cancers, mesothelioma, soft tissue sarcomas, breast cancer, AIDS-Related Kaposi's Sarcoma, multiple myeloma, cervical cancer, prostate cancer, and ovarian cancer. For metastatic melanoma, 145 mg/m2 semaxanib is administered intravenously twice-weekly in combination with thalidomide, commencing at 200 mg daily with intrapatient dose escalation as tolerated; or 85 or 145 mg/m2 in combination with standard irinotecan/bolus 5-fluorouracil/leucovorin (IFL) for 4 weeks on/2 weeks off. For solid tumors, semaxanib is administered at a dose of 145 mg/m2 twice weekly. For metastatic colon cancer, semaxanib is administered at a dose of 85 or 145 mg/m2 twice weekly in combination with fluorouracil and leucovorin (given either weekly or daily for 5 days every 4 weeks). For Kaposi's sarcoma, semaxanib is administered at a dose of 65-145 mg/m2 i.v. biw for six cycles (of 29 days).


In embodiments, the VEGF-pathway inhibitor is pomalidomide. Pomalidomide (POMALYST) is a thalidomide analogue indicated for the treatment of adult patients with multiple myeloma (MM) who have received at least two prior therapies including lenalidomide and a proteasome inhibitor and have demonstrated disease progression on or within 60 days of completion of the last therapy; in combination with dexamethasone. POMALYST is also indicated for adult patients with AIDS-related Kaposi sarcoma (KS) after failure of highly active antiretroviral therapy (HAART) or in patients with KS who are HIV negative. For MM, pomalidomide is administered at a dose of 4 mg per day orally on days 1 through 21 of repeated 28-day cycles in combination with dexamethasone until disease progression. For KS, pomalidomide is administered at a dose of 5 mg per day taken orally on Days 1 through 21 of repeated 28-day cycles until disease progression or unacceptable toxicity. Coadministration with strong CYP1A2 Inhibitors should be avoided, but if unavoidable, pomalidomide dosing should be reduced to 2 mg. The dosage form of pomalidomide is 1 mg, 2 mg, 3 mg, or 4 mg capsules. Deep venous thrombosis (DVT), pulmonary embolism (PE), myocardial infarction, and stroke may occur in patients with multiple myeloma treated with POMALYST.


In embodiments, the VEGF-pathway inhibitor is alitretinoin. Alitretinoin (PANRETIN) is a gel indicated for topical treatment of cutaneous lesions in patients with AIDS-related Kaposi's sarcoma. Panretin gel is not indicated when systemic anti-KS therapy is required (e.g., more than 10 new KS lesions in the prior month, symptomatic lymphedema, symptomatic pulmonary KS, or symptomatic visceral involvement). Panretin gel should initially be applied two (2) times a day to cutaneous KS lesions. The application frequency can be gradually increased to three (3) or four (4) times a day according to individual lesion tolerance. Panretin gel is available in tubes containing 60 grams.


In embodiments, the VEGF-pathway inhibitor is imiquimod. Imiquimod is marketed as ALDARA and ZYCLARA. ALDARA is a 5% cream supplied in single-use packets (24 per box), each of which contains 250 mg of the cream, equivalent to 12.5 mg of imiquimod. ZYCLARA is provided as a 2.5% or 3.75% cream in packets or a pump. Imiquimod is indicated for the topical treatment of clinically typical, nonhyperkeratotic, nonhypertrophic actinic keratoses (AK) on the face or scalp in immunocompetent adults; biopsy-confirmed, primary superficial basal cell carcinoma (sBCC) in immunocompetent adults; maximum tumor diameter of 2.0 cm on trunk, neck, or extremities (excluding hands and feet), only when surgical methods are medically less appropriate and patient follow-up can be reasonably assured; and external genital and perianal warts/condyloma acuminata in patients 12 years old or older.


In embodiments, the VEGF-pathway inhibitor is sinecatechins. Sinecatechins (VEREGEN) is a 15% topical ointment indicated for the treatment of external genital and perianal warts (Condylomata acuminata) in immunocompetent patients 18 years and older. VEREGEN is to be applied three times per day to all external genital and perianal warts.


In embodiments, the VEGF-pathway inhibitor is vismodegib. Vismodegib (ERIVEDGE) is a hedgehog pathway inhibitor indicated for the treatment of adults with metastatic basal cell carcinoma, or with locally advanced basal cell carcinoma that has recurred following surgery or who are not candidates for surgery and who are not candidates for radiation. The recommended dosage is 150 mg orally once daily. The dosage form is 150 mg capsules.


In embodiments, the VEGF-pathway inhibitor is sonidegib. Sonidegib (ODOMZO) is a hedgehog pathway inhibitor indicated for the treatment of adult patients with locally advanced basal cell carcinoma (BCC) that has recurred following surgery or radiation therapy, or those who are not candidates for surgery or radiation therapy. The recommended dosage is 200 mg orally once daily taken on an empty stomach, at least 1 hour before or 2 hours after a meal. Serum creatine kinase (CK) levels and renal function tests are prior to initiating ODOMZO treatment. The dosage form is 200 mg capsules.


In embodiments, the VEGF-pathway inhibitor is pegaptanib sodium. Pegaptanib sodium (MACUGEN) is indicated for the treatment of neovascular (wet) age-related macular degeneration. MACUGEN is administered in a dose of 0.3 mg once every six weeks by intravitreous injection into the eye. The dosage form is a 0.3 mg/90 μL solution in a single-use syringe for intravitreal injection.


In embodiments, the VEGF-pathway inhibitor is dexamethasone. Dexamethasone intravitreal implant (OZURDEX) is a corticosteroid indicated for the treatment of macular edema following branch retinal vein occlusion (BRVO) or central retinal vein occlusion (CRVO), the treatment of non-infectious uveitis affecting the posterior segment of the eye, or the treatment of diabetic macular edema. The dosage form is an intravitreal implant containing 0.7 mg dexamethasone in the NOVADUR solid polymer drug delivery system.


In embodiments, the VEGF-pathway inhibitor is fluocinolone acetonide. Fluocinolone acetonide (ILUVIEN) contains a corticosteroid and is indicated for the treatment of diabetic macular edema (DME) in patients who have been previously treated with a course of corticosteroids and did not have a clinically significant rise in intraocular pressure. The dosage form is a non-bioerodible intravitreal implant containing 0.19 mg fluocinolone acetonide in a drug delivery system, and is intended for intravitreal injection.


In embodiments, the VEGF-pathway inhibitor is conbercept. Conbercept (COMPAQ SIQQ) is indicated for treatment of age-related macular degeneration (AMD) and other macular diseases, Idiopathic Choroidal Neovascularization, Diabetic Retinopathy, Macular Edema, Central Retinal Vein Occlusion, Tractional Retinal Detachment, Circumscribed Choroidal Haemangioma, uveitis, Polypoidal Choroidal Vasculopathy, and Corneal Neovascularization. For AMD and other retinal vascular disorders, conbercept may be administered at a dose of 0.5 mg/eye monthly for 3 months followed by 0.5 mg/eye every 3 months; or just 0.5 mg/eye every 3 months without the 3 month loading period; or 0.5 mg or 2.0 mg for 3 consecutive monthly doses, after which either monthly or as-needed (PRN) therapy is administered at the same previous dose; or 0.5 mg every 8 weeks and 1.0 mg every 12 weeks after 3 monthly injections as a loading phase.


In embodiments, the VEGF-pathway inhibitor is brolucizumab. Brolucizumab-dbll (BEOVU) is a human vascular endothelial growth factor (VEGF) inhibitor indicated for the treatment of AMD. BEOVU is administered by intravitreal injection. The recommended dose for BEOVU is 6 mg (0.05 mL of 120 mg/mL solution) monthly (approximately every 25-31 days) for the first three doses, followed by one dose of 6 mg (0.05 mL) every 8-12 weeks. The dosage form is a 6 mg/0.05 mL solution for intravitreal injection in a single-dose vial. There is a potential risk of arterial thromboembolic events (ATE) following intravitreal use of VEGF inhibitors


In embodiments, the VEGF-pathway inhibitor is selpercatinib. Selpercatinib (RETEVMO) is a kinase inhibitor indicated for the treatment of adult patients with metastatic RET fusion-positive NSCLC, adult and pediatric patients 12 years of age and older with advanced or metastatic RET-mutant medullary thyroid cancer (MTC) who require systemic therapy, and adult and pediatric patients 12 years of age and older with advanced or metastatic RET fusion-positive thyroid cancer who require systemic therapy and who are radioactive iodine-refractory (if radioactive iodine is appropriate). Patients are selected for treatment with RETEVMO based on the presence of a RET gene fusion (NSCLC or thyroid) or specific RET gene mutation (MTC). The recommended dosage in adults and pediatric patients 12 years of age or older is based on weight as follows. Less than 50 kg: 120 mg orally twice daily; 50 kg or greater: 160 mg orally twice daily. RETEVMO may be administered orally twice daily (approximately every 12 hours) until disease progression or unacceptable toxicity. Concomitant use of strong and moderate CYP3A inhibitors should be avoided, but if it cannot be avoided, the RETEVMO dose may be reduced as follows. If taking 120 mg twice daily: reduce to 80 mg twice daily with a moderate inhibitor and 40 mg twice daily with a strong inhibitor; if taking 160 mg twice daily: reduce to 120 mg twice daily with a moderate inhibitor and 80 mg twice daily with a strong inhibitor. Concomitant use of a PPI, a histamine-2 (H2) receptor antagonist, or a locally-acting antacid with RETEVMO should be avoided, but if it cannot be avoided, RETEVMO may be administered with food and/or 2 hours before or 10 hours after an H2 receptor antagonist; or 2 hours before or 2 hours after a locally-acting antacid. Dosing may also be reduced for severe hepatic impairment. The dosage form is 40 mg and 80 mg capsules. RETEVMO should not be initiated in patients with uncontrolled hypertension. Blood pressure should be monitored and RETEVMO should be withheld, reduced in dose, or permanently halted based on severity.


In embodiments, the VEGF-pathway inhibitor is nintedanib (OFEV). Nintedanib is a kinase inhibitor indicated for treatment of idiopathic pulmonary fibrosis (IPF), treatment of chronic fibrosing interstitial lung diseases (ILDs) with a progressive phenotype, and for slowing the rate of decline in pulmonary function in patients with systemic sclerosis-associated interstitial lung disease. Nintedanib is administered at a dose of 150 mg twice daily, about 12 hours apart. The dosage form is 150 mg or 100 mg capsules. Arterial thromboembolic events have been reported. Caution should be taken when treating patients at higher cardiovascular risk including known coronary artery disease. Treatment may be interrupted in patients who develop signs or symptoms of acute myocardial ischemia. For patients with mild hepatic impairment, the dose may be modified to 100 mg twice daily approximately 12 hours apart. In addition to symptomatic treatment, if applicable, dose reduction or temporary interruption may be indicated for the management of adverse reactions, until the specific adverse reaction resolves to levels that allow continuation of therapy. Treatment may be resumed at the full dosage (150 mg twice daily), or at the reduced dosage (100 mg twice daily), which subsequently may be increased to the full dosage. If a patient does not tolerate 100 mg twice daily, treatment with nintedanib may be discontinued. Dose modifications or interruptions may be necessary for liver enzyme elevations. Liver function tests (aspartate aminotransferase (AST), alanine aminotransferase (ALT), and bilirubin) may be conducted prior to initiation of treatment with nintedanib, at regular intervals during the first three months of treatment, and periodically thereafter or as clinically indicated. In patients who report symptoms that may indicate liver injury, including fatigue, anorexia, right upper abdominal discomfort, dark urine or jaundice, liver tests may be measured promptly. In patients with AST or ALT greater than 3 times the upper limit of normal (ULN) with signs or symptoms of liver injury and for AST or ALT elevations greater than 5 times the upper limit of normal, treatment may be discontinued. For AST or ALT greater than 3 times to less than 5 times the ULN without signs of liver damage, treatment may be interrupted or reduced to 100 mg twice daily. Once liver enzymes have returned to baseline values, treatment may be reintroduced at a reduced dosage (100 mg twice daily), which subsequently may be increased to the full dosage (150 mg twice daily).


In embodiments, the VEGF-pathway inhibitor is apatinib. Apatinib is indicated for treatment of advanced or metastatic gastric carcinoma, metastatic breast cancer, advanced hepatocellular carcinoma, metastatic colorectal cancer, esophageal cancer (advanced esophageal squamous cell carcinoma), and glioblastoma. Apatinib generally may be administered at a dose of 750 mg once daily. Other possible doses include 250, 500, 750, 850, and 1000 mg once daily. For advanced or metastatic gastric carcinoma, apatinib may be administered at a dose of 850 mg once daily or 425 mg twice daily. For advanced progressed lung adenocarcinoma patients with EGFR-TKI resistance, apatinib may be administered at a dose of 500 mg/m2 per day for 21 consecutive days alone or in combination with traditional chemotherapy drugs pemetrexed (50 mg/m2, once every 21 days) and docetaxel (75 mg/m2, once every 21 days). For metastatic colorectal cancer, apatinib may be administered at a dose of 125 mg, 250 mg, 500 mg, 850 mg once per day, alone or in combination with other agents in either 21 or 28 day cycles. For advanced esophageal squamous cell carcinoma, apatinib may be administered at a dose of 500 mg daily in a 28 day cycle, which may be reduced to 250 mg.


In embodiments, the VEGF-pathway inhibitor is motesanib. Motesanib is indicated for thyroid cancer (progressive or symptomatic, advanced or metastatic medullary thyroid cancer; progressive differentiated thyroid cancer), non-small cell lung cancer (advanced nonsquamous), gastrointestinal stromal cancer, colorectal cancer, breast cancer (HER2-negative locally recurrent or metastatic breast cancer), persistent or recurrent ovarian cancer, fallopian tube and primary peritoneal carcinomas, advanced solid tumors, and low-grade neuroendocrine tumors. For advanced nonsquamous non-small-cell lung cancer (NSCLC), motesanib may be administered at a dose of 125 mg once daily, or 75 mg twice daily (5 days on/2 days off), both with carboplatin (AUC, 6 mg/ml min) and paclitaxel (200 mg/m2) for up to six 3-week cycles. For HER2-negative locally recurrent or metastatic breast cancer: motesanib 125 mg orally once per day with paclitaxel (90 mg/m 2 on days 1, 8, and 15 every 3 weeks). For progressive or symptomatic, advanced or metastatic medullary thyroid cancer, progressive differentiated thyroid cancer, advanced solid tumors, and for persistent or recurrent ovarian, fallopian tube, and primary peritoneal carcinomas, motesanib may be administered at a dose of 125 mg daily. For ow-grade neuroendocrine tumors, motesanib may be administered at a dose of 125 mg once daily in combination with octreotide-LAR (30 mg administered on day 1 of each cycle 28-day cycle).


VEGF-pathway inhibitors may be administered in combination with one or more additional anti-cancer therapies. For example, VEGF-pathway inhibitors may be administered in combination with surgical therapy, radiation therapy, chemotherapy, immunotherapies (e.g. checkpoint inhibitors, adoptive cell transfer, antibodies, vaccines, cytokines, etc.), targeted therapies (e.g. small-molecule drugs, antibodies), hormone therapy, stem-cell transplant, and the like. The subject may be a candidate for or currently provided with any suitable combination of therapies prior to determination of risk of VEGF-inhibitor toxicities in the subject. Any suitable combination of therapies (e.g. VEGF-inhibitors, other anti-cancer therapies, supportive therapies, or any combination thereof) may be provided to the subject following determination of risk in the subject.


Any of the therapies described herein (e.g. VEGF-pathway inhibitors, supportive therapies, other anti-cancer therapies) may be provided by any suitable route. For example, the therapy may be provided orally. Alternatively, the therapy may be provided parenterally. Suitable doses and modes of administration may be determined based upon various factors, including the age, sex, weight, health of the subject, other medications being administered to the subject, and the like, using routine techniques known in the art.


By way of example and not of limitation, examples of the present disclosure will now be provided.


EXPERIMENTAL EXAMPLES
Example 1

The objective of the current study was to perform a GWAS of four randomized phase III clinical trials from the Cancer and Leukemia Group B (CALGB, now Alliance for Clinical Trials in Oncology, Alliance) to identify novel genes and genetic variants that showed a consistent risk of toxicity across the different studies.


Methods


Patients and Randomized, Phase III Clinical Trials


CALGB 80303 was conducted in advanced pancreatic cancer patients treated with gemcitabine and either 10 mg/kg bevacizumab or placebo. CALGB 40503 was conducted in hormone receptor-positive advanced-stage breast cancer patients treated with letrozole and either 15 mg/kg bevacizumab or placebo. CALGB 90401 was conducted in metastatic castration-resistant prostate cancer patients treated with docetaxel/prednisone with either 15 mg/kg bevacizumab or placebo. CALGB 40502 was conducted in locally recurrent or metastatic breast cancer patients treated with either nab-paclitaxel, ixabepilone, or paclitaxel, all administered in combination with 10 mg/kg bevacizumab. Patient eligibility, characteristics, stratifications, treatments, and the methods to detect progression of disease have been previously described.


Toxicity


Proteinuria and hypertension were recorded according to Common Toxicity Criteria for Adverse Events (CTCAE) version 3.0 (Table 1), per protocol. The composite toxicity is defined as the occurrence of either proteinuria or hypertension or both. For CALGB 40502, data on proteinuria and composite toxicity were not available. Urine protein levels were measured on day 1 and every four weeks after starting treatment in CALGB 80303; on day 1 of the 1st cycle and up to 5 days before or on the day of treatment for subsequent cycles in CALGB 40503; and within 48 hours prior to every treatment cycle in CALGB 90401. Blood pressure was obtained on day 1 of each cycle in all trials, and plus on day 15 in CALGB 80303.









TABLE 1







Hypertension and proteinuria grades of toxicity according


to Common Toxicity Criteria of Adverse Events (CTCAE) v3.0.


Urine dipstick test result: 1+ (15-30 mg/dL), 2+ (100-300 mg/dL), 3+


(300-1000 mg/dL), and 4+ (>1000 mg/dL). WNL within normal limits.












Toxicity
Grade 1
Grade 2
Grade 3
Grade 4
Grade 5





Proteinuria
1+ or
2+ to 3+ or
4+ or
Nephrotic
Death



0.15-1.0
>1.0-3.5
>3.5
syndrome




g/24 hrs
g/24 hrs
g/24 hrs




Hyper-
Asympto-
Recurrent or
Requiring
Life-
Death


tension
matic,
persistent
more than
threatening




transient
(>24 hrs) or
one
conse-




(<24 hrs)
symptomatic

quences




increase by
increase by
drug or
(e.g.,




>20 mmHg
>20 mmHg
more
hyper-




(diastolic)
(diastolic) or
intensive
tensive




or to
to >150/100
therapy
crisis)




>150/100 if
if previously
than





previously
WNL;
previously





WNL;
monotherapy






intervention
may be






not
indicated






indicated









Bevacizumab-related toxicity was defined as the occurrence of toxicity (grade≥2 or grade≥3 of hypertension, proteinuria, or either proteinuria or hypertension—composite toxicity) after the start of treatment. Only toxicities with attribution of “possibly related” or higher were included. The occurrence of treatment-terminating events was used for censoring, as they determined the exit of the patients from the trial. Treatment-terminating events included death, disease progression, other toxicities defined per protocol, withdrawal of consent, loss to follow up, or unknown recorded events. The time to event was reconstructed manually for each patient in each study, as performed previously. The time to event was calculated as the time from the first administration of bevacizumab to the first date of experiencing the toxicity of interest, or other treatment-terminating events, whichever occurred first.


Genotyping and Quality Control


DNA for genotyping was obtained from peripheral blood. The genotyping platforms used in each study are described in Table 2, and the number of SNPs used for analysis after quality control (QC) are described in FIG. 1. Additional information on the quality control procedures can be found in the individual publications of the GWAS data.









TABLE 2







Patients of European ancestry treated with bevacizumab used in the GWAS data.


CALGB Cancer and Leukemia Group B, SD standard deviation, composite toxicity is defined


as the occurrence of either proteinuria or hypertension or both.














80303
40503
90401
40502











CALGB trial
n = 154
n = 105
n = 316
n = 466















Age
Mean (SD)
64.1 (10.2)
68.4 (8.3)
56.9 (11.7)
57.2 (10.7)


Gender
Male
90
0
316
0



Female
64
105
0
466











Cancer type
Advanced
Hormone receptor-
Metastatic castration-
Recurrent or














pancreatic cancer
positive advanced-
resistant prostate
metastatic breast





stage breast cancer
cancer
cancer











Treatment
Gemcitabine 1,000
Letrozole 2.5 mg
Docetaxel 75 mg/m2
Paclitaxel 90 mg/m2 or














mg/m2 on days 1,
orally/day plus either
in combination with
nab-paclitaxel 150




8, and 15 plus
placebo or
prednisone 5 mg
mg/m2 or ixabepilone




either placebo or
bevacizumab 15
orally on day 1 plus
16 mg/m2 on days 1,




bevacizumab 10
mg/kg every 21 days
either placebo or
8, and 15 plus




mg/kg on days 1

bevacizumab 15
bevacizumab 10




and 15

mg/kg every 21 days
mg/kg on days 1 and







15











Genotype platform
IIlumina
IIlumina Human
IIlumina
IIlumina Human














HumanHap550-
OmniExpressExome-8
HumanHap610-Quad
OmniExpressExome-8




Quad





















Grade ≥ 2
Grade ≥ 3
Grade ≥ 2
Grade ≥ 3
Grade ≥ 2
Grade ≥ 3
Grade ≥ 2
Grade ≥ 3















Hypertension (n, %)
26 (16.9)
19 (12.3)
53 (50.5)
29 (27.6)
47 (15.0)
22 (7.0)
143 (30.7)
50 (10.7)














Proteinuria (n, %)
26 (16.9)
9 (5.8)
32 (30.5)
10 (9.5) 
20 (6.4) 
 5 (1.6)



Composite toxicity (n, %)
43 (27.9)
26 (16.9)
73 (69.5)
34 (32.4)
61 (19.4)
26 (8.2)










Statistical Analysis


SNP-Based Association Testing


The association between SNPs and toxicities (grade≥2 or grade≥3) was tested in genetic European patients in the bevacizumab arm. Ethnicity information was determined by estimating the genetic ancestral origin of patients using the principal components analysis software implemented in Eigenstrat. A cause-specific Cox model, where the outcome is defined as the pair of time event and the censoring indicator, was fitted to obtain the estimate of the SNP effect (and the corresponding standard error estimate) on toxicity in each individual study. The analyses were powered against an additive genetic model. The inverse variance formula was used to combine the SNP effect in each study to obtain the estimate (β) of the SNP-toxicity association and its standard error. The heterogeneity across studies was examined by the Cochran's test (no heterogeneity was detected). Cox analyses for each variant, adjusting for age and gender, were performed by adding those variables as covariates in the model. The reported results are unadjusted, unless stated otherwise. The reported p values are not corrected for multiple comparisons. Quantile-quantile (Q-Q) plots were generated.


Gene-Based Association Testing


Under the same model described above, a gene-based analysis was also performed. First, all the human protein-coding genes were mapped to SNPs according to the location of SNPs with a margin equaling 50 by using the R package “snplist”. Next, the cause-specific Cox model was fitted to obtain the score statistics for SNP by toxicity association in each study. Last, the Sequence Kernel Association Test (SKAT) was used to combine the SNP-level test statistics. This method allowed for different directions of the SNP effect in a gene and could accommodate also common alleles. From the SKAT test, the weighted quadratic statistics were computed using the MASS software, with p-values determined by the re-sampling method. The reported results are unadjusted, unless stated otherwise. The reported p values are not corrected for multiple comparisons. Q-Q plots were also generated for this analysis.


Functional Annotation of Variants


Functional annotation of SNPs and genes was performed using the SCAN database. Variants were analyzed by the LDlink web-based application for analyses of linkage disequilibrium (LD). UCSC Genome Browser (http://genome.ucsc.edu/), RegulomeDB and Haploreg v4 were used for functional inference. The Genotype-Tissue Expression project (GTEx v7) and NephQTL were used for expression quantitative trait loci (eQTL) analyses.


Results


A total of 1,041 cancer patients of European ancestry treated with bevacizumab with available genotyping information were included in the study. The characteristics of patients from each trial, as well as the prevalence of toxicities, are shown in Table 2. Grade≥2 hypertension (15.0%-50.5%) was more prevalent than grade≥2 proteinuria (5.4-30.5%). The prevalence of either grade≥2 proteinuria or grade≥2 hypertension (composite toxicity) was 19.4-69.5%. Considering only the patients who had both toxicities, the prevalence was 1.9%-11.4%. The prevalence of these toxicities was higher in female patients in the breast cancer studies (CALGB 40502 and 40503) than in male patients in the prostate cancer study (CALGB 90401). A higher prevalence was also observed in females compared to males in the pancreatic cancer study (CALGB 80303) (Table 3).









TABLE 3







Prevalence of hypertension and proteinuria in CALGB 80303 by gender.


Composite toxicity is defined as the occurrence of


either proteinuria or hypertension or both.










Grade ≥2
Grade 3












Female
Male
Female
Male



(n = 64)
(n = 90)
(n = 64)
(n = 90)





Hypertension (n, %)
14 (21.9)
12 (13.3)
 9 (14.1)
10 (11.1)


Proteinuria (n, %)
11 (17.2)
15 (16.7)
6 (9.4)
3 (3.3)


Composite toxicity (n, %)
20 (31.2)
23 (25.6)
14 (21.9)
12 (13.3)









Variants and Genes Associated with Bevacizumab-Induced Proteinuria


For the SNP-based analysis of grade≥2, the Manhattan and Q-Q plots are shown in FIG. 2. 90 variants were identified as associated with bevacizumab-induced proteinuria (Table 4).









TABLE 4







SNP's associated with Proteinuria (grade ≥ 2)

























effect
reference
MAF
MAF
MAF










SNP
CH
BP
allele
allele
80303
40503
90401
gene
feature
Flanking gene
Flanking gene
p-value unadjusted
effect (β) unadjusted
p-value adjusted
effect (β) adjusted

























rs339947
5
14071067
A
C
0.12
.
0.14
NA
NA
DNAH5
TRIO
7.66E−08
1.27
1.58E−07
1.26


rs13293961
9
104807170
A
C
.
.
0.08
CYLC2
missense
LOC100131879
SMC2
2.39E−06
1.56
2.60E−06
1.61


rs12612153
2
44755864
C
A
0.11
.
0.11
C2orf34
intron
PREPL
LOC100130502
3.89E−06
1.16
6.93E−06
1.15


rs7180310
15
22890430
A
C
0.06
0.05
.
NA
NA
SNORD116-24
SNORD116-25
4.10E−06
1.54
4.19E−06
1.55


rs12482855
21
42065030
A
G
0.06
0.06
0.06
NA
NA
RIPK4
PRDM15
6.28E−06
1.20
1.09E−05
1.20


rs408130
5
14059289
A
G
0.21
.
0.28
NA
NA
DNAH5
TRIO
6.33E−06
1.07
6.94E−06
1.09


rs418173
5
14058033
A
G
0.21
.
0.28
NA
NA
DNAH5
TRIO
6.33E−06
1.07
6.94E−06
1.09


rs11716628
3
35851495
G
A
.
0.18
.
NA
NA
ARPP-21
LOC100131711
6.87E−06
1.39
1.04E−05
1.39


rs7959783
12
67109382
G
A
0.31
0.26
0.33
NA
NA
MDM1
LOC729376
7.01E−06
0.72
6.56E−06
0.73


rs627761
11
125330918
G
A
0.10
.
0.09
LOC338667
intron
DDX25
CDON
7.49E−06
1.19
1.34E−05
1.18


rs2688994
3
126300783
A
G
0.13
0.14
0.14
SLC12A8
intron
HEG1
ZNF148
8.13E−06
0.92
4.38E−06
0.98


rs10486445
7
24980507
G
A
0.42
0.35
0.39
OSBPL3
intron
DFNA5
CYCS
1.17E−05
0.75
1.11E−05
0.78


rs17345945
8
68674808
A
G
0.09
.
0.08
CPA6
intron
LOC100132812
PREX2
1.36E−05
1.15
1.30E−05
1.19


rs13276511
8
86959167
G
A
0.06
.
.
NA
NA
REXO1L7P
LOC642137
1.39E−05
1.40
4.01E−05
1.37


rs17624773
12
33136580
A
G
0.10
0.06
0.14
NA
NA
ASSP14
SYT10
1.79E−05
0.96
1.59E−05
0.97


rs1509247
4
22952896
G
A
0.43
0.43
0.52
LOC643751
intron
GBA3
PPARGC1A
1.83E−05
0.70
1.09E−05
0.72


rs12345440
9
102993955
G
A
0.09
.
0.10
RP11-35N6.1
intron
LOC392374
LOC347275
1.89E−05
1.23
1.45E−05
1.28


rs4916009
1
65144006
A
G
0.08
.
0.09
JAK1
intron
RAVER2
LOC100130270
2.10E−05
1.17
8.86E−06
1.24


rs2378865
14
30952224
G
A
.
0.42
.
NA
NA
HEATRSA
C14orf126
2.35E−05
1.11
2.10E−05
1.14


rs2064949
20
19756654
G
A
.
0.19
.
NA
NA
RPL12L3
RIN2
2.38E−05
1.07
6.46E−06
1.07


rs12536799
7
133378576
C
A
0.11
.
0.08
EXOC4
intron
FAM10A7
LRGUK
2.82E−05
1.24
6.20E−06
1.25


rs6483735
11
20844275
A
G
0.19
0.20
0.17
NELL1
intron
LOC100132634
LOC100130160
2.92E−05
0.80
1.61E−05
0.83


rs12352151
9
102995858
A
G
0.10
.
0.10
RP11-35N6.1
intron
LOC392374
LOC347275
3.07E−05
1.20
2.60E−06
1.22


rs1431477
9
102994274
C
A
0.10
.
0.10
RP11-35N6.1
intron
LOC392374
LOC347275
3.07E−05
1.20
4.19E−06
1.22


rs11662763
18
5847091
A
G
0.14
0.11
0.13
NA
NA
LOC645355
TTMA
3.11E−05
0.78
1.87E−05
0.79


rs4780054
15
27387295
A
G
0.38
0.40
0.40
NA
NA
NDNL2
LOC100130736
3.16E−05
0.72
1.11E−05
0.70


rs17725486
7
25037388
A
G
.
0.30
.
NA
NA
OSBPL3
CYCS
3.26E−05
1.00
4.38E−06
1.03


rs2391081
7
25034923
A
G
.
0.30
.
NA
NA
OSBPL3
CYCS
3.26E−05
1.00
6.18E−06
1.03


rs879965
7
46015867
G
A
0.46
0.47
0.44
NA
NA
LOC222052
LOC730338
3.29E−05
0.71
5.05E−05
0.68


rs5927577
X
30558644
A
G
.
0.38
.
NA
NA
LOC652904
GK
3.53E−05
1.13
1.34E−05
1.12


rs12910488
15
59578470
C
T
.
0.42
.
NA
NA
RORA
VPS13C
3.60E−05
−1.32
6.94E−06
−1.33


rs7616936
3
85886475
C
A
0.08
.
0.12
CADM2
intron
LOC440970
LOC728144
3.71E−05
1.04
3.43E−05
1.01


rs13255802
8
80730920
G
A
.
0.23
.
STMN2
intron
LOC100128963
HEY1
3.85E−05
1.16
3.15E−05
1.15


rs11532247
12
19614829
A
G
0.50
.
0.49
NA
NA
AEBP2
LOC400013
3.90E−05
0.91
2.09E−05
0.95


rs7614155
3
74196658
G
A
0.25
.
0.27
NA
NA
LOC100129282
HSP90AB5P
3.95E−05
0.90
8.86E−06
0.90


rs11196791
10
116323964
G
A
.
0.23
.
ABLIM1
intron
AFAP1L2
PPIAP19
3.97E−05
1.16
1.61E−05
1.15


rs2901044
10
116317439
A
G
.
0.23
.
ABLIM1
intron
AFAP1L2
PPIAP19
3.97E−05
1.16
1.73E−05
1.15


rs6996073
8
18594558
C
T
.
0.06
.
PSD3
intron
NAT2
NSAP11
4.21E−05
1.36
1.72E−04
1.39


rs972433
8
18599078
C
T
.
0.06
.
PSD3
intron
NAT2
NSAP11
4.30E−05
1.35
1.77E−04
1.38


rs2491608
1
105673803
A
G
0.44
.
0.46
NA
NA
LOC642337
LOC100130867
4.32E−05
0.94
3.25E−05
0.92


rs13275710
8
41514221
A
G
0.17
.
0.13
GINS4
intron
KRT18P37
AGPAT6
4.57E−05
1.05
1.45E−05
1.06


rs12777350
10
90351816
A
G
0.06
0.07
0.06
LIPJ
intron
C10orf59
LOC389992
4.69E−05
1.10
3.74E−05
1.10


rs6597976
11
1101474
A
G
0.06
0.06
0.07
NA
NA
MUC2
LOC100132635
5.03E−05
0.99
3.87E−05
1.01


rs5904577
X
21604594
A
G
.
0.05
.
NA
NA
KLHL34
SMPX
6.06E−05
1.68
2.10E−05
1.71


rs2328452
20
19713174
A
G
.
0.17
.
LOC100130408
intron
SLC24A3
RPL12L3
6.46E−05
0.98
5.10E−05
0.97


rs6112574
20
19710695
G
A
.
0.17
.
LOC100130408
intron
SLC24A3
RPL12L3
6.46E−05
0.98
5.31E−05
0.97


rs7804806
7
75433618
A
G
0.32
0.29
.
POR
intron
SNORA14A
TMEM120A
6.67E−05
0.74
7.41E−05
0.73


rs4579610
9
89230980
G
A
0.25
0.26
.
NA
NA
LOC100132348
DAPK1
6.82E−05
0.76
1.25E−04
0.74


rs546913
6
112396275
A
G
0.05
.
0.05
NA
NA
FYN
WISP3
6.84E−05
1.41
2.61E−05
1.51


rs689328
6
112393380
A
G
0.05
.
0.05
NA
NA
FYN
WISP3
6.84E−05
1.41
2.61E−05
1.51


rs1358206
3
74198360
G
A
0.30
.
0.31
NA
NA
LOC100129282
HSP90AB5P
7.03E−05
0.86
3.29E−05
0.87


rs2980872
8
126486102
A
G
0.47
0.44
0.49
NA
NA
NSMCE2
TRIB1
7.10E−05
−0.70
4.93E−05
−0.70


rs2899258
22
34685304
C
A
0.10
.
0.09
RBM9
intron
LOC100131802
APOL3
7.11E−05
1.16
1.02E−04
1.14


rs5750200
22
34641716
C
A
0.10
.
0.09
RBM9
intron
NDUFA9P1
LOC100131802
7.11E−05
1.16
1.02E−04
1.14


rs339429
5
14032101
G
A
0.14
0.13
0.16
NA
NA
DNAH5
TRIO
7.34E−05
0.85
1.20E−04
0.84


rs11794832
9
18900581
C
T
.
0.22
.
ADAMTSL1
utr-3
LOC100129109
FAM154A
7.41E−05
1.24
3.15E−05
1.24


rs6737965
2
159744839
A
G
0.08
.
0.10
TANC1
intron
BTF3L4P
WDSUB1
7.49E−05
1.00
1.82E−04
−0.96


rs4676847
3
72081959
C
T
.
0.15
.
NA
NA
PROK2
CCDC137P
7.66E−05
1.15
4.62E−05
1.21


rs2184352
10
121762442
G
A
0.10
0.07
0.07
NA
NA
LOC651144
LOC729402
7.74E−05
0.89
4.98E−05
0.89


rs7552510
1
243234661
A
C
0.09
0.08
0.10
EFCAB2
intron
LOC100129656
LOC100128825
7.93E−05
0.93
3.63E−05
0.95


rs17262815
8
130560347
C
T
.
0.14
.
NA
NA
LOC100129525
LOC100130376
8.10E−05
1.25
5.66E−05
1.24


rs11020388
11
92880495
A
C
0.18
0.17
0.17
C11orf75
intron
CCDC67
LOC729466
8.12E−05
0.75
4.98E−05
0.77


rs555397
11
125341540
A
G
0.11
0.07
0.09
CDON
intron
LOC338667
LOC729561
8.22E−05
0.97
1.66E−04
−0.95


rs1874797
12
30027638
G
A
0.14
0.15
0.16
NA
NA
TMTC1
IPO8
8.35E−05
0.80
2.16E−04
0.76


rs11919628
3
111812972
T
G
.
0.08
.
NA
NA
LOC440973
LOC389141
8.48E−05
1.48
1.53E−04
−1.47


rs17298333
7
25010467
A
C
.
0.31
.
NA
NA
OSBPL3
CYCS
8.52E−05
0.97
7.04E−05
0.99


rs1563591
4
180515297
G
A
0.10
.
0.10
NA
NA
LOC391719
hCG_2025798
8.71E−05
1.25
7.35E−05
1.27


rs294027
11
26485638
A
G
0.15
.
0.19
TMEM16C
intron
LOC645705
MUC15
8.77E−05
1.00
3.92E−05
1.02


rs17017895
2
36029204
A
G
0.10
0.09
0.11
NA
NA
MRPL50P1
CRIM1
8.78E−05
0.88
1.04E−05
0.93


rs6884748
5
31527072
G
A
0.06
.
0.07
RNASEN
intron
CDH6
C5orf22
8.82E−05
1.13
2.61E−05
1.19


rs6884823
5
31526878
A
G
0.06
.
0.07
RNASEN
intron
CDH6
C5orf22
8.82E−05
1.13
2.61E−05
1.19


rs2757491
1
170533424
A
G
0.06
.
0.06
DNM3
intron
LOC100128178
LOC100131486
8.85E−05
1.10
1.17E−04
−1.08


rs2757500
1
170545644
A
G
0.06
.
0.06
DNM3
intron
LOC100128178
LOC100131486
8.85E−05
1.10
1.17E−04
−1.08


rs12777191
10
95052323
G
A
0.14
0.14
0.14
NA
NA
LOC643863
FER1L3
9.06E−05
0.77
1.10E−04
0.76


rs957615
4
23518663
T
C
.
0.10
.
NA
NA
PPARGC1A
LOC729175
9.22E−05
1.33
5.67E−05
1.36


rs11898024
2
58115520
C
A
0.08
.
0.10
NA
NA
LOC100131953
VRK2
9.24E−05
1.15
6.94E−06
1.25


rs10169411
2
42491253
A
G
.
0.13
.
NA
NA
COX7A2L
KCNG3
9.25E−05
1.16
1.22E−04
−1.14


rs11693549
2
42543983
T
C
.
0.13
.
KCNG3
intron
COX7A2L
LOC100129718
9.25E−05
1.16
1.22E−04
−1.14


rs222468
2
42496035
A
G
.
0.13
.
NA
NA
COX7A2L
KCNG3
9.25E−05
1.16
1.22E−04
−1.14


rs222471
2
42491561
G
A
.
0.13
.
NA
NA
COX7A2L
KCNG3
9.25E−05
1.16
1.22E−04
1.14


rs3794002
11
92892707
G
A
0.18
.
0.16
C11orf75
intron
CCDC67
LOC729466
9.29E−05
0.91
6.50E−05
0.95


rs11028782
11
25574425
A
G
0.24
.
0.18
NA
NA
LOC554234
LOC645705
9.40E−05
0.86
1.26E−04
−0.85


rs2076766
13
106979661
A
G
0.18
0.16
0.16
FAM155A
intron
RP11-282A11.1
LIG4
9.43E−05
0.71
1.65E−04
−0.70


rs1871072
10
54571008
A
G
.
0.31
.
NA
NA
MBL2
PCDH15
9.49E−05
1.21
1.42E−04
−1.07


rs6750890
2
208719259
T
G
.
0.10
.
CRYGB
near-gene-5
CRYGB
CRYGA
9.49E−05
1.08
1.93E−04
−1.20


rs6712962
2
234577772
G
A
0.49
0.42
0.45
TRPM8
intron
LOC100130859
SPP2
9.60E−05
−0.70
1.39E−04
−0.69


rs318422
1
82792064
A
G
0.44
0.40
0.41
NA
NA
LPHN2
TTLL7
9.70E−05
0.64
1.21E−04
−0.63


rs17182641
14
21146287
G
A
0.11
0.08
0.13
NA
NA
OR10G1P
TRA@
9.71E−05
0.92
1.09E−05
0.97


rs10179237
2
42369005
T
C
.
0.12
.
EML4
intron
SGK493
COX7A2L
9.81E−05
1.19
1.35E−04
−1.18


rs2053349
2
42369709
A
G
.
0.12
.
EML4
intron
SGK493
COX7A2L
9.81E−05
1.19
1.35E−04
−1.18









Fifty-nine out of 90 variants had the same direction of effect (either reduced or increased risk) in at least two out of the three studies (cutoff p<1×10−4). The top ten most statistically significant variants of that list are shown in Table 5.









TABLE 5







Ten most statistically significant variants, according to unadjusted p values,


associated with grade 22 proteinuria, hypertension and composite toxicity with the same


direction of effect (either reduced or increased risk) in at least two out of three trials for


proteinuria and composite toxicity, and three out of four trials for hypertension. Ch


chromosome, NA Intergenic SNP, MAF minor allele frequencies in CALGB 80303, 40503,


90401, and 40502 respectively, “—” SNP not present in the genotype platform of the trial,


“.” data on proteinuria were not available. Composite toxicity is defined as the occurrence


of either proteinuria or hypertension or both.






















Base

Effect



SNP
Ch
Gene
Feature
Flanking gene
Flanking gene
change
MAF
size (β)
p-value










Proteinuria
















rs339947
5
NA
NA
DNAH5
TRIO
C > A
0.12/_/0.14/.
1.27
7.66 × 10−8


rs12612153
2
C2orf34
Intron
PREPL
LOC100130502
A > C
0.11/_/0.11/.
1.16
3.89 × 10−6


rs7180310
15
NA
NA
SNORD116-24
SNORD116-25
C > A
0.06/0.05/_/.
1.54
4.10 × 10−6


rs12482855
21
NA
NA
RIPK4
PRDM15
G > A
0.06/0.06/0.06/.
1.20
6.28 × 10−6


rs408130
5
NA
NA
DNAH5
TRIO
G > A
0.21/_/0.28/.
1.07
6.33 × 10−6


rs418173
5
NA
NA
DNAH5
TRIO
G > A
0.21/_/0.28/.
1.07
6.33 × 10−6


rs7959783
12
NA
NA
MDM1
LOC729376
A > G
0.31/0.26/0.33/.
0.72
7.01 × 10−6


rs627761
11
LOC338667
Intron
DDX25
CDON
A > G
0.10/_/0.09/.
1.19
7.49 × 10−6


rs2688994
3
SLC12A8
Intron
HEG1
ZNF148
G > A
0.13/0.14/0.14/.
0.92
8.13 × 10−6


rs10486445
7
OSBPL3
Intron
DFNA5
CYCS
A > G
0.42/0.35/0.39/.
0.75
1.17 × 10−5







Hypertension
















rs13135230
4
NA
NA
CCDC149
LGI2
G > A
0.27/0.28/0.25/0.28
0.46
1.26 × 10−6


rs2350620
8
ASPH
Intron
hCG_1988300
LOC645551
A > G
0.32/0.26/0.32/0.32
−0.49
1.44 × 10−6


rs6770663
3
KCNAB1
Intron
LOC751837
SSR3
A > G
0.09/0.09/0.08/0.09
0.57
4.79 × 10−6


rs1145786
6
NA
NA
MAP3K7
LOC100129847
A > G
0.33/0.32/0.34/0.33
0.39
5.10 × 10−6


rs7130734
11
NA
NA
LRRC4C
LOC100131020
C > A
0.35/0.30/_/0.33
0.42
1.17 × 10−5


rs2179218
20
PTPRT
Intron
LOC6431 72
PPIAL
G > A
0.13/0.15/0.14/0.13
0.49
1.99 × 10−5


rs10519829
5
NA
NA
LOC644659
LOC100130551
G > A
0.44/0.46/0.47/0.47
0.36
2.28 × 10−5


rs1530837
15
PLA2G4E
Intron
EHD4
PLA2G4D
A > G
0.23/0.19/0.18/0.17
0.43
2.59 × 10−5


rs2000611
14
KCNK10
Intron
KCNK10
SPATA 7
A > G
0.44/0.43/0.50/0.48
−0.37
3.49 × 10−5


rs4611262
12
NUP37
Intron
CCDC53
C12orf48
G > A
0.20/0.25/0.23/0.23
0.39
3.74 × 10−5







Composite toxicity
















rs11662763
18
NA
NA
LOC645355
TTMA
G > A
0.14/0.11/0.13/.
0.67
9.19 × 10−7


rs8006648
14
NA
NA
LOC730121
GALC
G > A
0.27/0.28/0.26/.
0.58
2.33 × 10−6


rs2456761
10
NA
NA
LOC729184
CDC2
C > A
0.35/_/0.34/.
0.72
2.80 × 10−6


rs1000032
2
NA
NA
KIAA1 715
EVX2
C > A
0.13/0.18/0.19/.
0.62
3.21 × 10−6


rs2687640
7
CPVL
Intron
KIAA0644
LOC100131724
G > A
0.06/_/0.06/.
1.03
3.55 × 10−6


rs9310707
3
CNTN4
Intron
LOC727810
LOC100130346
G > A
0.37/0.37/0.36/.
0.53
4.03 × 10−6


rs13156044
5
DNAH5
Intron
LOC391738
TRIO
G > A
0.15/0.11/0.11/.
0.60
8.51 × 10−6


rs12328055
2
NA
NA
FSHR
LOC130728
G > A
0.06/_/0.05/.
0.99
9.19 × 10−6


rs4799369
18
DTNA
Intron
LOC646842
MAPRE2
A > G
0.20/0.20/0.18/.
0.59
1.14 × 10−5


rs2757491
1
DNM3
Intron
LOC100128178
LOC100131486
G > A
0.06/_/0.06/.
0.90
1.21 × 10−5









rs339947 (C>A, minor allele frequency, MAF 0.12-0.14) was the most statistically significant (p=7.66×10-8, β=1.27), with the A allele increasing the risk of proteinuria (FIG. 3). rs339947 is an intergenic variant located 73 kb 5′ from DNAH5 and 130 kb 5′ from TRIO (FIG. 4A). rs408130 and rs418173 (G>A and MAF 0.21-0.28 for both) are among the ten most statistically significant variants and in complete LD with each other (R2=1.00) and in moderate LD with rs339947 (R2=0.51). rs12482855 (G>A, MAF 0.06) had the same direction of effect in all three trials (p=6.28×10−6, β=1.20), with the A allele increasing the risk of proteinuria (FIG. 3). rs12482855 is 4.7 kb 5′ from RIPK4, an intergenic variant and does not have any variant in high LD (r2>0.8) with it (FIG. 4C).


For the SNP-based analysis of grade the Manhattan and Q-Q plots are shown in FIG. 5. 67 variants were identified as associated with proteinuria. Results are shown in Table 6.









TABLE 6







SNPs associated with proteinuria (grade ≥ 3)























effect
reference
MAF
MAF
MAF





effect


SNP
CH
BP
allele
allele
80303
40503
90401
gene
feature
Flanking gene
Flanking gene
p-value
(β)























rs2303028
5
150485987
A
G
0.19
0.20
0.16
ANXA6
intron
TNIP1
CCDC69
5.75E−07
1.57


rs3792775
5
150483530
A
G
0.25
0.24
0.21
ANXA6
intron
TNIP1
CCDC69
1.56E−06
1.49


rs17525472
15
49756960
G
A
0.14
.
0.12
NA
NA
DMXL2
SCG3
2.05E−06
1.98


rs7579312
2
189590930
A
G
.
0.06
.
NA
NA
COL3A1
COL5A2
3.65E−06
2.49


rs7761644
6
6933004
G
A
.
0.08
.
NA
NA
RP11-320C15.1
LOC643936
5.28E−06
1.96


rs6772933
3
136335379
G
A
0.05
0.10
0.07
EPHB1
intron
LOC645218
PPP2R3A
5.31E−06
1.85


rs10188246
2
189879253
G
A
.
0.06
0.06
NA
NA
COL5A2
KRT18P19
5.86E−06
1.68


rs12636883
3
133912212
A
C
0.13
0.13
0.15
NPHP3
intron
UBA5
NCRNA00119
6.57E−06
1.49


rs9502527
6
6930995
G
A
.
0.08
.
NA
NA
RP11-320C15.1
LOC643936
9.56E−06
1.94


rs2070492
3
38332821
A
G
0.09
0.10
0.10
SLC22A14
missense
SLC22A13
XYLB
1.04E−05
1.77


rs7341475
7
103192051
A
G
0.16
0.11
0.15
RELN
intron
SLC26A5
ORC5L
1.07E−05
1.66


rs6434309
2
189591411
A
C
0.08
0.08
0.10
NA
NA
COL3A1
COL5A2
1.22E−05
1.47


rs2105632
11
131842137
G
A
0.14
0.14
0.13
OPCML
intron
HNT
LOC100128095
1.36E−05
1.61


rs1590347
9
10325382
A
G
.
0.12
.
PTPRD
intron
RN7SLP2
LOC646087
1.48E−05
1.90


rs17460569
3
85702141
G
A
0.08
.
0.13
NA
NA
LOC440970
CADM2
1.55E−05
2.33


rs10061011
5
36478917
G
A
.
0.07
0.05
NA
NA
RANBP3L
SLC1A3
1.77E−05
2.57


rs7341301
6
6930714
A
G
0.11
0.08
0.09
NA
NA
RP11-320C15.1
LOC643936
2.20E−05
1.28


rs12248682
10
131200410
A
G
0.09
0.07
0.10
MGMT
intron
hCG_1795091
LOC100129103
2.36E−05
1.65


rs12864893
13
97867240
A
C
0.06
.
0.08
FARP1
intron
RNF113B
STK24
2.56E−05
1.87


rs893911
15
64715542
A
G
0.19
0.14
0.18
NA
NA
LCTL
SMAD6
2.56E−05
1.28


rs280877
16
76215748
G
A
0.19
0.14
0.16
NA
NA
ADAMTS18
NUDT7
2.70E−05
1.22


rs7581769
2
105053248
A
G
0.11
.
0.09
MRPS9
intron
LOC100128684
LOC100133048
2.82E−05
1.62


rs2974319
8
42594234
G
A
0.06
0.08
0.08
NA
NA
C8orf40
CHRNB3
2.88E−05
1.92


rs61737465
7
94378463
A
G
.
0.06
.
NA
NA
ARF1P1
PON1
2.89E−05
1.84


rs551112
9
14433468
A
C
0.05
0.09
0.07
NA
NA
NFIB
ZDHHC21
2.92E−05
1.61


rs6781294
3
86413784
G
A
0.07
0.12
0.12
NA
NA
CADM2
VGLL3
2.93E−05
1.48


rs1999184
1
176940266
G
A
0.09
.
0.07
NA
NA
C1orf220
LOC646976
3.03E−05
2.29


rs9860570
3
86372146
G
A
0.07
0.12
0.12
NA
NA
CADM2
VGLL3
3.15E−05
1.48


rs9899787
17
62161091
G
A
.
0.10
.
PRKCA
intron
APOH
CACNG5
3.34E−05
2.46


rs7875861
9
10275562
G
A
.
0.08
.
PTPRD
intron
RN7SLP2
LOC646087
3.47E−05
2.87


rs10184895
2
189788608
A
T
.
0.06
.
NA
NA
COL5A2
KRT18P19
3.53E−05
1.67


rs9864170
3
85693598
A
G
0.13
.
0.18
NA
NA
LOC440970
CADM2
3.77E−05
1.68


rs280866
16
76211348
A
G
0.07
0.07
0.07
NA
NA
ADAMTS18
NUDT7
3.87E−05
1.59


rs282999
16
76151802
G
A
0.22
0.17
0.19
NA
NA
ADAMTS18
NUDT7
4.13E−05
1.29


rs9912154
17
62159169
A
G
.
0.11
.
PRKCA
intron
APOH
CACNG5
4.21E−05
2.44


rs4979476
9
116740531
G
A
0.09
0.09
0.08
NA
NA
TNFSF8
TNC
4.26E−05
1.50


rs4916009
1
65144006
A
G
0.08
.
0.09
JAK1
intron
RAVER2
LOC100130270
4.39E−05
1.96


rs1583609
18
26882002
A
G
0.10
0.10
0.11
NA
NA
DSC3
DSC2
4.46E−05
1.72


rs10798628
1
176918995
A
G
0.10
.
0.08
NA
NA
C1orf220
LOC646976
4.76E−05
2.29


rs7826830
8
95723804
A
G
0.17
0.13
0.14
RBM35A
intron
K1AA1429
DPY19L4
5.25E−05
1.36


rs8116164
20
61083073
A
G
0.13
0.08
0.12
NA
NA
LOC100128172
BHLHB4
5.38E−05
1.49


rs12486323
3
133913494
G
A
.
0.16
.
NPHP3
intron
UBA5
NCRNA00119
5.56E−05
1.84


rs9922975
16
26847848
G
A
0.13
0.11
0.12
NA
NA
HS3ST4
C16orf82
5.57E−05
1.27


rs661198
9
10289084
A
G
0.10
0.10
0.09
PTPRD
intron
RN7SLP2
LOC646087
5.61E−05
1.33


rs17717970
5
150954894
G
A
.
0.11
.
NA
NA
FAT2
SPARC
5.79E−05
1.71


rs11965083
6
45935458
G
A
.
0.18
.
NA
NA
RUNX2
CLIC5
5.96E−05
1.80


rs7637944
3
132912301
A
C
0.15
0.14
0.13
CPNE4
intron
MRPL3
LOC729674
5.98E−05
1.26


rs12533538
7
105218549
A
C
0.06
0.06
0.07
ATXN7L1
intron
LOC100131028
LOC100129553
6.14E−05
1.47


rs546913
6
112396275
A
G
0.05
.
0.05
NA
NA
FYN
WISP3
6.73E−05
2.19


rs689328
6
112393380
A
G
0.05
.
0.05
NA
NA
FYN
WISP3
6.73E−05
2.19


rs1332175
9
25493034
G
A
0.07
0.06
0.06
NA
NA
C9orf134
TUSC1
6.78E−05
1.65


rs4479482
20
59037337
A
G
0.11
0.10
0.09
NA
NA
MTCO2L
CDH4
6.98E−05
1.53


rs445775
13
32422448
A
G
.
0.06
0.06
NA
NA
PDS5B
hCG_1643176
7.14E−05
1.84


rs10959051
9
10320850
G
A
0.24
0.30
0.22
PTPRD
intron
RN7SLP2
LOC646087
7.23E−05
1.17


rs10516313
4
17028411
A
G
0.14
.
0.16
NA
NA
LOC729006
LOC645097
7.55E−05
1.78


rs7948079
11
96725167
A
G
0.10
0.09
0.08
NA
NA
LOC100131233
LOC643381
7.74E−05
1.29


rs2167171
8
133556707
C
A
0.08
0.09
0.07
KCNQ3
intron
HHLA1
LRRC6
7.77E−05
1.39


rs2277719
18
54350509
A
C
0.06
.
0.07
ALPK2
intron
NEDD4L
LOC100128163
7.79E−05
1.77


rs3844600
10
49353903
A
G
0.22
0.20
0.22
ARHGAP22
intron
MAPK8
WDFY4
7.90E−05
1.23


rs1285295
17
75513707
A
C
.
0.09
.
NA
NA
CBX4
TBC1D16
8.12E−05
1.71


rs2723129
2
23438312
G
A
0.09
0.07
0.09
NA
NA
LOC100130841
KLHL29
8.33E−05
1.33


rs1330656
5
26084219
A
C
0.17
0.17
0.13
NA
NA
MSNL1
LOC100132866
8.68E−05
1.50


rs10065544
5
136592476
G
A
0.20
0.19
0.21
SPOCK1
intron
LOC391834
KLHL3
8.78E−05
1.19


rs992803
3
86325620
A
C
0.14
0.16
0.19
NA
NA
CADM2
VGLL3
8.83E−05
1.20


rs9825532
3
89169850
A
G
.
0.27
.
NA
NA
LOC728432
EPHA3
9.32E−05
2.36


rs2302840
18
41326985
A
G
0.13
.
0.11
NA
NA
LOC100131669
SLC14A2
9.40E−05
1.93


rs17237607
3
126170122
A
G
0.08
0.10
0.08
HEG1
utr-3
MUC13
SLC12A8
9.87E−05
1.36









Forty-nine out of 67 variants had the same direction of effect (either reduced or increased risk) in at least two out of the three studies (cutoff p<1×10−4). The top ten most statistically significant variants of that list are shown in Table 7. rs2303028 (G>A, MAF 0.16-0.20) was the most statistically significant (p=5.75×10−7, β=1.57), with the A allele increasing the risk of proteinuria. rs2303028 is an intronic variant in ANXA6 (FIG. 6). rs3792775 (G>A and MAF 0.21-0.25) was the next most statistically significant variant (p=1.56×10-6, β=1.49), also located in intron of ANXA6 and in moderate LD with rs2303028 (R2=0.77) (FIG. 6), with the A allele increasing the risk of proteinuria. rs12636883 (A>G, MAF 0.05-0.10) also had the same direction of effect in all three trials (p=5.57×10−6, β=1.49), with the A allele increasing the risk of proteinuria. rs12636883 is an intronic variant in NPHP3 (FIG. 6).









TABLE 7







Ten most statistically significant variants, according to unadjusted p values


grade ≥ 3, associated with proteinuria, hypertension and composite toxicity with the same


direction of effect (either reduced or increased risk) in at least two out of three trials for


proteinuria and composite toxicity, and three out of four trials for hypertension. Ch


chromosome, NA Intergenic SNP, MAF minor allele frequencies in CALGB 80303, 40503,


90401, and 40502 respectively, “_” SNP not present in the genotype platform of the trial,


“.” data on proteinuria were not available. Composite toxicity is defined as the occurrence


of either proteinuria or hypertension or both.






















Base

Effect



SNP
Ch
Gene
Feature
Flanking gene
Flanking gene
change
MAF
size (β)
p-value










Proteinuria
















rs2303028
5
ANXA6
Intron
TNIP1
CCDC69
G > A
0.19/0.20/0.16/.
1.57
5.75 × 10−7


rs3792775
5
ANXA6
Intron
TNIP1
CCDC69
G > A
0.25/0.24/0.21/.
1.49
1.56 × 10−6


rs17525472
15
NA
NA
DMXL2
SCG3
A > G
0.14/_/0.12/.
1.98
2.05 × 10−6


rs6772933
3
EPHB1
Intron
LOC645218
PPP2R3A
A > G
0.05/0.10/0.07/.
1.85
5.31 × 10−6


rs10188246
2
NA
NA
COL5A2
KRT18P19
A > G
_/0.06/0.06/.
1.68
5.86 × 10−6


rs12636883
3
NPHP3
Intron
UBA5
NCRNA00119
C > A
0.13/0.13/0.15/.
1.49
5.57 × 10−6


rs2070492
3
SLC22A14
Missense
SLC22A13
XYLB
G > A
0.09/0.10/0.10/.
1.77
1.04 × 10−5


rs7341475
7
RELN
Intron
SLC26A5
ORC5L
G > A
0.16/0.11/0.15/.
1.66
1.07 × 10−5


rs6434309
2
NA
NA
COL3A1
COL5A2
C > A
0.08/0.08/0.10/.
1.47
1.22 × 10−5


rs2105632
11
OPCML
Intron
HNT
LOC100128095
A > G
0.14/0.14/0.13/.
1.61
1.36 × 10−5







Hypertension
















rs4782946
16
ATP2C2
Intron
WFDC1
KIAA1609
G > A
0.37/0.38/0.37/0.43
0.66
3.09 × 10−7


rs17439529
14
AKAP6
Intron
MTCO1P2
NPAS3
G > A
0.36/0.40/0.38/0.40
−0.72
2.08 × 10−6


rs1530837
15
PLA2G4E
Intron
EHD4
PLA2G4D
A > G
0.23/0.19/0.18/0.17
0.66
4.87 × 10−6


rs11863271
16
ATP2C2
Intron
WFDC1
KIAA1609
G > A
0.20/0.17/0.19/0.22
0.63
5.23 × 10−6


rs1171065
13
DCLK1
Intron
NBEA
SOHLH2
A > C
0.19/0.26/0.19/0.21
0.62
5.73 × 10−6


rs670362
18
NA
NA
VAPA
APCDD1
G > A
0.18/0.14/0.11/0.12
0.67
6.10 × 10−6


rs2665917
8
NIBP
Intron
C8orf17
LOC100131910
G > A
0.44/0.48/0.47/0.47
0.63
7.13 × 10−6


rs10967306
9
VLDLR
Intron
FL135024
KCNV2
G > A
0.07/0.07/0.09/0.08
0.87
8.16 × 10−6


rs1320881
8
NA
NA
LOC100132107
ADAM28
G > A
0.24/0.18/0.21/0.24
0.61
9.86 × 10−6


rs4691370
4
NA
NA
hCG_1814936
PDGFC
A > G
0.06/0.09/_/0.07
0.82
1.00 × 10−5







Composite toxicity
















rs10867852
9
NA
NA
LOC442427
RASEF
G > A
0.08/0.07/0.06/.
1.16
1.46 × 10−6


rs7717673
5
SLC25A48
Intron
LOC153328
IL9
G > A
0.11/0.12/0.12/.
0.94
3.93 × 10−6


rs2454331
8
NA
NA
LOC100129100
RIPK2
A > G
0.43/0.40/0.43/.
−0.77
1.43 × 10−6


rs873224
8
NA
NA
FL143860
LOC100131146
A > G
0.11/0.10/0.08/.
0.86
1.48 × 10−6


rs966439
14
NA
NA
LOC283584
LOC283585
A > G
0.21/0.17/0.16/.
0.70
1.52 × 10−6


rs7849777
9
COL5A1
Intron
RXRA
LOC100130622
G > A
0.09/0.05/0.06/.
1.31
1.56 × 10−6


rs10869538
9
PIP5K1B
Intron
LOC100131240
PRKACG
A > G
0.15/0.16/0.15/.
0.74
1.74 × 10−6


rs11664759
18
NA
NA
LOC400655
FBX015
G > A
0.11/0.15/0.15/.
0.83
2.21 × 10−6


rs1978259
14
NA
NA
LOC283584
LOC283585
C > A
0.20/_/0.16/.
0.81
2.63 × 10−6


rs17109031
12
NA
NA
SMUG1
LOC100132010
G > A
0.13/0.08/0.10/.
0.85
2.93 × 10−6









For the gene-based analysis of grade the Q-Q plot is shown in FIG. 7. Identified genes associated with proteinuria, hypertension, and composite toxicity are shown in Table 8.









TABLE 8







Genes associated with proteinuria, hypertension, or composite toxicity (grade ≥ 2)









Proteinuria
Hypertension
Composite toxicity
















p-value
p-value

p-value
p-value

p-value
p-value


Gene
unadjusted
adjusted
Gene
unadjusted
adjusted
Gene
unadjusted
adjusted





C1D
2.00E−08
2.00E−08
UNC50
2.30E−05
3.20E−05
SLC25A24
4.00E−06
3.00E−06


IL17F
1.80E−07
5.90E−07
KATNB1
2.50E−05
7.30E−05
SMS
5.00E−06
5.00E−06


MCM3
5.10E−07
1.15E−06
MGAT4A
4.60E−05
6.10E−05
CEP295
1.00E−05
7.00E−06


SMPX
1.20E−05
8.91E−06
FBXO9
5.10E−05
3.60E−05
YWHAE
1.60E−05
1.30E−05


KLHL34
1.26E−05
1.50E−05
STRIP1
9.80E−05
1.05E−04
PTPN3
4.00E−05
7.10E−05


EAPP
2.70E−05
2.70E−05
CCDC54
1.01E−04
7.70E−05
KLHL35
4.50E−05
3.50E−05


CNKSR2
3.50E−05
2.70E−05
COA5
1.06E−04
1.46E−04
H6PD
5.10E−05
4.00E−05


LIPJ
4.80E−05
7.10E−05
KIFC3
1.18E−04
2.76E−04
MBTPS2
7.50E−05
7.10E−05


ITGB6
5.00E−05
5.50E−05
ICK
1.21E−04
7.70E−05
CRK
1.37E−04
1.51E−04


XCR1
5.70E−05
1.86E−04
AHCYL1
1.45E−04
1.75E−04
SLC17A6
1.50E−04
1.44E−04


RFPL4AL1
1.03E−04
1.42E−04
CAPZA2
1.63E−04
1.36E−04
ALDH4A1
2.13E−04
2.42E−04


PDE3A
1.48E−04
7.86E−04
A4GALT
2.96E−04
1.93E−04
HSD3B2
2.43E−04
2.37E−04


SNX6
1.81E−04
1.11E−04
LUZP4
3.10E−04
2.59E−04
ZNF217
2.74E−04
3.05E−04


PWWP2A
1.82E−04
3.60E−04
CFAP69
3.80E−04
3.21E−04
STAT4
3.44E−04
1.97E−04


NDFIP2
2.01E−04
6.17E−04
STK10
4.30E−04
4.79E−04
TAS1R2
3.46E−04
3.42E−04


VCP
2.09E−04
2.13E−03
TMPRSS12
5.03E−04
4.01E−04
HDAC11
3.55E−04
4.02E−04


CRYBB2
2.34E−04
9.40E−05
AQP12A
5.12E−04
5.00E−04
AZI2
4.00E−04
4.26E−04


RFPL4A
2.38E−04
2.24E−04
CYSLTR2
5.38E−04
3.81E−04
CMC1
4.26E−04
4.35E−04


CRYBB3
2.47E−04
9.00E−05
DTD1
6.85E−04
5.41E−04
FAM155B
4.36E−04
2.96E−04


ALDH6A1
2.87E−04
3.69E−04
BRD1
6.94E−04
9.23E−04
TGM3
6.14E−04
4.83E−04


CTRB2
3.03E−04
5.53E−04
CSRP2
7.46E−04
7.00E−04
MC3R
6.37E−04
1.07E−03


FANCG
3.12E−04
3.94E−03
FUK
7.74E−04
6.71E−04
IL17F
6.75E−04
5.61E−04


PIGO
3.21E−04
4.29E−03
ST3GAL2
8.16E−04
5.12E−04
HSD3B1
6.93E−04
6.49E−04


KIAA1671
3.29E−04
1.14E−04
CDK14
8.68E−04
8.26E−04
RGPD6
7.04E−04
6.84E−04


DDB2
3.33E−04
1.75E−04
SEPT2
9.21E−04
1.14E−03
RPS3
9.49E−04
1.01E−03


ACP2
3.38E−04
1.99E−04
SF3B3
9.23E−04
6.91E−04
MALL
1.09E−03
7.92E−04


MSANTD1
3.61E−04
4.62E−04
RDH14
9.27E−04
9.37E−04
SPAG4
1.10E−03
1.32E−03


TGFA
3.78E−04
4.88E−04
CCDC58
1.03E−03
7.33E−04
MYH11
1.16E−03
1.47E−03


CTRB1
3.81E−04
6.26E−04
COLGALT2
1.05E−03
8.33E−04
RBL1
1.16E−03
1.43E−03


C9orf131
3.85E−04
1.73E−03
ZDHHC22
1.05E−03
7.83E−04
MRPL9
1.22E−03
1.30E−03


SPRY4
4.63E−04
1.02E−03
NT5C1B
1.10E−03
1.02E−03
SKAP1
1.24E−03
1.58E−03


DIRC2
5.26E−04
2.13E−04
CSTA
1.14E−03
9.29E−04
IFFO2
1.25E−03
1.21E−03


PTGR2
5.43E−04
8.58E−04
IL33
1.16E−03
1.06E−03
C1QTNF7
1.26E−03
7.18E−04


GPX5
6.26E−04
3.13E−04
RYR2
1.20E−03
1.97E−03
GDPD5
1.32E−03
1.11E−03


DNAJB5
6.38E−04
4.62E−04
ACKR3
1.27E−03
8.26E−04
PIK3C2B
1.32E−03
1.03E−03


RGS12
6.72E−04
1.02E−03
EPB41L4B
1.28E−03
1.68E−03
RASGRF1
1.34E−03
1.07E−03


URB2
8.40E−04
4.09E−04
CTSK
1.35E−03
2.17E−03
CCDC172
1.54E−03
1.46E−03


MLH1
8.86E−04
1.38E−03
MFSD2A
1.39E−03
1.48E−03
TMEM182
1.59E−03
1.08E−03


RAN
1.02E−03
1.91E−04
S100P
1.44E−03
1.28E−03
GLRA3
1.76E−03
1.72E−03


FZD6
1.02E−03
1.07E−03
COG4
1.45E−03
1.49E−03
HOMER1
1.88E−03
1.98E−03


TTC1
1.03E−03
9.29E−04
CASR
1.46E−03
1.02E−03
NEFM
1.90E−03
1.60E−03


GNG7
1.04E−03
5.33E−04
CNBD2
1.48E−03
1.19E−03
TET1
2.01E−03
2.22E−03


TAF5L
1.08E−03
5.84E−04
PDE4DIP
1.48E−03
9.00E−04
SLC25A16
2.02E−03
2.01E−03


ZBTB3
1.14E−03
1.75E−04
TIAL1
1.60E−03
1.47E−03
MCM3
2.03E−03
1.87E−03


PITPNM2
1.15E−03
1.39E−03
UBE4B
1.62E−03
1.22E−03
PLCL1
2.03E−03
2.18E−03


CALCR
1.16E−03
1.82E−03
ARNT
1.75E−03
2.47E−03
GABRA3
2.10E−03
2.09E−03


POLR2G
1.18E−03
2.76E−04
ARHGAP42
1.81E−03
1.61E−03
MPP3
2.10E−03
1.93E−03


SLC25A24
1.21E−03
1.21E−03
LRRC3B
1.83E−03
1.42E−03
NPTX2
2.10E−03
2.27E−03


RWDD2B
1.22E−03
6.29E−04
NYAP2
1.86E−03
1.84E−03
NFS1
2.11E−03
2.48E−03


CCT8
1.24E−03
7.50E−04
SSX5
1.89E−03
2.53E−03
RBM12
2.15E−03
2.09E−03


STOML2
1.32E−03
1.85E−02
PAQR4
1.93E−03
2.15E−03
SEMA5B
2.26E−03
2.36E−03


KRTAP12-4
1.35E−03
1.60E−03
KREMEN2
2.02E−03
2.20E−03
GPATCH2
2.28E−03
1.33E−03


STX2
1.35E−03
2.65E−04
SNX11
2.06E−03
3.48E−03
CPNE1
2.29E−03
2.39E−03


PRB3
1.40E−03
2.34E−03
FLYWCH1
2.07E−03
2.31E−03
PEX11G
2.32E−03
1.93E−03


FER1L6
1.41E−03
2.01E−03
PKMYT1
2.10E−03
2.48E−03
XYLB
2.40E−03
2.87E−03


PRB4
1.45E−03
7.21E−02
PACSIN2
2.28E−03
1.79E−03
ADAM12
2.43E−03
1.92E−03


MPP3
1.48E−03
1.08E−03
GP1BA
2.32E−03
1.98E−03
SCYL2
2.43E−03
2.67E−03


OR4N5
1.54E−03
1.82E−03
KIF1A
2.38E−03
1.39E−03
YY2
2.52E−03
2.09E−03


PLEKHB1
1.61E−03
1.06E−03
NBPF9
2.45E−03
1.79E−03
TMEM165
2.56E−03
2.11E−03


RBM7
1.62E−03
1.51E−03
SKAP1
2.50E−03
3.75E−03
RHAG
2.58E−03
2.42E−03


KRTAP12-3
1.63E−03
2.14E−03
STEAP2
2.50E−03
2.45E−03
ANAPC5
2.61E−03
2.70E−03


FAM214B
1.64E−03
1.83E−02
RBM42
2.52E−03
3.81E−03
CHRNG
2.66E−03
2.17E−03


TMEM223
1.74E−03
5.45E−04
TMEM115
2.69E−03
2.31E−03
BIVM
2.73E−03
3.12E−03


PHOSPHO2
1.79E−03
2.85E−03
CIPC
2.70E−03
2.17E−03
CAM KK2
2.78E−03
2.43E−03


NXF1
1.88E−03
5.13E−04
ARFGAP3
2.80E−03
2.01E−03
LMTK3
2.83E−03
2.37E−03


TMEM179B
1.90E−03
5.93E−04
C10orf142
2.83E−03
2.07E−03
C1D
2.92E−03
2.62E−03


OR4M1
1.94E−03
3.15E−03
TTLL5
2.91E−03
1.63E−03
DLL3
2.92E−03
2.65E−03


TAF6L
1.99E−03
5.44E−04
PRDM2
2.93E−03
3.37E−03
ERCC5
2.94E−03
3.90E−03


SCYL2
2.02E−03
1.99E−03
ZC2HC1B
3.04E−03
3.48E−03
RBM39
2.97E−03
3.34E−03


GRHL2
2.04E−03
1.01E−02
LTV1
3.10E−03
3.23E−03
TNKS
2.98E−03
3.51E−03


TTC9C
2.04E−03
3.82E−04
CCNI
3.29E−03
3.61E−03
ZNF835
3.07E−03
2.27E−03


DLG5
2.13E−03
1.62E−03
IL23R
3.30E−03
3.29E−03
EIF4E2
3.10E−03
1.94E−03


OR4Q3
2.19E−03
3.31E−03
MRFAP1L1
3.33E−03
3.55E−03
PRPF38A
3.16E−03
2.94E−03


PPP1R16A
2.26E−03
3.27E−03
CLDN9
3.38E−03
4.11E−03
TLK1
3.17E−03
3.19E−03


GCNT2
2.29E−03
1.51E−02
ZBED4
3.45E−03
3.96E−03
TMC1
3.24E−03
2.78E−03


GPT
2.29E−03
3.28E−03
ENO3
3.52E−03
2.97E−03
TRAPPC4
3.28E−03
3.96E−03


MFSD3
2.29E−03
3.23E−03
ZNF774
3.55E−03
3.04E−03
PPP1R15B
3.31E−03
2.80E−03


LRRC24
2.32E−03
3.41E−03
SEL1L
3.59E−03
3.43E−03
CCDC84
3.35E−03
3.88E−03


FOXH1
2.33E−03
3.27E−03
NDNF
3.64E−03
2.61E−03
RPS25
3.35E−03
3.69E−03


C11orf71
2.39E−03
1.97E−03
AP2B1
3.76E−03
3.88E−03
KCTD12
3.43E−03
3.24E−03


SLC40A1
2.40E−03
3.24E−03
COX6B1
3.83E−03
4.82E−03
TCOF1
3.45E−03
2.60E−03


RFC3
2.42E−03
3.46E−03
CLDN6
3.97E−03
3.87E−03
SLC37A4
3.49E−03
4.14E−03


RECQL4
2.45E−03
3.25E−03
ETV2
3.97E−03
5.02E−03
TIMM50
3.63E−03
3.14E−03


NCOA3
2.46E−03
1.42E−03
PFN1
3.98E−03
3.33E−03
TIGD1
3.76E−03
2.34E−03


STX5
2.47E−03
6.63E−04
DGKE
4.11E−03
4.43E−03
TRIM28
3.84E−03
3.09E−03


WDR37
2.47E−03
1.75E−03
SLC25A11
4.23E−03
3.71E−03
PDZRN3
3.91E−03
3.97E−03


LGALS2
2.51E−03
9.13E−04
ZNF485
4.23E−03
3.78E−03
KATNB1
3.92E−03
3.13E−03


CYHR1
2.53E−03
3.66E−03
TSPAN33
4.41E−03
3.42E−03
RIIAD1
3.99E−03
4.39E−03


DSG1
2.54E−03
3.00E−03
FBXW11
4.52E−03
6.35E−03
CHMP2A
4.02E−03
2.98E−03


KIFC2
2.54E−03
3.64E−03
IL2
4.52E−03
5.88E−03
MZF1
4.04E−03
3.34E−03


BBS5
2.55E−03
5.94E−03
TBX5
4.55E−03
3.19E−03
UBE2M
4.04E−03
3.17E−03


TONSL
2.56E−03
3.72E−03
C17orf100
4.57E−03
6.94E−03
FBXO47
4.27E−03
4.89E−03


LRRC14
2.58E−03
3.01E−03
XAGE2
4.60E−03
5.24E−03
PGLS
4.49E−03
5.44E−03


REXO2
2.62E−03
3.09E−03
HNMT
4.68E−03
4.21E−03
RALY
4.49E−03
4.18E−03


CCDC173
2.74E−03
2.83E−03
ASPH
4.69E−03
5.83E−03
ZBTB45
4.51E−03
3.64E−03


CYLC1
2.75E−03
2.05E−03
RNF167
4.73E−03
3.72E−03
CTNNB1
4.60E−03
4.57E−03


PCBP2
2.75E−03
5.19E−03
DAB2IP
4.84E−03
4.68E−03
NAMPT
4.73E−03
2.83E−03


SOST
2.79E−03
1.74E−03
KIF1B
4.86E−03
4.48E−03
STAT1
4.77E−03
3.79E−03


DLGAP1
2.82E−03
6.77E−03
CENPL
4.88E−03
2.88E−03
CRISP3
4.81E−03
4.96E−03


SMIM18
2.83E−03
6.26E−04
NUP155
4.88E−03
2.56E−03
PLEKHA6
4.89E−03
4.08E−03


SNRPA
2.84E−03
2.93E−03
ATP10A
4.97E−03
1.06E−02
SLC22A14
4.93E−03
5.34E−03


KLHL41
2.88E−03
6.49E−03
FOXG1
5.02E−03
4.55E−03
CGB8
5.05E−03
4.18E−03


RNF19A
2.89E−03
2.69E−03
CRHR2
5.16E−03
5.36E−03
ZNF446
5.08E−03
3.84E−03


EFNA5
2.90E−03
3.64E−03
ZNF707
5.17E−03
4.53E−03
UBC
5.18E−03
3.48E−03


RC3H1
2.94E−03
2.07E−03
HOMER1
5.18E−03
4.44E−03
PTAR1
5.20E−03
2.76E−03


SP1
2.94E−03
1.57E−03
PIM2
5.18E−03
5.38E−03
NPHP1
5.24E−03
5.06E−03


FASTKD1
2.95E−03
6.60E−03
GPAT2
5.32E−03
4.94E−03
TEX13B
5.24E−03
5.56E−03


NUMBL
3.02E−03
2.90E−03
AQP12B
5.38E−03
5.56E−03
IGF1R
5.25E−03
4.61E−03


ZNF256
3.05E−03
2.69E−03
TNFRSF12A
5.48E−03
6.02E−03
LHB
5.31E−03
3.58E−03


ITPKC
3.12E−03
3.79E−03
CPNE6
5.50E−03
1.24E−02
CD74
5.36E−03
3.92E−03


ACCSL
3.15E−03
7.81E−02
HS6ST1
5.61E−03
1.29E−02
DNAJB5
5.38E−03
6.12E−03


VWA5B1
3.15E−03
3.67E−03
HERC5
5.66E−03
5.20E−03
CITED1
5.39E−03
3.93E−03


DUSP3
3.18E−03
1.79E−03
GPR139
5.69E−03
7.03E−03
KLHL26
5.39E−03
4.53E−03


SERPINC1
3.25E−03
2.56E−03
FLYWCH2
5.73E−03
6.61E−03
C9orf135
5.42E−03
4.63E−03


RNLS
3.26E−03
3.51E−03
TXNDC2
5.76E−03
5.92E−03
ROMO1
5.51E−03
5.81E−03


C19orf54
3.30E−03
3.12E−03
HCFC1R1
5.77E−03
6.77E−03
ZCCHC11
5.55E−03
4.16E−03


ZNF429
3.36E−03
2.88E−03
ZXDA
5.84E−03
7.91E−03
DIRC2
5.59E−03
4.89E−03


C2orf88
3.45E−03
4.75E−03
THOC6
5.85E−03
6.99E−03
DIRAS2
5.62E−03
5.21E−03


KRT25
3.45E−03
3.73E−03
GSTA2
5.94E−03
6.16E−03
AKAP1
5.63E−03
5.12E−03


SHMT1
3.60E−03
2.50E−05
CETP
5.95E−03
5.20E−03
KCNJ14
5.63E−03
5.16E−03


HERC6
3.71E−03
2.85E−03
RIMBP2
5.95E−03
4.68E−03
TXNL1
5.86E−03
3.61E−03


KRTAP10-10
3.74E−03
5.55E−03
C1QTNF7
6.15E−03
5.50E−03
ELOVL2
5.91E−03
8.74E−03


MIA
3.74E−03
4.27E−03
ZNF592
6.21E−03
1.16E−02
ZDHHC7
5.94E−03
3.65E−03


SMCR8
3.81E−03
2.06E−03
GIPC2
6.22E−03
5.12E−03
DUSP3
6.01E−03
6.00E−03


RAB6A
3.82E−03
1.96E−03
ARHGAP15
6.34E−03
5.07E−03
SOST
6.04E−03
6.47E−03


TAS2R42
3.82E−03
5.90E−03
PLAGL1
6.43E−03
6.22E−03
MPZ
6.06E−03
6.28E−03


RBPMS
3.84E−03
1.33E−03
ZNF787
6.44E−03
7.05E−03
COPG2
6.08E−03
5.69E−03


EVPLL
3.88E−03
3.10E−05
ZNF835
6.45E−03
8.13E−03
ETAA1
6.09E−03
7.90E−03


ST6GALNAC3
3.93E−03
1.03E−02
NAPEPLD
6.46E−03
1.10E−02
NF2
6.11E−03
6.26E−03


RAB4B
4.00E−03
4.65E−03
FAM83H
6.49E−03
5.92E−03
SLC27A5
6.13E−03
5.15E−03


KRTAP10-11
4.06E−03
4.98E−03
CNTF
6.52E−03
7.36E−03
GRWD1
6.23E−03
5.43E−03


OVOL2
4.06E−03
6.26E−03
MAPK15
6.55E−03
5.72E−03
COLGALT1
6.28E−03
7.51E−03


SLC25A33
4.10E−03
2.97E−03
SMO
6.55E−03
6.00E−03
CTSH
6.32E−03
4.97E−03


WDR1
4.24E−03
5.07E−03
CCDC166
6.68E−03
5.83E−03
CELF3
6.34E−03
5.66E−03


RPUSD2
4.26E−03
7.35E−04
GOLGA78
6.69E−03
7.37E−03
FAM129C
6.38E−03
7.67E−03


BOD1L1
4.39E−03
4.92E−03
GATAD1
6.73E−03
8.39E−03
DRC7
6.40E−03
5.35E−03


ID12
4.56E−03
3.28E−03
C3orf38
6.75E−03
6.86E−03
MAP9
6.56E−03
2.67E−03


WDR74
4.59E−03
1.58E−03
ATP182
6.79E−03
6.32E−03
VCX2
6.56E−03
5.70E−03


EGLN2
4.66E−03
5.51E−03
MED12
6.83E−03
2.72E−02
YTHDF2
6.60E−03
6.20E−03


IDI1
4.68E−03
4.16E−03
UR82
6.83E−03
8.02E−03
OR4M1
6.68E−03
1.16E−02


MEDI
4.73E−03
1.80E−03
PCED18
6.88E−03
9.27E−03
MACROD2
6.70E−03
4.69E−03


MAGEA1
4.82E−03
7.16E−03
MOAP1
6.89E−03
7.75E−03
MAPK15
6.71E−03
5.51E−03


KLHL35
4.83E−03
5.01E−03
NLGN3
6.90E−03
2.77E−02
UGGT1
6.72E−03
1.89E−02


MSTN
4.93E−03
3.60E−03
HAUS5
6.91E−03
8.60E−03
CGB5
6.74E−03
4.91E−03


CLIC4
4.96E−03
9.75E−03
OTOP1
6.97E−03
7.63E−03
PIM3
6.81E−03
6.29E−03


SLC3A2
4.96E−03
1.95E−03
TMEM251
7.05E−03
7.71E−03
GUCD1
6.87E−03
7.38E−03


CYP781
5.25E−03
6.55E−03
DARS2
7.08E−03
4.44E−03
KANSL1
6.95E−03
7.57E−03


PTGIS
5.40E−03
6.26E−03
WASF3
7.08E−03
1.10E−02
OR4Q3
6.97E−03
1.12E−02


VPS28
5.43E−03
6.67E−03
RGPD6
7.13E−03
7.15E−03
FAM83H
6.99E−03
5.87E−03


ZNF138
5.47E−03
6.10E−03
MAPK8IP3
7.19E−03
8.33E−03
RNF103
7.08E−03
5.69E−03


RPS10
5.53E−03
4.86E−03
UACA
7.23E−03
9.30E−03
UBXN11
7.16E−03
6.68E−03


SLC30A1
5.61E−03
4.78E−03
GRIPAP1
7.25E−03
7.16E−03
CREB3L3
7.19E−03
9.51E−03


CDC42EP1
5.69E−03
4.23E−03
MEF2D
7.33E−03
6.78E−03
LIPJ
7.30E−03
8.04E−03


HSPA13
5.83E−03
7.30E−03
CRTAC1
7.40E−03
9.06E−03
EFHD1
7.34E−03
5.26E−03


SMIM10L1
5.90E−03
4.24E−03
OR5M1
7.59E−03
5.59E−03
SATL1
7.34E−03
5.24E−03


BANP
6.22E−03
8.91E−03
ZFP91
7.61E−03
5.47E−03
IZUMO2
7.43E−03
7.49E−03


CDK2AP1
6.28E−03
7.38E−03
TUBGCP3
7.62E−03
9.74E−03
CGB1
7.49E−03
5.21E−03


IRF5
6.31E−03
7.71E−03
CERS5
7.70E−03
9.45E−03
LARP1B
7.49E−03
6.48E−03


NXPH3
6.32E−03
8.94E−03
GSTP1
7.74E−03
8.33E−03
CGB2
7.56E−03
5.27E−03


SULT1C2
6.40E−03
6.67E−03
HEY1
7.93E−03
1.00E−02
KLF14
7.65E−03
5.81E−03


BIRC7
6.45E−03
1.08E−02
BLOC1S4
8.04E−03
7.91E−03
CYTH2
7.67E−03
7.05E−03


KPNA3
6.51E−03
1.72E−03
CLIC6
8.06E−03
7.77E−03
MAP3K7
7.68E−03
8.11E−03


FGFR1OP
6.57E−03
1.86E−03
RGL4
8.22E−03
1.89E−02
TTLL10
7.71E−03
6.72E−03


PASD1
6.58E−03
7.01E−03
WFIKKN2
8.30E−03
6.80E−03
ZNF707
7.71E−03
6.07E−03


ABCB10
6.64E−03
5.38E−03
HSD3B1
8.45E−03
9.51E−03
PPP2R1A
7.73E−03
5.78E−03


NKAIN4
6.65E−03
1.10E−02
SPAG4
8.49E−03
7.10E−03
HSPA13
7.77E−03
8.48E−03


DSG4
6.81E−03
9.69E−03
11-Sep
8.62E−03
9.72E−03
NBPF4
7.77E−03
7.72E−03


NKX3-2
6.82E−03
4.65E−03
SST
8.64E−03
1.15E−02
PAIP2
7.86E−03
8.55E−03


AMHR2
6.86E−03
4.81E−03
UPK1A
8.86E−03
8.32E−03
SCAND1
7.91E−03
8.12E−03


PRR13
6.90E−03
5.07E−03
ADAMTS20
8.93E−03
8.28E−03
DHRS7
7.99E−03
7.25E−03


OGT
6.93E−03
7.99E−03
CXCL3
8.94E−03
9.32E−03
NCL
8.02E−03
7.61E−03


MR0H9
6.95E−03
9.50E−03
C17orf67
8.98E−03
1.07E−02
KRT25
8.05E−03
8.57E−03


A1CF
7.00E−03
6.01E−03
WDR87
8.99E−03
9.91E−03
GPR63
8.08E−03
8.11E−03


MAPT
7.12E−03
7.20E−03
TOB1
9.37E−03
5.88E−03
ALPK2
8.21E−03
7.95E−03


MFHAS1
7.12E−03
1.86E−02
BCAR1
9.47E−03
7.97E−03
CABP5
8.23E−03
9.68E−03


TAF1
7.13E−03
8.69E−03
CPNE4
9.48E−03
1.34E−02
HES7
8.23E−03
9.19E−03


ATG101
7.28E−03
6.35E−03
MGARP
9.55E−03
1.06E−02
DEFB112
8.24E−03
9.00E−03


TOP3A
7.37E−03
4.99E−03
TERT
9.55E−03
6.65E−03
PCGF6
8.26E−03
7.65E−03


EFHB
7.44E−03
6.63E−03
FMOD
9.67E−03
5.49E−03
ORC1
8.32E−03
7.96E−03


NR1H3
7.46E−03
5.63E−03
LYPD3
9.68E−03
9.51E−03
CD300LG
8.52E−03
8.06E−03


PET117
7.52E−03
7.36E−03
SUCLA2
9.71E−03
8.49E−03
NEFL
8.60E−03
7.96E−03


PPIG
7.57E−03
1.95E−02
TNMD
9.72E−03
9.27E−03
HNRNPD
8.61E−03
8.20E−03


DAZAP2
7.66E−03
4.69E−03
NREP
9.86E−03
8.78E−03
STAG2
8.64E−03
7.66E−03


PPP1R14D
7.78E−03
3.53E−03
FBXO3
9.91E−03
6.76E−03
FBRS
8.82E−03
8.84E−03


ZFYVE19
7.85E−03
3.07E−03
STON1
9.97E−03
9.49E−03
CC2D2A
8.88E−03
7.08E−03


SNTG1
7.89E−03
8.43E−03
HTRA3
9.99E−03
1.03E−02
CCDC166
8.94E−03
7.44E−03


PRPS1
7.94E−03
8.51E−03



CFAP69
8.98E−03
8.17E−03


SLC36A4
7.95E−03
5.05E−03



TFB1M
9.12E−03
1.16E−02


SMAGP
8.02E−03
4.61E−03



C14orf177
9.17E−03
8.13E−03


CD300LG
8.10E−03
7.00E−03



IQCA1
9.17E−03
8.03E−03


CTXN2
8.11E−03
1.02E−02



MROH8
9.20E−03
8.00E−03


ZSWIM6
8.17E−03
1.52E−03



AUTS2
9.21E−03
7.21E−03


KRTAP10-12
8.24E−03
1.05E−02



SMG1
9.26E−03
1.06E−02


PRRG3
8.26E−03
7.78E−03



NSUN3
9.32E−03
9.80E−03


DEPDC4
8.30E−03
6.83E−03



SSBP3
9.38E−03
1.02E−02


CTHRC1
8.34E−03
1.36E−02



ING3
9.47E−03
1.18E−02


C19orf18
8.39E−03
7.28E−03



SND1
9.50E−03
7.05E−03


KRTAP12-1
8.42E−03
1.04E−02



KPNA3
9.51E−03
5.29E−03


SOCS4
8.44E−03
5.01E−03



NCALD
9.55E−03
1.10E−02


PLSCR5
8.48E−03
1.18E−02



TERT
9.55E−03
7.97E−03


AVP
8.58E−03
5.39E−03



KLF3
9.56E−03
1.09E−02


NR2E1
8.69E−03
2.43E−02



UBN2
9.74E−03
9.79E−03


C4orf36
8.79E−03
7.50E−03



ZFP37
9.76E−03
6.02E−03


GNGT1
8.83E−03
1.04E−01



GPI
9.80E−03
1.03E−02


MANSC1
8.83E−03
1.10E−02



ODF1
9.84E−03
8.11E−03


YTHDF1
8.91E−03
1.08E−02



HIST2H2BF
9.98E−03
9.42E−03


MUCS5AC
9.02E−03
2.03E−02








GTPBP4
9.10E−03
6.79E−03








SEMA5B
9.11E−03
6.34E−03








ZNF410
9.13E−03
1.16E−02








MADD
9.28E−03
6.45E−03








ETNPPL
9.30E−03
5.88E−03








ATP1A1
9.31E−03
2.53E−02








FREM3
9.35E−03
6.61E−03








SLC22A2
9.40E−03
1.04E−02








SLC25A26
9.41E−03
2.16E−02








KRTAP12-2
9.42E−03
1.21E−02








FBN1
9.43E−03
1.05E−02








OXT
9.44E−03
6.54E−03








TRAF5
9.48E−03
3.38E−03








GDPD5
9.52E−03
1.07E−02








BIN2
9.58E−03
5.65E−03








C9orf47
9.64E−03
6.01E−03








PTCHD4
9.71E−03
1.31E−02








SNCAIP
9.79E−03
3.00E−02









The ten most statistically significant genes are shown in Table 9. CID (p=2.00×10−8) was the most significant, followed by IL17F (p=1.80×10−7).









TABLE 9







Ten most statistically significant genes, according to unadjusted p values,


associated with proteinuria, hypertension, and composite toxicity from the gene-based


association analysis grade ≥2. Composite toxicity is defined as the occurrence of either proteinuria or hypertension or both.









Proteinuria
Hypertension
Composite toxicity












Gene
p-value
Gene
p-value
Gene
p-value





C1D
2.00 × 10−8
UNC50
2.30 × 10−5
SLC25A24
4.00 × 10−6


IL17F
1.80 × 10−7
KATNB1
2.50 × 10−5
SMS
5.00 × 10−6


MCM3
5.10 × 10−7
MGAT4A
4.60 × 10−5
CEP295
1.00 × 10−5


SMPX
1.20 × 10−5
FBXO9
5.10 × 10−5
YWHAE
1.60 × 10−5


KLHL34
1.26 × 10−5
STRIP1
9.80 × 10−5
PTPN3
4.00 × 10−5


EAPP
2.70 × 10−5
CCDC54
1.01 × 10−4
KLHL35
4.50 × 10−5


CNKSR2
3.50 × 10−5
COA5
1.06 × 10−4
H6PD
5.10 × 10−5


LIPJ
4.80 × 48−5
KIFC3
1.18 × 10−4
MBTPS2
7.50 × 10−5


ITGB6
5.00 × 10−5
ICK
1.21 × 10−4
CRK
1.37 × 10−4


XCR1
5.70 × 10−5
AHCYL1
1.45 × 10−4
SLC17A6
1.50 × 10−4









Variants and Genes Associated with Bevacizumab-Induced Hypertension


For the SNP-based analysis of grade hypertension, the Manhattan and Q-Q plots are shown in FIG. 2. 104 variants associated with hypertension were identified (Table 10).









TABLE 10







SNPs associated with hypertension (grade ≥ 2).


























effect
reference
MAF
MAF
MAF
MAF




p-value
effect (β)

effect


SNP
CH
BP
allele
allele
80303
40503
90401
40502
gene
feature
Flanking gene
Flanking gene
unadjusted
unadjusted
p-value adjusted
(β) adjusted


























rs3793027
6
70727823
G
A
0.09
.
.
.
COL19A1
intron
LMBRD1
COL9A1
1.21E−06
1.87
4.12E−06
2.00


rs13135230
4
24605796
A
G
0.27
0.28
0.25
0.28
NA
NA
CCDC149
LGI2
1.26E−06
0.46
1.36E−06
0.47


rs2350620
8
62660161
G
A
0.32
0.26
0.32
0.32
ASPH
intron
hCG_1988300
LOC645551
1.44E−06
−0.49
1.23E−06
−0.50


rs7204266
1
98760046
G
A
0.28
.
0.28
.
GRIN2A
intron
LOC653737
LOC727844
3.61E−06
0.76
2.58E−06
0.79


rs6770663
3
157514872
G
A
0.09
0.09
0.08
0.09
KCNAB1
intron
LOC751837
SSR3
4.79E−06
0.57
4.16E−06
0.58


rs1145786
6
91678597
G
A
0.33
0.32
0.34
0.33
NA
NA
MAP3K7
LOC100129847
5.10E−06
0.39
7.18E−06
0.39


rs7038808
9
91931116
A
G
0.13
.
0.15
.
NA
NA
IL6RL1
OR7E31P
5.20E−06
0.91
9.36E−06
0.90


rs11036390
11
41387322
C
A
.
0.27
.
0.31
NA
NA
LRRC4C
LOC100131020
5.23E−06
0.46
5.57E−06
0.47


rs10905087
10
7082276
A
G
.
0.25
.
0.23
NA
NA
LOC439949
SFMBT2
6.01E−06
−0.64
5.30E−06
−0.65


rs12316952
12
46238282
G
A
0.06
.
0.08
.
NA
NA
LOC100127978
RPAP3
6.17E−06
1.14
8.30E−06
1.14


rs17097718
14
98252288
T
C
.
0.06
.
.
C14orf177
missense
LOC100132612
RPL3P4
8.56E−06
1.48
8.45E−03
−0.54


rs757354
12
46233818
C
A
0.06
.
0.08
.
NA
NA
LOC100127978
RPAP3
1.11E−05
1.11
1.42E−05
1.11


rs7553399
1
3406309
C
A
.
0.25
.
.
MEGF6
missense
ARHGEF16
TPRG1L
1.14E−05
1.06
1.34E−05
1.06


rs7130734
11
41385931
A
C
0.35
0.30
.
0.33
NA
NA
LRRC4C
LOC100131020
1.17E−05
0.42
8.77E−06
0.43


rs13176984
5
151653739
C
T
.
0.11
.
0.18
NA
NA
GLRA1
NMUR2
1.20E−05
0.55
6.10E−06
0.57


rs11714367
3
176714180
A
G
0.14
.
0.17
.
NAALADL2
intron
LOC647212
LOC100128870
1.40E−05
0.83
1.49E−05
0.82


rs2179218
20
40502874
A
G
0.13
0.15
0.14
0.13
PTPRT
intron
LOC643172
PPIAL
1.99E−05
0.49
3.00E−05
0.48


rs16986558
20
40207824
A
G
0.06
.
0.06
.
PTPRT
intron
LOC643172
PPIAL
2.18E−05
0.93
1.02E−05
0.99


rs10519829
5
125045325
A
G
0.44
0.46
0.47
0.47
NA
NA
LOC644659
LOC100130551
2.28E−05
0.36
1.84E−05
0.37


rs1530837
15
40069082
G
A
0.23
0.19
0.18
0.17
PLA2G4E
intron
EHD4
PLA2G4D
2.59E−05
0.43
2.28E−05
0.44


rs4697273
4
21844894
A
G
.
0.28
.
0.20
NA
NA
KCNIP4
GPR125
2.60E−05
0.50
3.76E−05
0.49


rs2949929
17
62943076
T
C
.
0.27
.
0.25
PITPNC1
intron
LOC729822
NOL11
2.98E−05
0.48
3.75E−05
0.48


rs1564470
8
136290117
A
C
0.30
.
0.32
.
NA
NA
ZFAT
LOC286094
3.10E−05
0.74
2.70E−05
0.75


rs7201930
16
9866156
G
A
0.29
.
0.33
.
GRIN2A
intron
LOC653737
LOC727844
3.15E−05
0.72
2.35E−05
0.74


rs2125944
4
42421675
A
G
0.08
.
0.10
.
NA
NA
ATP8A1
GRXCR1
3.19E−05
0.86
5.09E−05
0.84


rs10828545
10
18669609
A
G
.
0.34
.
0.37
CACNB2
intron
SLC39Al2
NSUN6
3.21E−05
−0.47
1.79E−05
−0.49


rs4688081
3
119398144
G
A
.
0.41
.
0.40
NA
NA
LOC728873
IGSF11
3.38E−05
−0.44
4.05E−05
−0.44


rs9921541
16
9899263
A
C
0.23
.
0.24
.
GRIN2A
intron
LOC653737
LOC727844
3.38E−05
0.71
3.17E−05
0.72


rs4899947
14
0.88769467
C
T
.
0.36
.
0.32
KCNK10
intron
KCNK10
SPATA7
3.48E−05
0.44
1.75E−05
0.45


rs2000611
14
87837079
G
A
0.44
0.43
0.50
0.48
KCNK10
intron
KCNK10
SPATA7
3.49E−05
−0.37
2.25E−05
−0.38


rs11732343
4
89722914
A
G
0.08
.
.
.
NA
NA
LOC100129137
HERC3
3.62E−05
1.70
2.22E−05
1.78


rs4611262
12
101026889
A
G
0.20
0.25
0.23
0.23
NUP37
intron
CCDC53
C12orf48
3.74E−05
0.39
1.59E−05
0.40


rs9512328
13
26149803
G
A
0.06
0.09
0.09
0.08
WASF3
intron
LOC646527
GPR12
3.84E−05
0.54
8.30E−05
0.52


rs996784
3
164707301
T
G
.
0.23
.
0.27
NA
NA
LOC647107
LOC730129
3.86E−05
0.45
5.91E−05
0.44


rs13161952
5
125046494
G
A
.
0.30
.
0.21
NA
NA
LOC644659
LOC100130551
3.96E−05
0.45
2.11E−05
0.46


rs1517527
2
206252547
A
G
0.41
.
0.42
.
NA
NA
PARD3B
NRP2
4.11E−05
0.69
7.39E−05
0.68


rs760122
21
40701616
A
G
0.23
.
0.26
.
DSCAM
intron
PCP4
BACE2
4.15E−05
0.69
7.05E−05
0.69


rs11713383
3
63523900
A
G
0.38
.
0.35
.
SYNPR
intron
LOC100129031
S100A1L
4.17E−05
0.71
7.36E−05
0.71


rs9933832
16
9856135
A
G
0.29
.
0.32
.
GRIN2A
intron
LOC653737
LOC727844
4.19E−05
0.70
3.09E−05
0.73


rs1350117
4
34666752
G
A
0.40
0.33
0.38
0.39
NA
NA
LOC727819
LOC100132690
4.32E−05
−0.39
3.35E−05
−0.40


rs2220706
9
104673784
G
A
0.05
.
0.06
0.07
NA
NA
LOC100131879
CYLC2
4.40E−05
0.65
6.89E−05
0.64


rs17648695
11
100363635
C
T
.
0.14
.
0.11
LOC100129602
intron
FLJ32810
TMEM133
4.41E−05
0.54
3.70E−05
0.55


rs17654410
11
100369356
T
C
.
0.14
.
0.11
TMEM133
utr-3
LOC100129602
PGR
4.41E−05
0.54
3.70E−05
0.55


rs2456761
10
62200548
A
C
0.35
.
0.34
.
NA
NA
LOC729184
CDC2
4.57E−05
0.74
5.35E−05
0.74


rs7738087
6
939790
G
A
0.42
0.40
0.37
0.37
NA
NA
EXOC2
FOXQ1
4.67E−05
0.36
6.59E−05
0.36


rs17787479
8
140579876
A
C
0.21
0.26
0.20
0.20
NA
NA
COL22A1
KCNK9
4.68E−05
0.40
5.88E−05
0.40


rs7618831
3
63531349
A
G
0.38
.
0.36
.
SYNPR
intron
LOC100129031
S100A1L
4.69E−05
0.71
8.08E−05
0.70


rs873766
2
106042957
C
T
.
0.12
.
0.10
NA
NA
LOC100132455
C2orf40
4.71E−05
0.57
5.40E−05
0.57


rs2886725
5
37770836
A
G
.
0.14
.
.
NA
NA
WDR70
GDNF
4.80E−05
1.02
6.25E−05
1.07


rs10087981
8
23282409
A
C
.
0.32
.
0.28
LOXL2
intron
R3HCC1
ENTPD4
4.84E−05
−0.49
6.10E−05
−0.49


rs6302
6
87782302
T
C
.
0.10
.
0.08
HTR1E
reference
LOC643971
CGA
4.85E−05
0.63
8.23E−05
0.61


rs365277
13
61808609
G
A
0.47
0.46
0.41
0.45
NA
NA
LOC100133193
LOC647259
4.93E−05
−0.37
6.04E−05
−0.37


rs3858416
11
100230559
T
C
.
0.06
.
0.05
FLJ32810
intron
LOC100128386
LOC100129602
4.95E−05
0.66
3.14E−05
0.68


rs7821773
8
9748866
G
A
0.08
0.05
0.08
.
NA
NA
TNKS
MSRA
4.97E−05
0.78
2.07E−03
0.46


rs10842185
12
23625382
G
A
0.10
0.13
0.10
0.10
SOX5
intron
LOC100131418
LOC100129937
4.97E−05
0.50
2.92E−05
0.52


rs6445360
3
63523420
A
G
0.38
.
0.36
.
SYNPR
intron
LOC100129031
S100A1L
5.26E−05
0.71
9.10E−05
0.70


rs2825322
21
19343047
G
A
0.27
0.34
0.27
0.26
NA
NA
PPIAL3
SLC6A6P
5.51E−05
−0.43
5.98E−05
−0.43


rs805772
20
5619460
T
G
.
0.13
.
0.12
NA
NA
RPS-1022P6.2
C20orf196
5.58E−05
0.57
5.50E−05
0.58


rs1352981
9
104625739
G
A
0.08
.
0.08
.
NA
NA
LOC100131879
CYLC2
5.74E−05
0.85
6.63E−05
0.85


rs12170867
22
30292076
A
G
.
0.09
.
0.11
SFI1
intron
LOC100128535
PISD
5.76E−05
0.57
8.56E−05
0.56


rs2278495
18
52838811
A
G
0.25
.
0.24
.
WDR7
intron
LOC100130858
FAM44C
6.11E−05
0.72
8.93E−05
0.71


rs2729007
3
2132357
A
G
0.21
0.26
0.22
0.22
CNTN4
intron
LOC727810
LOC100130346
6.14E−05
0.40
8.80E−05
0.39


rs2991492
13
78625387
A
G
.
0.48
.
0.48
NA
NA
LOC390415
LOC100128339
6.15E−05
−0.43
9.05E−05
−0.42


rs2267796
16
9884214
C
A
0.24
.
0.24
.
GRIN2A
intron
LOC653737
LOC727844
6.60E−05
0.69
5.78E−05
0.70


rs2232030
4
24614069
G
A
0.15
0.18
0.13
0.15
LGI2
utr-3
CCDC149
SEPSECS
6.67E−05
0.46
7.23E−05
0.47


rs7659172
4
24609653
A
G
.
0.18
.
0.15
NA
NA
CCDC149
LGI2
6.83E−05
0.53
9.37E−05
0.53


rs1171566
1
154766593
C
T
.
0.28
.
0.32
IQGAP3
reference
MEF2D
TTC24
6.84E−05
0.41
7.42E−05
0.41


rs1370215
18
52839937
G
A
0.25
.
0.24
.
WDR7
intron
LOC100130858
FAM44C
6.99E−05
0.72
1.02E−04
0.70


rs540509
7
17071448
G
A
.
0.19
.
0.23
NA
NA
LOC100131425
LOC100131512
7.03E−05
0.45
4.91E−05
0.46


rs1288934
1
224894661
G
A
0.24
0.27
0.24
0.26
ITPKB
intron
C1orf95
PSEN2
7.05E−05
−0.43
7.60E−05
−0.43


rs3745539
19
56219853
A
G
0.08
.
0.06
.
KLK11
missense
KLK10
KLK12
7.08E−05
0.93
7.94E−05
0.92


rs2860529
4
105672170
G
A
0.22
0.20
0.23
0.23
NA
NA
LOC728847
LOC391679
7.11E−05
0.37
8.67E−05
0.37


rs2172102
5
125024395
G
A
.
0.28
.
0.19
NA
NA
LOC644659
LOC100130551
7.12E−05
0.44
5.08E−05
0.45


rs1219508
10
123451644
A
G
0.22
0.24
0.23
0.23
NA
NA
LOC729426
ATE1
7.14E−05
−0.46
1.42E−04
0.44


rs4580675
4
80827274
A
G
0.43
0.47
0.44
0.47
NA
NA
0 R7E94 P
GDEP
7.15E−05
−0.36
8.47E−05
−0.36


rs12480201
20
59812166
A
G
0.14
.
0.15
.
CDH4
intron
LOC100131417
TAF4
7.18E−05
0.85
4.39E−05
0.88


rs1268663
14
64335834
A
G
0.20
0.22
0.20
0.21
SPTB
intron
LOC100129913
CH URC1
7.34E−05
0.41
5.26E−05
0.42


rs4775610
15
61119110
A
G
.
0.31
.
0.28
NA
NA
TLN2
TPM1
7.37E−05
0.42
7.35E−05
0.42


rs11133274
4
53994137
A
G
0.21
0.20
0.21
0.20
FIP1L1
intron
LOC100130982
LNX1
7.50E−05
0.38
2.46E−05
0.41


rs4813886
20
912652
G
A
0.11
0.12
0.12
0.12
RSPO4
intron
ANGPT4
PSMF1
7.61E−05
0.46
5.87E−05
0.47


rs4743599
9
104651778
G
A
0.08
.
0.08
.
NA
NA
LOC100131879
CYLC2
7.73E−05
0.84
9.03E−05
0.84


rs2713289
4
134759843
A
G
0.48
0.49
0.49
0.47
NA
NA
PCDH10
PABPC4L
7.89E−05
0.34
8.57E−05
0.34


rs1884114
20
914504
T
G
.
0.08
.
0.08
RSPO4
intron
ANGPT4
PSMF1
7.90E−05
0.62
5.11E−05
0.64


rs338248
1
58703893
C
A
0.29
0.24
0.27
0.29
NA
NA
DAB1
OMA1
7.90E−05
0.37
8.49E−05
0.37


rs3767867
1
210624222
G
A
0.35
.
0.38
.
TMEM206
intron
PPP2R5A
NENF
7.91E−05
−0.81
1.00E−04
−0.80


rs9530488
13
75370156
A
G
0.36
.
0.42
.
NA
NA
FLJ35379
LOC100132423
8.04E−05
0.68
1.49E−04
−0.66


rs11251166
10
2357939
C
A
.
.
.
0.28
NA
NA
LOC728209
LOC727878
8.22E−05
0.50
7.30E−05
0.51


rs1452232
12
83750362
C
A
0.37
.
0.37
.
NA
NA
LOC100128335
SLC6A15
8.38E−05
0.69
1.03E−04
0.69


rs7667510
4
41913903
G
A
.
0.15
.
0.15
NA
NA
BEND4
SHISA3
8.39E−05
0.49
9.27E−05
0.49


rs2687640
7
29138781
A
G
0.06
.
0.06
0.05
CPVL
intron
KIAA0644
LOC100131724
8.45E−05
0.66
9.57E−05
0.66


rs711272
6
91667454
A
G
0.28
0.27
0.30
0.27
NA
NA
MAP3K7
LOC100129847
8.72E−05
0.35
8.10E−05
0.36


rs16924767
12
22260834
G
A
0.13
.
0.16
.
ST8SIA1
intron
CMAS
KIAA0528
8.98E−05
0.89
9.26E−05
0.90


rs12757197
1
233657182
A
G
0.07
.
0.10
.
TBCE
intron
GGPS1
B3GALNT2
9.19E−05
0.83
4.07E−05
0.91


rs11164023
1
84861990
G
A
0.20
0.17
0.19
0.22
NA
NA
CTBS
C1orf180
9.25E−05
0.40
5.75E−05
0.41


rs4948291
10
59770095
T
C
.
0.33
.
0.36
UBE2D1
intron
CISD1
TFAM
9.30E−05
0.40
7.00E−05
0.41


rs17156773
10
1740763
A
G
.
0.07
.
0.09
ADARB2
intron
C10orf109
LOC100129465
9.42E−05
0.63
8.49E−05
0.64


rs2288502
5
156582630
A
G
0.07
0.07
0.06
0.06
ITK
intron
FAM71B
CYFIP2
9.45E−05
0.61
1.04E−04
−0.61


rs1362972
12
94599424
A
C
0.12
.
0.18
.
NTN4
intron
LOC100132594
SNRPF
9.47E−05
0.79
1.73E−04
−0.78


rs1480802
8
136293393
C
A
0.37
.
0.38
.
NA
NA
ZFAT
LOC286094
9.54E−05
0.71
6.70E−05
0.73


rs6681946
1
17358138
G
A
0.20
.
0.21
.
NA
NA
PADI2
LOC400743
9.59E−05
0.73
1.18E−04
0.72


rs4735993
8
1141126
G
A
.
0.27
.
0.26
NA
NA
LOC401442
DLGAP2
9.70E−05
0.42
4.38E−05
0.45


rs2515034
8
119565108
G
A
0.06
.
.
.
SAMD12
intron
EXT1
LOC441377
9.86E−05
1.68
7.67E−05
1.77


rs4691370
4
157809201
G
A
0.06
0.09
.
0.07
NA
NA
hCG_1814936
PDGFC
9.91E−05
0.59
1.02E−04
0.60


rs2077923
16
9788282
G
A
0.29
.
0.32
.
GRIN2A
intron
LOC653737
LOC727844
9.95E−05
0.68
8.64E−05
0.69









Thirty-four out of the 104 variants had the same direction of effect in at least three out of the four studies (cutoff p<1×10−4). The top ten most statistically significant variants of that list in shown in Table 5. rs13135230 (G>A, MAF 0.25-0.28) was the most statistically significant (p=1.26×10−6, β=0.46), with the A allele increasing the risk of hypertension (FIG. 3). rs13135230 is 3.8 kb 3′ from LGI2 (FIG. 4B). rs2350620 (A>G, MAF 0.26-0.32) is the next most statistically significant (p=1.44×10−6, β=0.49) with the G allele decreasing the risk of hypertension (FIG. 13). rs2350620 is located in the intron 14 of ASPH (FIG. 4B). rs6770663 (A>G, MAF 0.08-0.09) is the next most statistically significant (p=4.79×10−6, β=0.57) with the G allele increasing the risk of hypertension (FIG. 13). rs6770663 is located in the intron 1 of KCNAB1 (FIG. 4C) Among these ten variants, the only two with p-value<0.05 in three out of the four studies were rs2350620 and rs6770663 (Table 5). FIG. 13 shows the cumulative incidence of grade≥2 hypertension for rs2350620 and rs6770663. For the SNP-based analysis of grade the Manhattan and Q-Q plots are shown in FIG. 5. 106 variants were identified as associated with hypertension (Table 11).


Forty-seven out of 106 variants had the same direction of effect (either reduced or increased risk) in at least three out of the four studies (cutoff p<1×10−4). The top ten most statistically significant variants of that list are shown in Table 7. rs4782946 (G>A, MAF 0.37-0.43) was the most statistically significant (p=3.09×10−7, β=0.66) with the A allele increasing the risk of hypertension. rs4782946 is an intronic variant in ATP2C2 (FIG. 6). rs17439529 (G>A, MAF 0.36-0.40) was the next most statistically significant (p=2.08×10-6, β=−0.72) with the A allele decreasing the risk of hypertension. rs17439529 is located in the intron of AKAP6 (FIG. 6).









TABLE 11







SNPs associated with hypertension (grade ≥3)

























refer-















effect
ence
MAF
MAF
MAF
MAF


Flanking
Flanking

effect


SNP
CH
BP
allele
allele
80303
40503
90401
40502
gene
feature
gene
gene
p-value
(β)
























rs-
16
82979663
A
G
0.37
0.38
0.37
0.43
ATP2C2
intron
WFDC1
KIAA1609
3.09E−07
0.66


4782946
















rs-
11
100230559
A
G
.
0.06
.
0.05
FLJ32810
intron
LOC-
LOC-
7.29E−07
1.06


3858416










100128386
100129602




rs-
3
120338347
C
A
.
.
0.06
.
IGSF11
intron
LOC728873
C3orf30
1.27E−06
1.70


6807110
















rs-
14
32253709
A
G
0.36
0.40
0.38
0.40
AKAP6
intron
MTCO1P2
NPAS3
2.08E−06
−0.72


17439529
















rs-
14
77017051
G
A
.
0.06
.
0.09
THSD3
intron
AHSA1
SPTLC2
3.47E−06
1.04


10129969
















rs-
16
78434745
G
A
0.06
.
0.05
.
NA
NA
LOC440389
LOC729847
4.68E−06
1.44


9933396
















rs-
15
40069082
G
A
0.23
0.19
0.18
0.17
PLA2G4E
intron
EHD4
PLA2G4D
4.87E−06
0.66


1530837
















rs-
16
82980316
A
G
0.20
0.17
0.19
0.22
ATP2C2
intron
WFDC1
KIAA1609
5.23E−06
0.63


11863271
















rs-
13
35359822
C
A
0.19
0.26
0.19
0.21
DCLK1
intron
NBEA
SOHLH2
5.73E−06
0.62


1171065
















rs-
14
77018319
G
A
.
0.07
.
0.09
THSD3
intron
AHSA1
SPTLC2
5.92E−06
1.01


8010861
















rs-
18
10056414
A
G
0.18
0.14
0.11
0.12
NA
NA
VAPA
APCDD1
6.10E−06
0.67


670362
















rs-
2
182712983
G
A
0.07
.
0.06
.
NA
NA
PPP1R1C
PDE1A
7.08E−06
1.60


17649232
















rs-
8
141032458
A
G
0.44
0.48
0.47
0.47
NIBP
intron
C8orf17
LOC-
7.13E−06
0.63


2665917











100131910




rs-
14
77209741
A
C
.
0.18
.
0.18
ALKBH1
utr-3
SPTLC2
RPL21P10
7.63E−06
0.78


1048147
















rs-
14
77207812
A
G
.
0.18
.
0.18
ALKBH1
near-
SPTLC2
ALKBH1
7.63E−06
0.78


11624101









gene-3






rs-
14
77250973
G
A
.
0.18
.
0.18
C14orf156
intron
ALKBH1
SNW1
7.63E−06
0.78


176955
















rs-
9
2630805
A
G
0.07
0.07
0.09
0.08
VLDLR
intron
FLJ35024
KCNV2
8.16E−06
0.87


10967306
















rs-
10
115923895
A
G
0.13
.
0.10
.
C10orf118
utr-5
ADRB1
TDRD1
9.41E−06
1.17


17091403
















rs-
13
95897355
G
A
0.06
.
0.07
.
HS6ST3
intron
UGCGL2
HSP90AB6P
9.44E−06
1.35


732121
















rs-
14
77270338
C
A
.
0.18
.
0.18
SNW1
intron
C14orf156
C14orf178
9.68E−06
0.77


12887282
















rs-
8
23934297
A
G
0.24
0.18
0.21
0.24
NA
NA
LOC-
ADAM28
9.86E−06
0.61


1320881










100132107





rs-
4
124693385
G
A
.
0.16
.
0.17
NA
NA
SPRY1
LOC644624
1.00E−05
0.77


10011590
















rs-
4
157809201
G
A
0.06
0.09
.
0.07
NA
NA
hCG_1814936
PDGFC
1.00E−05
0.82


4691370
















rs-
14
77330548
A
G
.
0.18
.
0.18
NA
NA
C14orf178
ADCK1
1.06E−05
0.77


1008988
















rs-
15
68821216
C
A
.
0.13
.
0.09
UACA
intron
TLE3
LOC729611
1.08E−05
0.93


11852645
















rs-
14
77317035
A
G
.
0.18
.
0.18
NA
NA
C14orf178
ADCK1
1.09E−05
0.77


4632066
















rs-
5
58097612
A
G
0.19
0.18
0.17
0.16
RAB3C
intron
GAPT
PDE4D
1.12E−05
0.64


10073306
















rs-
18
10052583
G
A
.
0.10
.
0.10
NA
NA
VAPA
APCDD1
1.26E−05
0.84


8088993
















rs-
2
178188309
A
G
0.09
0.10
0.08
0.08
TTC30A
utr-3
TTC30B
PDE11A
1.31E−05
0.83


3821004
















rs-
10
30375128
G
A
.
0.40
.
.
KIAA1462
intron
SVIL
LOC729663
1.33E−05
1.27


2505083
















rs-
7
36284221
A
G
0.07
0.13
0.09
0.07
EEPD1
intron
LOC-
KIAA0895
1.37E−05
0.75


196584










100131181





rs-
9
84353502
A
G
0.08
0.07
0.06
0.06
NA
NA
LOC442427
RASEF
1.54E−05
1.01


10867852
















rs-
11
130222650
G
A
.
0.45
.
0.49
NA
NA
C11orf44
SNX19
1.54E−05
0.72


1944142
















rs-
6
1657305
C
A
.
0.20
.
0.15
GMDS
intron
FLJ46552
LOC-
1.68E−05
0.78


7765461











100128372




rs-
3
5538371
A
G
0.12
0.15
0.09
0.12
NA
NA
MRPS35P1
MRPS36P1
1.72E−05
0.70


17749328
















rs-
5
58106740
A
C
0.14
0.17
0.14
0.13
RAB3C
intron
GAPT
PDE4D
1.76E−05
0.67


10051270
















rs-
16
88183752
A
G
0.45
0.47
0.50
0.48
CPNE7
intron
RPL13
DPEP1
1.86E−05
0.58


464349
















rs-
22
48127214
G
A
.
0.20
.
0.19
NA
NA
LOC643653
FLJ44385
2.04E−05
0.75


2858536
















rs-
6
116992250
C
A
0.19
0.16
0.19
0.19
NA
NA
FAM26D
RWDD1
2.09E−05
0.64


17078062
















rs-
20
17569201
A
G
0.08
.
0.08
.
RRBP1
intron
DSTN
BANF2
2.10E−05
1.30


7267054
















rs-
15
99119567
G
A
.
.
0.41
.
NA
NA
ASB7
LOC440313
2.27E−05
1.42


7174784
















rs-
5
156582630
A
G
0.07
0.07
0.06
0.06
ITK
intron
FAM71B
CYFIP2
2.47E−05
0.89


2288502
















rs-
7
17071448
G
A
.
0.19
.
0.23
NA
NA
LOC-
LOC-
2.64E−05
0.73


540509










100131425
100131512




rs-
18
57190720
A
G
0.08
0.12
0.09
0.09
NA
NA
hCG_1659830
LOC-
2.66E−05
0.77


8084568











100129867




rs-
2
165199471
G
A
.
0.26
.
0.29
NA
NA
GRB14
COBLL1
2.77E−05
0.70


4425091
















rs-
3
2330167
A
G
.
0.30
0.33
0.34
CNTN4
intron
LOC727810
LOC-
2.99E−05
−0.75


11129096











100130346




rs-
2
29947713
C
A
0.11
0.15
0.17
0.21
ALK
intron
CLIP4
YPEL5
3.06E−05
0.60


7574859
















rs-
2
226443471
G
A
.
0.09
.
0.11
NA
NA
KIAA1486
LOC646736
3.13E−05
0.88


35969878
















rs-
3
182528567
G
A
.
0.45
.
0.42
NA
NA
DNAJC19
SOX2OT
3.21E−05
0.68


2879464
















rs-
2
46019476
G
A
0.13
0.12
0.14
0.12
PRKCE
intron
SRBD1
EPAS1
3.50E−05
0.70


10206343
















rs-
15
27520966
G
A
0.32
0.34
0.34
0.35
NA
NA
NDNL2
LOC-
3.54E−05
0.55


511092











100130736




rs-
15
68781337
A
G
.
0.13
.
0.09
UACA
intron
TLE3
LOC729611
3.68E−05
0.89


6494889
















rs-
22
27789732
G
A
0.22
0.22
0.24
.
NA
NA
C22orf31
KREMEN1
3.71E−05
0.73


760628
















rs-
14
77217446
A
G
.
0.19
.
0.20
ALKBH1
intron
SPTLC2
RPL21P10
3.76E−05
0.69


2267760
















rs-
8
141012685
G
A
0.45
0.48
0.47
0.48
NIBP
intron
KCNK9
LOC-
3.78E−05
0.58


2233230











100131910




rs-
11
104627661
A
G
.
0.49
.
0.46
NA
NA
OR2AL1P
GRIA4
3.85E−05
−0.72


4320922
















rs-
2
174261681
C
A
0.13
0.11
0.14
0.11
NA
NA
LOC-
LOC644056
4.04E−05
0.73


752280










100129456





rs-
17
11806187
A
G
0.20
0.18
0.19
0.18
DNAH9
missense
FLJ45455
ZNF18
4.11E−05
0.59


1990236
















rs-
3
23458540
A
G
0.40
0.40
0.43
0.45
UBE2E2
intron
LOC-
UBE2E1
4.17E−05
0.53


13062101










100130785





rs-
1
54625582
C
A
.
0.44
.
.
SSBP3
intron
C1orf191
LOC645436
4.18E−05
−1.19


11206344
















rs-
7
1106944
A
C
0.19
.
.
0.21
C7orf50
intron
GPER
ZFAND2A
4.18E−05
0.75


6463224
















rs-
15
68789686
G
A
.
0.13
.
0.09
UACA
intron
TLE3
LOC729611
4.32E−05
0.88


16954699
















rs-
15
68792114
C
A
.
0.13
.
0.09
UACA
intron
TLE3
LOC729611
4.32E−05
0.88


2059322
















rs-
10
76203313
A
G
0.07
.
0.08
.
NA
NA
LOC645646
MYST4
4.36E−05
1.10


7075347
















rs-
9
130559781
G
A
0.45
.
0.46
.
ZER1
intron
ZDHHC12
TBC1D13
4.39E−05
−1.09


10988111
















rs-
16
85631051
C
A
0.30
0.33
0.32
0.34
NA
NA
LOC729979
LOC730018
4.39E−05
0.52


1364075
















rs-
15
49594756
A
C
.
0.14
.
0.15
DMXL2
intron
GLDN
SCG3
4.48E−05
0.76


11855184
















rs-
8
68660493
G
A
.
.
.
0.11
CPA6
intron
LOC-
PREX2
4.50E−05
1.02


16933415










100132812





rs-
11
104720707
A
G
.
0.15
.
0.16
NA
NA
OR2AL1P
GRIA4
4.52E−05
0.79


1449047
















rs-
15
31357207
G
A
0.11
0.08
0.06
0.08
NA
NA
FMN1
RYR3
4.64E−05
0.81


1514035
















rs-
13
92633700
A
C
.
0.20
.
0.20
NA
NA
GPC5
GPC6
4.88E−05
0.71


9584088
















rs-
14
48194882
A
G
0.34
0.44
0.44
0.41
NA
NA
RPL18P1
ATP5GP2
4.92E−05
0.54


2585348
















rs-
6
90700670
G
A
0.23
0.22
0.25
0.22
BACH2
intron
GJA10
LOC-
5.03E−05
0.56


17708487











100129711




rs-
15
21400911
G
A
.
0.11
.
0.13
NA
NA
MKRN3
MAGEL2
5.15E−05
0.83


7173605
















rs-
19
5031647
A
G
0.09
.
0.08
.
JMJD2B
intron
UHRF1
LOC-
5.26E−05
1.12


11673509











100128439




rs-
15
68795974
A
G
.
0.12
.
0.09
UACA
intron
TLE3
LOC729611
5.32E−05
0.87


1078097
















rs-
5
58117438
A
G
0.17
0.20
0.18
0.17
RAB3C
intron
GAPT
PDE4D
5.54E−05
0.61


406992
















rs-
13
102681443
G
A
.
0.10
.
0.10
NA
NA
SLC10A2
LOC728183
6.04E−05
0.79


6650294
















rs-
17
11825241
A
G
0.20
0.18
0.19
0.18
ZNF18
intron
DNAH9
MAP2K4
6.18E−05
0.58


10852800
















rs-
11
335595
A
G
0.35
0.37
0.29
0.31
NA
NA
IFITM3
B4GALNT4
6.23E−05
−0.62


6598035
















rs-
5
13323090
A
G
.
0.17
0.17
0.14
NA
NA
CTNND2
LOC391738
6.28E−05
0.66


6554770
















rs-
15
68818494
A
G
.
0.13
.
0.09
UACA
intron
TLE3
LOC729611
6.30E−05
0.88


1011236
















rs-
17
11809087
G
A
0.21
0.18
0.19
0.19
DNAH9
intron
FLJ45455
ZNF18
6.34E−05
0.56


12449769
















rs-
3
182516536
G
A
0.44
0.46
0.42
0.43
NA
NA
DNAJC19
SOX2OT
6.36E−05
0.53


6778227
















rs-
2
178196274
A
G
0.07
0.08
.
0.06
PDE11A
utr-3
TTC30A
LOC-
6.59E−05
0.87


2293473











100131480




rs-
11
112699658
C
A
0.15
0.12
0.12
0.11
TTC12
intron
NCAM1
ANKK1
6.62E−05
0.62


723079
















rs-
9
111119949
A
G
0.39
0.37
0.35
0.36
EPB41L4B
intron
C9orf4
PTPN3
6.69E−05
−0.60


966697
















rs-
11
129067604
G
A
.
0.16
.
0.16
NA
NA
BARX2
LOC729717
6.74E−05
0.74


11221807
















rs-
2
205209582
A
C
0.09
.
0.08
.
PARD3B
intron
LOC-
NRP2
6.78E−05
1.12


1978368










100132669





rs-
5
113989891
A
C
0.10
0.09
0.06
0.09
NA
NA
KCNN2
TRIM36
6.84E−05
0.76


17365340
















rs-
15
68823323
C
A
.
0.13
0.10
0.09
UACA
intron
TLE3
LOC729611
6.91E−05
0.83


16954789
















rs-
18
10055917
G
A
0.21
0.15
0.15
0.15
NA
NA
VAPA
APCDD1
6.99E−05
0.57


1292299
















rs-
19
9175135
C
A
0.14
0.16
0.18
0.15
NA
NA
OR7E16P
OR7E25P
7.00E−05
0.59


10415904
















rs-
16
72370567
A
C
0.32
.
0.30
.
NA
NA
C16orf47
LOC441506
7.03E−05
0.89


2386717
















rs-
13
103355842
G
A
0.12
0.11
0.11
0.13
NA
NA
LOC728183
DAOA
7.27E−05
0.69


7328957
















rs-
1
182693445
G
A
0.08
.
0.07
0.07
C1orf21
intron
TSEN15
LOC-
7.57E−05
0.93


13374607











100129573




rs-
12
22260834
G
A
0.13
.
0.16
.
ST8SIA1
intron
CMAS
KIAA0528
7.58E−05
1.17


16924767
















rs-
5
89989605
A
G
0.06
.
0.08
.
GPR98
synony-
LYSMD3
LOC729040
7.77E−05
1.12


17543819









mous






rs-
13
103339702
G
A
0.10
0.11
0.09
0.11
NA
NA
LOC728183
DAOA
7.85E−05
0.67


17344132
















rs-
13
72567440
A
G
.
0.06
.
0.06
NA
NA
KLF5
FABP5L1
8.96E−05
0.90


2503697
















rs-
5
90031559
G
A
0.06
.
0.08
.
GPR98
intron
LYSMD3
LOC729040
9.33E−05
1.11


17622455
















rs-
5
135239365
A
G
0.11
0.12
0.12
0.11
NA
NA
LOC153328
IL9
9.37E−05
0.68


7717673
















rs-
18
63045205
A
G
.
0.10
.
0.08
NA
NA
CDH19
DSEL
9.42E−05
0.83


4519437
















rs-
11
84849951
A
G
0.07
.
.
0.07
NA
NA
DLG2
TMEM126B
9.49E−05
0.94


1213236
















rs-
2
36780787
G
A
0.13
0.11
0.14
0.14
VIT
intron
FEZ2
STRN
9.93E−05
0.6266


17019472
















rs-
16
75154359
G
A
0.40
.
0.41
.
NA
NA
CNTNAP4
LOC-
9.93E−05
−1.0612


4506930











100128497











For the gene-based analysis of grade≥2, the Q-Q plot is shown in FIG. 7. Table 9 shows the ten most statistically significant genes. UNC50 was the most statistically significant gene (p=2.30×10−5).


Variants and Genes Associated with Bevacizumab-Induced Proteinuria and Hypertension (Composite Toxicity)


For the SNP-based analysis of grade≥2, the Manhattan and Q-Q plots are shown in FIG. 2. 100 variants associated with composite toxicity were identified (Table 12).









TABLE 12







SNPs associated with composite toxicity (grade ≥2)


























reference
MAF
MAF
MAF










SNP
CH
BP
effect allele
allele
80303
40503
90401
gene
feature
Flanking gene
Flanking gene
p-value unadjusted
effect (β) unadjusted
p-value adjusted
effect (β) adjusted

























rs17084411
6
122692679
A
G
.
0.11
.
NA
NA
LOC644502
HSF2
4.24E−08
1.52
4.74E−08
1.55


rs1927869
6
122627419
T
C
.
0.11
.
NA
NA
LOC644502
HSF2
4.24E−08
1.52
4.74E−08
1.55


rs17084371
6
122612111
G
A
.
0.11
.
NA
NA
LOC644502
HSF2
7.24E−08
1.47
8.05E−08
1.49


rs11036390
11
41387322
C
A
.
0.27
.
NA
NA
LRRC4C
LOC100131020
2.15E−07
1.02
2.37E−07
1.02


rs11662763
18
5847091
A
G
0.14
0.11
0.13
NA
NA
LOC645355
TTMA
9.19E−07
0.67
9.48E−05
0.61


rs2937754
5
17308803
G
A
.
0.19
.
BASP1
intron
FLJ34047
LOC646012
1.52E−06
0.95
1.52E−06
0.97


rs8006648
14
87359052
A
G
0.27
0.28
0.26
NA
NA
LOC730121
GALC
2.33E−06
0.58
2.87E−05
0.55


rs2456761
10
62200548
A
C
0.35
.
0.34
NA
NA
LOC729184
CDC2
2.80E−06
0.72
4.57E−05
0.69


rs1000032
2
176643771
A
C
0.13
0.18
0.19
NA
NA
KIAA1715
EVX2
3.21E−06
0.62
9.26E−06
0.63


rs2203208
12
57257435
G
A
.
0.20
.
NA
NA
LOC100127973
LRIG3
3.54E−06
0.96
3.05E−06
1.00


rs2687640
7
29138781
A
G
0.06
.
0.06
CPVL
intron
KIAA0644
LOC100131724
3.55E−06
1.03
1.09E−06
1.13


rs9310707
3
2307104
A
G
0.37
0.37
0.36
CNTN4
intron
LOC727810
LOC100130346
4.03E−06
0.53
1.33E−05
0.52


rs7197696
16
6110274
G
A
.
0.14
.
A2BP1
intron
LOC100129334
LOC440337
5.95E−06
1.15
6.41E−06
1.16


rs9991738
4
182341049
C
T
.
0.49
.
NA
NA
hCG_2025798
LOC132386
7.26E−06
0.84
5.79E−06
0.86


rs12597709
16
6102147
G
A
.
0.13
.
A2BP1
intron
LOC100129334
LOC440337
7.29E−06
1.14
7.36E−06
1.14


rs13156044
5
13920851
A
G
0.15
0.11
0.11
DNAH5
intron
LOC391738
TRIO
8.51E−06
0.60
7.40E−05
0.59


rs12328055
2
49824743
A
G
0.06
.
0.05
NA
NA
FSHR
LOC130728
9.19E−06
0.99
2.27E−03
0.76


rs4799369
18
30594128
G
A
0.20
0.20
0.18
DTNA
intron
LOC646842
MAPRE2
1.14E−05
0.59
1.63E−03
0.44


rs11610946
12
3985117
G
A
.
0.14
.
NA
NA
PARP11
LOC399988
1.19E−05
0.96
1.21E−05
0.96


rs750585
5
168644898
G
A
.
0.13
.
SLIT3
intron
LOC728095
CCDC99
1.24E−05
1.03
1.30E−05
1.04


rs2757491
1
170533424
A
G
0.06
.
0.06
DNM3
intron
LOC100128178
LOC100131486
1.25E−05
0.90
1.39E−02
−0.68


rs2757500
1
170545644
A
G
0.06
.
0.06
DNM3
intron
LOC100128178
LOC100131486
1.25E−05
0.90
1.39E−02
0.28


rs17752325
4
65927951
A
G
0.11
.
0.13
EPHA5
intron
LOC644682
LOC642828
1.38E−05
0.77
1.05E−05
0.82


rs7204266
16
9876004
G
A
0.28
.
0.28
GRIN2A
intron
LOC653737
LOC727844
1.44E−05
0.60
6.84E−06
0.69


rs12754186
1
19638913
T
G
.
0.11
.
CAPZB
intron
LOC100130193
C1orf151
1.65E−05
0.98
1.14E−05
0.99


rs7202526
16
6808380
A
G
0.30
0.30
0.29
A2BP1
intron
LOC100131413
LOC100131080
1.67E−05
0.51
2.35E−05
0.52


rs1001952
11
41421246
C
T
.
0.26
.
NA
NA
LRRC4C
LOC100131020
1.74E−05
0.87
1.74E−05
0.87


rs11154658
6
132422252
G
T
.
0.13
.
LOC100131774
intron
CTGF
MOXD1
1.75E−05
0.98
1.51E−05
0.99


rs7553399
1
3406309
C
A
.
0.25
.
MEGF6
missense
ARHGEF16
TPRG1L
1.81E−05
0.95
1.46E−05
0.91


rs1358206
3
74198360
G
A
0.30
.
0.31
NA
NA
LOC100129282
HSP90AB5P
1.81E−05
0.62
3.89E−03
0.45


rs17867545
4
118873138
T
C
.
0.10
.
NA
NA
NT5C3P1
NDST3
1.84E−05
1.20
1.57E−05
1.23


rs16945809
17
1241236
G
A
0.08
0.08
0.06
YWHAE
intron
TUSC5
LOC727845
2.00E−05
0.80
2.16E−06
0.94


rs7234672
18
5875157
A
G
0.15
.
0.14
NA
NA
LOC645355
TTMA
2.06E−05
0.72
1.03E−03
0.64


rs13062101
3
23458540
A
G
0.40
0.40
0.43
UBE2E2
intron
LOC100130785
UBE2E1
2.34E−05
0.45
4.35E−05
0.46


rs10820743
9
106711480
G
A
0.29
0.28
0.27
ABCA1
intron
NIPSNAP3B
SLC44A1
2.42E−05
0.48
8.05E−05
0.47


rs7201930
16
9866156
G
A
0.29
.
0.33
GRIN2A
intron
LOC653737
LOC727844
2.90E−05
0.60
4.51E−05
0.65


rs12706180
7
117784949
A
G
0.34
.
.
NA
NA
ANKRD7
LOC648442
3.03E−05
0.91
8.37E−04
0.97


rs9933832
16
9856135
A
G
0.29
.
0.32
GRIN2A
intron
LOC653737
LOC727844
3.24E−05
0.59
5.18E−05
0.64


rs6706281
2
190160993
C
A
.
0.26
.
NA
NA
SLC40A1
ASNSD1
3.27E−05
0.91
2.54E−05
0.94


rs1437883
2
190167713
C
T
.
0.25
.
NA
NA
SLC40A1
ASNSD1
3.35E−05
0.90
2.81E−05
0.93


rs4407684
6
85500368
A
G
0.47
.
0.53
TBX18
near-
LOC442233
TBX18
3.48E−05
0.59
1.40E−03
0.49











gene-

















3








rs4149265
9
106712319
A
G
0.29
0.28
0.27
ABCA1
intron
NIPSNAP3B
SLC44A1
3.57E−05
0.47
1.20E−04
0.46


rs17202944
8
13848320
G
T
.
0.33
.
NA
NA
C8orf48
SGCZ
3.70E−05
−0.82
2.53E−05
−0.85


rs4738274
8
56645881
A
C
0.29
.
0.27
NA
NA
XKR4
TMEM68
3.72E−05
0.60
3.16E−03
0.49


rs277311
5
154473983
A
G
0.14
0.14
0.14
NA
NA
LOC100131520
LOC100130088
3.88E−05
0.62
3.47E−04
0.60


rs2866223
4
101744971
G
A
0.19
0.18
0.21
NA
NA
EMCN
LOC728771
3.96E−05
0.56
2.40E−03
0.43


rs7614155
3
74196658
G
A
0.25
.
0.27
NA
NA
LOC100129282
HSP90AB5P
4.05E−05
0.61
8.67E−03
0.42


rs6966727
7
130025354
G
A
0.06
.
.
NA
NA
TSGA13
KLF14
4.07E−05
1.31
1.26E−01
0.78


rs6982610
8
14557840
C
A
.
0.36
.
SGCZ
intron
LOC100131565
TUSC3
4.39E−05
0.77
3.36E−05
0.78


rs924945
18
67586419
A
G
0.34
0.41
0.34
NA
NA
LOC100132647
CBLN2
4.48E−05
0.46
3.54E−05
0.49


rs17021160
2
37717573
T
G
.
0.07
.
NA
NA
QPCT
CDC42EP3
4.52E−05
1.29
4.99E−05
1.30


rs9921541
16
9899263
A
C
0.23
.
0.24
GRIN2A
intron
LOC653737
LOC727844
4.52E−05
0.59
5.20E−05
0.64


rs2250378
12
73914832
C
T
.
0.23
.
LOC100130268
near-
KCNC2
LOC100130268
4.63E−05
0.88
4.85E−05
0.89











gene-

















5








rs351572
8
16065839
G
A
0.40
0.49
0.44
MSR1
intron
hCG_1794003
LOC646440
4.81E−05
−0.46
1.43E−04
−0.45


rs11642239
16
9904081
G
A
0.25
0.28
0.25
GRIN2A
intron
LOC653737
LOC727844
4.83E−05
0.48
1.14E−04
0.49


rs1480802
8
136293393
C
A
0.37
.
0.38
NA
NA
ZFAT
LOC286094
4.97E−05
0.63
2.50E−05
0.70


rs2886725
5
37806593
A
G
.
0.14
.
NA
NA
WDR70
GDNF
4.99E−05
0.97
4.89E−05
1.02


rs1524145
2
35975892
T
G
.
0.43
.
NA
NA
MRPL50P1
CRIM1
5.01E−05
0.84
5.05E−05
0.84


rs12525751
6
109444416
A
G
0.24
0.19
0.22
SESN1
intron
ARMC2
C6orf182
5.04E−05
0.51
1.31E−03
0.43


rs2077923
16
9788282
G
A
0.29
.
0.32
GRIN2A
intron
LOC653737
LOC727844
5.21E−05
0.59
1.20E−04
0.61


rs7853963
9
82908731
A
G
0.15
.
0.14
NA
NA
LOC100128222
TLE1
5.21E−05
0.72
5.12E−03
0.56


rs1410171
6
85459030
A
G
0.47
.
0.53
NA
NA
LOC442233
TBX18
5.23E−05
0.57
2.18E−03
0.47


rs1904982
1
105061407
T
C
.
0.50
.
NA
NA
LOC642337
LOC100130867
5.24E−05
−0.75
3.54E−05
−0.80


rs12706181
7
117789716
A
G
0.34
.
.
NA
NA
ANKRD7
LOC648442
5.28E−05
0.88
1.09E−03
0.95


rs1345697
5
147922431
G
A
0.48
0.49
0.51
HTR4
intron
FBXO38
ADRB2
5.49E−05
−0.46
6.06E−04
−0.41


rs11255686
10
8496013
C
A
.
0.46
.
NA
NA
LOC389935
KRT8P16
5.56E−05
0.80
5.51E−05
0.81


rs1814343
11
129070462
A
G
0.23
0.23
0.26
NA
NA
BARX2
LOC729717
5.86E−05
0.50
1.32E−03
0.42


rs7724465
5
4723864
A
G
.
0.06
.
NA
NA
IRX1
LOC340094
5.92E−05
1.11
4.19E−05
1.15


rs13258175
8
13873685
A
G
.
0.45
.
NA
NA
C8orf48
SGCZ
5.97E−05
0.72
3.14E−05
0.77


rs7821773
8
9748866
G
A
0.08
0.05
0.08
NA
NA
TNKS
MSRA
5.98E−05
0.71
1.75E−05
0.80


rs1564470
8
136290117
A
C
0.30
.
0.32
NA
NA
ZFAT
LOC286094
6.02E−05
0.62
5.09E−06
0.75


rs6763279
3
74195448
G
A
0.25
0.29
0.27
NA
NA
LOC100129282
HSP90AB5P
6.28E−05
0.46
5.01E−03
0.34


rs2243628
10
7553828
A
G
0.37
.
0.34
NA
NA
LOC728777
ITIH5
6.39E−05
0.53
1.87E−03
0.46


rs10792038
11
56079983
G
A
0.34
.
0.38
NA
NA
OR5M11
OR5M10
6.59E−05
0.61
1.81E−05
0.72


rs13024296
2
224298740
A
G
0.17
.
0.20
NA
NA
LOC646696
AP1S3
6.83E−05
−0.97
4.35E−03
−0.71


rs7968026
12
83754187
A
G
0.31
.
0.30
NA
NA
LOC100128335
SLC6A15
6.89E−05
0.57
3.63E−05
0.64


rs41958
7
117760681
A
G
0.35
.
.
NA
NA
ANKRD7
LOC648442
7.07E−05
0.87
1.26E−03
0.94


rs2543540
17
7572396
A
G
.
0.40
.
DNAH2
intron
EFNB3
RPL29P2
7.09E−05
−0.77
7.26E−05
−0.77


rs17615862
14
43931394
T
C
.
0.25
.
NA
NA
YWHAZP1
LOC729165
7.21E−05
0.86
7.33E−05
0.86


rs693996
11
56046568
A
G
0.34
.
0.38
NA
NA
OR5M6P
OR5M5P
7.58E−05
0.60
2.16E−05
0.71


rs1123110
2
190152444
C
T
.
0.34
.
SLC40A1
intron
WDR75
ASNSD1
7.70E−05
0.72
7.56E−05
0.72


rs7754913
6
132423548
C
A
0.11
0.13
0.13
LOC100131774
intron
CTGF
MOXD1
8.10E−05
0.58
1.07E−04
0.60


rs9863361
3
177769362
G
A
.
.
0.03
NA
NA
LOC730168
TBL1XR1
8.36E−05
1.63
9.80E−05
1.62


rs2940774
4
22958441
A
G
0.17
.
0.25
LOC643751
intron
GBA3
PPARGC1A
8.60E−05
0.62
9.16E−04
0.58


rs1219769
1
108340149
A
G
0.32
.
0.32
NA
NA
VAV3
SLC25A24
8.65E−05
0.62
6.64E−03
0.47


rs2977983
8
71233342
A
G
0.06
.
.
NCOA2
intron
H2AFZP2
BTF3L2
8.76E−05
1.31
2.62E−03
1.36


rs4831257
8
13878742
A
G
.
0.40
.
NA
NA
C8orf48
SGCZ
8.93E−05
−0.72
6.57E−05
−0.74


rs8049793
16
7401978
C
A
0.19
0.17
0.17
A2BP1
intron
LOC100131413
LOC100131080
9.07E−05
−0.68
6.74E−04
−0.62


rs7725683
5
68255470
G
A
.
0.23
.
NA
NA
PIK3R1
LOC100130639
9.11E−05
0.82
9.54E−05
0.82


rs2206593
1
184909052
A
G
0.08
.
.
PTGS2
utr-3
LOC100131939
PLA2G4A
9.14E−05
1.30
3.03E−04
1.49


rs7038808
9
91931116
A
G
0.13
.
0.15
NA
NA
IL6RL1
OR7E31P
9.17E−05
0.68
4.55E−06
0.85


rs8098087
18
67662582
A
G
0.23
0.28
0.22
NA
NA
LOC100132647
CBLN2
9.23E−05
0.47
1.62E−04
0.49


rs17252114
3
41187757
A
G
0.45
0.50
0.52
NA
NA
RPS27P4
MRPS31P1
9.33E−05
−0.43
6.44E−04
−0.40


rs9805752
13
113894531
A
G
.
.
0.16
RASA3
intron
FAM70B
CDC16
9.44E−05
0.86
4.96E−05
0.90


rs12272563
11
32465808
A
G
.
0.20
.
NA
NA
WIT1
EIF3M
9.46E−05
0.85
8.00E−05
0.86


rs222151
21
26692482
A
G
0.25
0.23
0.22
NA
NA
APP
CYYR1
9.49E−05
−0.57
9.10E−06
−0.73


rs873930
10
7569980
G
A
0.46
0.47
0.43
NA
NA
LOC728777
ITIH5
9.58E−05
0.40
4.49E−04
0.39


rs10502634
18
30570172
G
A
0.11
0.09
0.10
DTNA
intron
LOC646842
MAPRE2
9.58E−05
0.67
1.56E−03
0.57


rs1349498
2
173300852
A
G
0.17
0.22
0.19
NA
NA
LOC100129169
RAPGEF4
9.73E−05
0.50
1.51E−03
0.45


rs2704783
2
146216429
C
T
.
0.28
.
NA
NA
LOC730124
LOC727713
9.84E−05
0.87
1.00E−04
0.87









Fifty-seven out of the 100 variants had the same direction of effect in at least two out of the three trials (cutoff p<1×10−4). The top ten most statistically significant variants of that list in shown in Table 5. rs11662763 (G>A, MAF 0.11-0.14) was the most statistically significant (p=9.19×10−7, (3=0.67), with the A allele increasing the risk of composite toxicity (FIG. 3). rs11662763 is 33 kb 3′ from TTMA (FIG. 4A).


For the SNP-based analysis of grade the Manhattan and Q-Q plots are shown in FIG. 5. 88 variants were identified as associated with composite toxicity (Table 13). Fifty-three out of 88 variants had the same direction of effect (either reduced or increased risk) in at least three out of the four studies (cutoff p<1×10−4). The top ten most statistically significant variants of that list are shown in Table 7. rs10867852 (G>A, MAF 0.06-0.08) was the most statistically significant (p=1.46×10−6, β=1.16), with the A allele increasing the risk of composite toxicity. rs10867852 is an intergenic variant located 430 kb 3′ from RASEF (FIG. 6). rs7717673 (G>A, MAF 0.11-0.12) was the next most statistically significant (p=3.93×10−6, β=0.94) with the A allele increasing the risk of composite toxicity. rs7717673 is located in the intron of SLC25A48 (FIG. 6).









TABLE 13







SNPs associated with composite toxicity (grade ≥3)
























refer-














Effect
ence
MAF
MAF
MAF


Flanking
Flanking

effect


SNP
CH
BP
allele
allele
80303
40503
90401
gene
feature
gene
gene
p-value
(β)























rs6807110
3
120338347
C
A
.
.
0.06
IGSF11
intron
LOC728873
C3orf30
1.29E−06
1.61


rs10867852
9
84353502
A
G
0.08
0.07
0.06
NA
NA
LOC442427
RASEF
1.46E−06
1.16


rs1022306
11
83629022
A
C
.
0.13
.
DLG2
intron
LOC-
LOC-
2.11E−06
1.32












100130985
100130066




rs6954042
7
109951683
G
A
.
0.06
.
NA
NA
LOC646620
IMMP2L
2.45E−06
1.76


rs7717673
5
135239365
A
G
0.11
0.12
0.12
SLC25A48
intron
LOC153328
IL9
3.93E−06
0.94


rs2478835
10
30357955
T
C
.
0.40
.
KIAA1462
synony-
SVIL
LOC729663
8.85E−06
1.22











mous






rs4842232
9
137279808
A
G
.
0.10
.
NA
NA
LOC401557
C9orf62
9.83E−06
1.55


rs4320922
11
104627661
A
G
.
0.49
.
NA
NA
OR2AL1P
GRIA4
1.27E−05
−1.24


rs6033941
20
14243645
C
A
.
0.29
.
MACROD2
intron
SCYE1P
FLRT3
1.40E−05
1.05


rs2454331
8
89957664
G
A
0.43
0.40
0.43
NA
NA
LOC-
RIPK2
1.43E−05
−0.77












100129100





rs873224
8
142600146
G
A
0.11
0.10
0.08
NA
NA
FLJ43860
LOC-
1.48E−05
0.86













100131146




rs10873360
14
25663831
T
G
.
0.11
.
NA
NA
LOC401767
NOVA1
1.49E−05
1.38


rs966439
14
86235074
G
A
0.21
0.17
0.16
NA
NA
LOC283584
LOC283585
1.52E−05
0.70


rs7849777
9
136812622
A
G
0.09
0.05
0.06
COL5A1
intron
RXRA
LOC-
1.56E−05
1.31













100130622




rs10869538
9
70729551
G
A
0.15
0.16
0.15
PIP5K1B
intron
LOC-
PRKACG
1.74E−05
0.74












100131240





rs11664759
18
69223208
A
G
0.11
0.15
0.15
NA
NA
LOC400655
FBXO15
2.21E−05
0.83


rs1978259
14
86265207
A
C
0.20
.
0.16
NA
NA
LOC283584
LOC283585
2.63E−05
0.81


rs7174784
15
99119567
G
A
.
.
0.41
NA
NA
ASB7
LOC440313
2.74E−05
1.25


rs17096208
14
73625022
A
G
0.08
.
0.07
LIN52
intron
ALDH6A1
VSX2
2.87E−05
1.05


rs4646864
14
73596456
A
G
0.08
.
0.07
ALDH6A1
near-
ENTPD5
ALDH6A1
2.87E−05
1.05











gene-3






rs17109031
12
52884634
A
G
0.13
0.08
0.10
NA
NA
SMUG1
LOC-
2.93E−05
0.85













100132010




rs4696433
4
154307393
A
G
0.12
0.10
0.12
NA
NA
FHDC1
TRIM2
3.01E−05
0.90


rs6739406
2
35467180
A
G
0.11
0.13
0.09
NA
NA
LOC-
MRPL50P1
3.11E−05
0.84












100130842





rs10988111
9
130559781
G
A
0.45
.
0.46
ZER1
intron
ZDHHC12
TBC1D13
3.21E−05
−0.97


rs491451
6
12836804
A
G
0.16
0.11
0.14
PHACTR1
intron
RPL15P3
LOC-
3.45E−05
0.80













100130357




rs16930838
8
65151961
C
T
.
0.11
.
NA
NA
IFITM8P
LOC-
3.50E−05
1.31













100130155




rs2505083
10
30375128
C
T
.
0.40
.
KIAA1462
intron
SVIL
LOC729663
3.55E−05
1.11


rs10129969
14
77017051
G
A
.
0.06
.
THSD3
intron
AHSA1
SPTLC2
3.73E−05
1.54


rs1452243
12
83695187
A
C
0.38
0.34
0.39
NA
NA
LOC-
SLC6A15
3.73E−05
0.68












100128335





rs11254929
10
7072177
G
A
0.16
.
0.17
NA
NA
LOC439949
SFMBT2
3.91E−05
0.94


rs710392
5
87060900
T
C
.
0.17
.
NA
NA
CCNH
TMEM161B
4.02E−05
1.20


rs1932065
1
70857226
G
A
.
0.23
.
NA
NA
LOC391048
PTGER3
4.03E−05
1.02


rs12157031
0
NA
T
C
.
0.08
.
NA
NA
RPS6KA3
CNKSR2
4.33E−05
1.52


rs7080002
10
109119252
G
A
.
0.06
.
NA
NA
SORCS1
LOC-
4.38E−05
1.64













100128304




rs3739998
4
118873138
G
C
.
0.40
.
NA
NA
NT5C3P1
NDST3
4.38E−05
1.06


rs17867545
14
61622536
T
C
.
0.10
.
SYT16
intron
MOCS3P
LOC-
4.57E−05
1.43













100128793




rs2154110
6
2465335
G
T
.
0.25
.
NA
NA
LOC-
C6orf195
4.68E−05
1.17












100128372





rs7764946
6
6613180
T
C
.
0.07
.
NA
NA
LY86
RP11-
5.05E−05
1.55













320C15.1




rs9405313
8
33984189
A
C
0.11
0.13
0.12
NA
NA
CYCSP3
LOC137107
5.07E−05
0.80


rs4493901
6
22511446
T
C
.
0.11
.
NA
NA
PRL
HDGFL1
5.10E−05
1.18


rs2655439
6
14056368
A
G
0.15
0.14
0.13
RNF182
intron
CCDC90A
MRPL35P1
5.42E−05
0.75


rs1192057
14
88559840
A
G
.
0.10
.
NA
NA
TTC8
LOC390501
5.55E−05
1.34


rs11628605
4
56789252
A
G
.
0.32
.
KIAA1211
intron
CEP135
MRPL22P1
5.56E−05
1.11


rs17751450
9
25541627
A
G
0.36
.
0.38
NA
NA
C9orf134
TUSC1
5.66E−05
0.75


rs7028018
20
40742146
G
A
0.29
0.38
.
PTPRT
intron
LOC643172
PPIAL
5.76E−05
0.73


rs2206428
12
72205105
A
G
0.25
.
0.30
NA
NA
TRHDE
LOC-
5.90E−05
0.81













100128674




rs12368298
10
76203313
G
A
0.19
.
.
NA
NA
LOC645646
MYST4
6.03E−05
1.31


rs7075347
7
36284221
A
G
0.07
.
0.08
EEPD1
intron
LOC-
KIAA0895
6.06E−05
1.01












100131181





rs196584
9
117317136
A
G
0.07
0.13
0.09
NA
NA
43800
C9orf27
6.13E−05
0.76


rs9408872
20
14192971
A
C
.
0.22
.
MACROD2
intron
SCYE1P
FLRT3
6.39E−05
1.06


rs1998238
11
104663936
A
G
.
0.29
.
NA
NA
OR2AL1P
GRIA4
6.42E−05
0.99


rs10895805
5
39716478
A
G
.
0.41
.
NA
NA
LOC-
LOC285634
6.42E−05
−1.28












100129040





rs10473145
1
25124011
T
G
.
0.15
.
RUNX3
intron
CLIC4
LOC391020
6.68E−05
1.07


rs742230
9
70717983
C
T
.
0.43
.
PIP5K1B
intron
LOC-
PRKACG
6.69E−05
−1.20












100131240





rs1414954
1
156145769
A
G
0.13
.
0.11
NA
NA
LOC649203
hCG_1994895
6.72E−05
0.85


rs4450009
12
74414178
G
A
0.16
0.13
0.13
NA
NA
LOC-
LOC-
6.72E−05
0.72












100130336
100131830




rs4831949
13
80958452
G
A
.
0.08
.
NA
NA
LOC-
PTMAP5
6.80E−05
1.48












100129023





rs9545728
20
40760195
A
G
0.19
.
.
PTPRT
intron
LOC643172
PPIAL
6.85E−05
1.38


rs6072833
9
116819754
A
G
0.25
.
0.30
NA
NA
TNFSF8
TNC
6.87E−05
0.80


rs1107373
5
92355984
A
G
0.06
0.08
0.09
NA
NA
CCT7P2
LOC391811
7.14E−05
0.83


rs12054859
10
30346810
G
A
0.07
.
.
KIAA1462
utr-3
SVIL
LOC729663
7.28E−05
1.87


rs2478839
13
66879378
T
C
.
0.42
.
NA
NA
LOC400141
LOC390411
7.37E−05
1.03


rs13378216
6
143400706
G
T
.
0.06
.
NA
NA
HIVEP2
AIG1
7.41E−05
1.39


rs12664681
18
55864775
C
A
0.06
0.06
0.08
NA
NA
LOC728115
LOC400652
7.65E−05
0.93


rs17066548
13
95897355
A
C
0.05
.
0.05
HS6ST3
intron
UGCGL2
HSP90AB6P
7.74E−05
1.34


rs732121
20
40763167
G
A
0.06
.
0.07
PTPRT
intron
LOC643172
PPIAL
7.93E−05
1.12


rs3092743
1
29428986
A
G
0.17
.
0.20
MECR
intron
SFRS4
PTPRU
8.19E−05
0.79


rs2819606
2
174388565
T
C
.
0.10
.
NA
NA
LOC-
LOC644056
8.19E−05
1.37












100129456





rs16862115
5
168644898
A
G
0.20
0.21
0.24
SLIT3
intron
LOC728095
CCDC99
8.61E−05
0.60


rs750585
6
134606559
G
A
.
0.13
.
NA
NA
SGK1
LOC442261
8.66E−05
1.06


rs9493871
16
78430806
A
C
0.09
0.07
0.08
NA
NA
LOC440389
LOC729847
8.66E−05
0.96


rs11644568
6
1773164
A
C
0.06
.
0.05
GMDS
intron
FLJ46552
LOC-
8.83E−05
1.18













100128372




rs9328072
2
50099333
G
A
0.28
0.26
0.31
NRXN1
intron
LOC130728
LOC730100
9.04E−05
0.63


rs7568888
4
109997382
A
G
.
.
0.15
COL25A1
intron
LOC-
ZCCHC23
9.10E−05
1.17












100129714





rs1377208
8
58380598
C
A
0.18
.
.
NA
NA
C8orf71
LOC-
9.11E−05
1.19













100130588




rs1878628
11
104715682
G
A
.
.
0.07
NA
NA
OR2AL1P
GRIA4
9.11E−05
1.35


rs4603276
11
104778916
G
A
.
0.41
.
NA
NA
OR2AL1P
GRIA4
9.13E−05
−1.22


rs7930393
8
24652844
C
T
.
0.41
.
NA
NA
ADAM7
NEFM
9.13E−05
−1.22


rs10091523
9
116740531
G
A
0.34
.
0.36
NA
NA
TNFSF8
TNC
9.31E−05
0.82


rs4979476
13
35359822
G
A
0.09
0.09
0.08
DCLK1
intron
NBEA
SOHLH2
9.33E−05
0.73


rs1171065
9
92388224
C
A
0.19
0.26
0.19
NA
NA
LOC340515
DIRAS2
9.34E−05
0.63


rs16906689
5
37808537
A
G
.
0.09
.
NA
NA
WDR70
GDNF
9.45E−05
1.43


rs10472291
7
3583940
A
C
.
0.37
.
SDK1
intron
LOC-
LOC730351
9.53E−05
1.04












100129603





rs9654994
17
67535422
G
A
0.14
0.15
0.15
NA
NA
hCG_1644301
FLJ37644
9.64E−05
0.76


rs12451606
1
61132767
G
A
.
.
0.03
NA
NA
C1orf87
NFIA
9.67E−05
1.83


rs1002005
8
24655238
G
A
0.06
0.08
0.07
NA
NA
ADAM7
NEFM
9.75E−05
0.83


rs4543550
10
93349774
G
A
0.34
.
0.36
NA
NA
HECTD2
PPP1R3C
9.92E−05
0.82


rs7903829
3
2307104
A
C
0.06
0.07
0.07
CNTN4
intron
LOC727810
LOC-
9.97E−05
0.90













100130346









For the gene-based analysis of grade≥2, the Q-Q plot is shown in FIG. 7. Table 9 shows the ten most statistically significant genes. SLC25A24 was the most significant (p=4.00×10−6).


Discussion

It is believed that this is the largest GWAS of bevacizumab-induced proteinuria and hypertension. The present study included 1,041 cancer patients, with different tumor types, from four randomized phase III clinical trials conducted at the Alliance. The relatively large sample size, the randomized design, and the standardized collection of the phenotypic and genotypic data are positive features that increase the value of these findings. The analysis of genetic associations that were consistent across different studies led to the identification of novel SNPs and genes associated with these toxicities.


This study has selected DNAH5, TRIO, RIPK4 and IL17F as genes involved bevacizumab-induced proteinuria. DNAH5 and TRIO are the closest genes from rs339947, the most statistically significant SNP associated with proteinuria (p=7.66×10−8). DNAH5 encodes a dynein protein (part of a microtubule-associated motor protein complex) that is important for the normal function of ciliated cells in many tissues, including kidney tubule. Mutations in DNAH5 cause a genetic disorder associated with polycystic kidney diseases. TRIO encodes a GDP to GTP exchange factor promoting the reorganization of the actin cytoskeleton, thereby playing a role in cell migration and growth. TRIO is highly expressed in podocytes and regulates the attachment of podocytes to glomerular basement membrane. TRIO also induces Rac 1 activity, which contributes to podocyte injury and proteinuria. DNAH5, or TRIO, or both could be involved in the mechanism of bevacizumab-induced proteinuria. Interestingly, our functional bioinformatic analysis that rs429023, in moderate LD with rs339947, is an eQTL increasing TRIO expression in the glomerulus (Table 14), potentially pointing towards TRIO as the putative gene of proteinuria.









TABLE 14







Bioinformatic analysis of rs13135230, rs2350620, and rs6770663 associated with hypertension, rs339947, rs12482855 and rs408130


associated with proteinuria, rs11662763 associated with composite toxicity, and SNPs in complete LD (R2 = 1.0) according to LDlink.















Data from Genome Browser, Regulome DB and/or HaploReg v4


















Regulome

Transcription
DNaseI







DB

factor
sensitivity
Chromatin
Histone


SNPs
eQTL
Region
Score
ChIP-seq
binding motifs
region
state
markers










Hypertension















rs13135230

 3.8 kb 3′
No data









from LGI2








rs2350620


4
FOXA1






rs35026059


2c
CTCF
CTCF





rs28695823

ASPH
5
SMARCC1

Yes
Enhancers
H3K4me1,




intron 14



(fetal heart)
(HUVEC,
H3K4me3,









aorta and
H3K27ac,









fetal heart)
H3K9ac










(HUVEC










and heart










tissue group)


rs6770663

KCNAB1
6




H3K4me1




intron 1





(HUVEC










and aorta)







Proteinuria















rs339947

 73 kb 5′
4
USF1


Repressed





from DNAH5




polycomb





130 kb 5′




(HUVEC)





from TRIO








rs408130


No data







rs418173

 60 kb 5′
5









from DNAH5








rs429023
TRIO in glomerulus
140 kb 5′
5
EBF1







(NES = 2.1, p = 0.039)
from TRIO








rs12482855

 4.7 kb
No data




H3K4me1




from RIPK4 5′





(fetal










kidney)







Composite toxicity















rs11662763
EPB41L3 in glomerulus
 33 kb 3′
No data








(NES = 22.8, p = 0.0055)
from TTMA









For Table 14, SNPs in bold are the selected SNPs from our study and the SNPs not in bold are SNPs in LD with them. Expression quantitative trait loci (eQTL) information was retrieved from the GTEx v7 and NephQTL. The RegulomeDB score represents the evidence that a variant has a regulatory function (1-strong evidence, 6-weak evidence). Data from Genome Browser, RegulomeDB and/or HaploReg v4 includes computational and experimental data from ENCODE and Roadmap Epigenomics Consortium. Only ChIP-seq and transcription binding motifs from experimental data are reported. Only DNaseI sensitivity region, chromatin state and histone markers for relevant cell lines (HUVEC or heart tissue group) are reported. Composite toxicity is defined as the occurrence of either proteinuria or hypertension or both. NES: normalized effect size.


In addition to TRIO, RIPK4 is also another putative new gene for proteinuria. RIPK4 (selected by rs12482855, 4.7 kb 5′) encodes a protein kinase that interacts with PKCδ, which is directly involved in renal damage by inducing apoptosis in podocytes and also in tubular cells. Finally, IL17F codes for interleukin-17F (IL-17F) and was selected by the gene based analysis. Using induced-nephrotoxic nephritis mouse model, IL-17F-deficient mice showed less severe nephritis, with lower albuminuria and better renal function, compared with wild-type mice. IL17F was the second most significant gene in our gene-based analysis after C1D, the biology of which cannot be reconciled with kidney damage by bevacizumab. Two less common variants (rs1413920 and rs763780, that did not pass the QC MAF<0.05 in SNP-based analysis) are driven the effect of IL17F in gene-based analysis. The G allele of rs1413920 (A>G, p=1.80×10-7, (ß=2.24, MAF 0.01-0.03) and of rs763780 (A>G, p=1.14×10-4, (ß=1.41, MAF 0.05) decreased the risk of proteinuria. rs1413920 is intergenic located 1.3 kb 3′ from MCM3 and 20 kb from IL17F (FIG. 8), with strong transcription in HUVEC. rs763780 is a non-synonymous variant that alters the histidine to arginine at amino acid 161 (H161R). The A allele (161H) has been associated with an anti-angiogenic effect by inhibition the angiogenesis in human endothelial cells. Inversely, patients who present the G allele (161R) could have an enhanced angiogenesis in these cells and be more prone to bevacizumab effect. The G allele was already associated with a better overall survival in CALGB 80303.


This study also proposes ASPH (selected by rs2350620, intronic, and by the gene-based 30 analysis) as novel candidate of bevacizumab-induced hypertension. ASPH encodes the junction protein that forms a quaternary complex with triadin, calsequestrin and the ryanodine receptor (RyR), involved in the release of Ca2+ from endoplasmic/sarcoplasmic reticulum. rs2350620 reduced the risk of bevacizumab-induced hypertension and has variants in complete LD that are located in regions of DNaseI sensitivity, chromatin state enhancers and enriched for histone modifications in HUVEC and cells from heart tissue group. The G allele of rs2350620 is likely to bind FOXA1 protein (in T-47D), which acts as a transcriptional activator. Therefore, rs2350620 might increase ASPH expression, which might contribute to confer a reduced risk of hypertension. Moreover, one of the variants in LD (rs35026059, →T) has 2c Regulome DB score (Table 14), due to strong evidence of binding of the T allele to CTCF motif, but not in relevant cell lines. CTCF can acts as a transcriptional activator or repressor and insulator.


Because genetic variants might have pleiotropic effects and hypertension and proteinuria share a common pathophysiology, we have also investigated the occurrence of the composite toxicity. rs11662763 had the same direction of effect in three trials, increasing the risk of either proteinuria or hypertension or both. rs1166276 is 33 kb from TTMA, also known as TMEM200C. rs11662763 was shown to be an eQTL for EPB41L3 in the glomerulus, increasing its expression (Table 14). EPB41L3 was also identified as a novel locus for kidney function, after an intronic SNP (rs9962915) was associated with lower glomerular filtration rate in a GWAS meta-analysis of more than 100,000 subjects. Furthermore, SLC25A24 was also selected by the gene-based analysis of the composite toxicity. SLC25A24 encodes a carrier protein that transports ATP-Mg exchanging it for phosphate.


The three most significant variants associated with composite toxicity (rs17084411, rs1927869 and rs17084371) had a p-value of 4.24-7.24×10−8 but only in CALGB 40503.


In conclusion, as a result of this study, DNAH5, TRIO, RIPK4, IL17F, ASPH, TTMA, EPB41L3 and SLC25A24, as well as all the top significant SNPs and genes associated with grade≥3 toxicities are proposed as new genes involved in bevacizumab-induced proteinuria and hypertension. Despite many years of use of bevacizumab, proteinuria and hypertension still represent an obstacle to full delivery of effective therapy, and pose a threat for patients and their quality of life. Because these toxicities are also shared by many other anti-angiogenesis drugs, the availability of these results in the public domain will incentivize the application of these findings to other drugs with a similar mechanism of action.


Example 2

Sorafenib is an orally administered multikinase inhibitor that targets multiple tyrosine kinases involved in angiogenesis, apoptosis, and tumor cell proliferation, including the vascular endothelial growth factor receptor 2 (VEGFR2). It is approved by the U.S. Food and Drug Administration (FDA) for the treatment of several tumors, including metastatic renal cell carcinoma (mRCC), advanced hepatocellular carcinoma and differentiated thyroid cancer. The clear-cell histology of RCC is characterized by overexpression of VEGF, which interacts with VEGFR2 to stimulate tumor angiogenesis. In addition to sorafenib, sunitinib, pazopanib, axitinib, lenvatinib and cabozantinib are also approved for mRCC, sharing the same mechanisms of VEGF-pathway inhibition.


Hypertension is one of the most frequent toxicities induced by sorafenib. A meta-analysis showed a prevalence of sorafenib-induced all-grade and grade≥3 hypertension of 19.1% and 4.3%, respectively. Patients with mRCC experience higher rates of hypertension when compared to other tumor types (all-grade: 24.9% vs 15.7%, high-grade: 8.6% versus 1.8%). Similar to sorafenib, other VEGF-pathway inhibitors can also induce hypertension, including bevacizumab, sunitinib and pazopanib.


The objective of this study was to identify and validate genetic biomarkers that are predictive of VEGF-pathway inhibitor-induced hypertension using a two-step, discovery-validation approach. Sorafenib-treated patients from the phase 3 Treatment Approaches in Renal Cancer Global Evaluation Trial (TARGET) were used as the discovery set, while a genome-wide association study (GWAS) of bevacizumab-treated patients from four Cancer and Leukemia Group B (CALGB, now Alliance for Clinical Trials in Oncology, Alliance) studies was used as a validation set.


TARGET was a double-blind, randomized, placebo-controlled phase III trial of patients with mRCC treated with 400 mg sorafenib orally twice daily or placebo. Hypertension was recorded according to CTCAE version 3.0. This analysis was conducted in patients who received at least one cycle (28 days) of sorafenib treatment. DNA was obtained from the peripheral blood of 140 patients treated with sorafenib. A total of 1,536 SNPs in 56 candidate genes were genotyped using the Illumina GoldenGate assay. Genes were selected based upon biological function, including genes involved in VEGF-pathway signaling, genes from additional signaling pathways targeted by sorafenib, genes associated with perycite survival, sorafenib disposition and toxicity, and genes associated with RCC prognosis/pathogenesis or general cancer prognosis. SNPs were excluded if the genotype call rate was <97.5% and were selected based upon a MAF>0.05 in Europeans from the 1,000 Genomes Project, and other criteria.


A flowchart showing the quality control for the study is provided as FIG. 9A. After quality control, a total of 973 of the 1,536 initial SNPs were used in this study. Tests for association between SNPs and grade≥2 hypertension were performed in the sorafenib arm by calculating the odds ratio (OR) from a logistic regression analysis, where grade≥2 hypertension was the binary outcome and SNPs were the independent variables, under an additive model. Age and gender were used as covariates. A p-value≤0.01 was used as a feature selection to identify SNPs for replication in the validation set.


For the validation cohort, the association between SNPs and hypertension was tested in genetic European patients treated with bevacizumab. A GWAS of four randomized phase III clinical trials from the CALGB/Alliance (CALGB 80303, 40503, 90401, and 40502) was used as the validation set. The details of the individual studies are described in Table 15. Patient eligibility, characteristics, stratifications and treatments can be found in the individual publications for all four trials. Blood pressure was measured on day 1 of each cycle in all four trials (and on day 15 in CALGB 80303), and hypertension was recorded according to CTCAE version 3.0. Bevacizumab-induced hypertension was defined as the occurrence of grade≥2 hypertension after the start of treatment. DNA was obtained from peripheral blood. The genotyping platforms used in each study are described in Table 15. A cause-specific Cox model, where the outcome was defined as the pair of time event and the censoring indicator (defined as the time from the first administration of bevacizumab to the first incidence of the toxicity of interest, or other treatment-terminating events, whichever occurred first, under a competing risk model), was fitted to obtain the estimate of the SNP effect on hypertension in each individual study. The analyses were powered against an additive genetic model. The inverse variance formula was used to combine the SNP effect in each study to obtain the estimate (β) of the SNP-hypertension association. Age and sex were added as covariates in the model. The exponential function of β was used to calculate OR.


The SNPs from the TARGET study (discovery set) associated with grade≥2 hypertension (p-value≤0.01) were tested in the CALGB GWAS (validation set). If the variant was not genotyped in the validation set, a SNP in high linkage disequilibrium (LD, R2>0.8, Europeans in the 1,000 Genomes Project) according to LDlink, was selected for testing. In the validation set, SNPs with a p-value≤0.01 for association and the same direction of effect (increased or reduced risk) were considered as validated.


Functional annotation of SNPs was performed using the SCAN database. LDlink was used for analyses of LD. RegulomeDB and SNPnexus were used for functional inference. The Genotype-Tissue Expression project (GTEx v7) was used for expression quantitative trait loci (eQTL) analysis. atSNP was also used to quantify impact of SNPs on transcription factor binding.


A total of 140 mRCC patients treated with sorafenib in TARGET were included in this study. The characteristics of the patients, and the prevalence of grade≥2 hypertension are shown in Table 15. Variants rs444904 (G>A, MAF 0.14) and rs1346563 (C>T, MAF 0.30) were both selected for testing in the validation set based on p<0.01 (Table 16). Both variants were associated with an increased risk of grade≥2 hypertension (OR=3.88, 95%, CI 1.54-9.81, p=0.0057 and OR=3.50, 95%, CI 1.48-8.24, p=0.0064, respectively) (Table 16).









TABLE 15







Patient characteristics and trials.










Discovery set
Validation set (n = 1,041)













(n = 140)
CALGB 80303
CALGB 40503
CALGB 90401
CALGB 40502


Trial
TARGET
n = 154
n = 105
n = 316
n = 466















Hypertension (n, %)







Grade ≥2
12 (8.6)
26 (16.9)
53 (50.5)
47 (15.0)
143 (30.7)


Grade 3
5 (3.6)
19 (12.3)
29 (27.6)
22 (7.0)
50 (10.7)


Age-Mean (SD)
59.6 (9.8)
64.1 (10.2)
68.4 (8.3)
56.9 (11.7)
57.2 (10.7)













Gender
Male
105
90
0
105
0



Female
35
64
316
0
466












Cancer type
Advanced and
Advanced
Hormone
Metastatic
Recurrent or



metastatic renal
pancreatic cancer
receptor-positive
castration-resistant
metastatic breast



cell carcinoma

advanced-stage
prostate cancer
cancer





breast cancer




Treatment
Sorafenib 400 mg
Gemcitabine 1,000
Letrozole 2.5 mg
Docetaxel 75 mg/m2
Paclitaxel 90 mg/m2



orally twice daily
mg/m2 on days 1,
orally/day plus
in combination with
or nab-paclitaxel



administered in 6-
8, and 15 plus
either placebo or
prednisone 5 mg
150 mg/m2 or



week cycles for
either placebo or
bevacizumab 15
orally on day 1 plus
ixabepilone 16



the first 24 weeks
bevacizumab 10
mg/kg every 21
either placebo or
mg/m2 on days 1, 8,



and in 8-week
mg/kg on days 1
days
bevacizumab 15
and 15 plus



cycles thereafter
and 15

mg/kg every 21 days
bevacizumab 10







mg/kg on days 1 and 15


Genotyping
Illumina
Illumina
Illumina Human
Illumina
Illumina Human


platform
GoldenGate
HumanHap550-
OmniExpressExome-8
HumanHap610-
OmniExpressExome-8




Quad

Quad
















TABLE 16







SNPs associated with sorafenib-induced hypertension in the TARGET study.


The SNPs in bold are the ones tested in the validation (p ≤ 0.01). Results are shown for


associations with p-value < 0.05, adjusted for age and gender. Chr: chromosome, NA:


Intergenic SNP, MAF: minor allele frequency, OR: odds ratio, SNP: single nucleotide


polymorphism.





















3′ Flanking
Base


p-


SNP
Chr
Gene
Feature
5′ Flanking gene
gene
change
MAF
OR (95% CI)
value



















rs444904
17
PIK3R5
Intron
PIK3R6
LOC100129978
G > A
0.14
3.88 (1.54-9.81)
0.0057


rs1346563
16
ADAMTS18
Intron
VN2R10P
NUDT7
C > T
0.30
3.50 (1.48-8.24)
0.0064


rs2330951
7
EGFR
Intron
LOC643168
LOC100133256
A > C
0.23
4.23 (1.78-10.05)
0.0118


rs11125039
2
PRKCE
Intron
SRBD1
EPAS1
A > G
0.24
3.51 (1.49-8.25)
0.0122


rs56367980
7
EGFR
Intron
LOC643168
LOC100133256
G > A
0.12
3.33 (1.27-8.76)
0.0188


rs16917099
10
NA
NA
RTKN2
ZNF365
T > C
0.13
3.58 (1.37-9.35)
0.0207


rs2740761
7
EGFR
Intron
LOC643168
LOC100130121
C > T
0.18
3.46 (1.39-8.59)
0.0222


rs3754565
2
PRKCE
Intron
SRBD1
EPAS1
G > T
0.11
4.07 (1.48-11.19)
0.0222


rs3754566
2
PRKCE
Intron
SRBD1
EPAS1
G > A
0.11
4.07 (1.48-11.19)
0.0222


rs4596024
2
PRKCE
Intron
SRBD1
EPAS1
A > G
0.11
4.07 (1.48-11.19)
0.0222


rs251312
5
NA
NA
NLN
ERBB2IP
C > T
0.48
3.26 (1.31-8.14)
0.0223


rs12366035
11
VEGFB
reference
DNAJC4
FKBP2
C > T
0.34
3.09 (1.31-7.24)
0.0227


rs35539903
4
KDR
Intron
LOC100132311
LOC100128865
A > G
0.15
3.44 (1.33-8.90)
0.0254


rs35597368
4
PDGFRA
Missense
LOC442108
KIT
T > C
0.10
3.69 (1.32-10.29)
0.0256


rs3797102
5
FLT4
Intron
SCGB3A1
OR2AI1P
T > C
0.42
2.78 (1.17-6.59)
0.0262


rs3804158
4
NUDT6/ FGF2
Intron/ UTR-3
BBS12
SPATA5
A > G
0.43
0.30 (0.11-0.84)
0.0272


rs45492196
1
PIK3C2B
Reference
PPP1R15B
LOC100130573
G > A
0.05
3.68 (1.07-12.60)
0.0279


rs7187665
16
WWOX
Intron
LOC100131126
LOC645947
T > C
0.45
0.34 (0.13-0.89)
0.0298


rs11980616
7
GNAIl
Intron
LOC100128030
GNAT3
A > G
0.13
3.24 (1.24-8.50)
0.0322


rs659441
3
NA
NA
UMPS
ITGB5
G > C
0.40
0.28 (0.11-0.73)
0.0327


rs315498
17
NA
NA
LOC100130112
C17orf79
T > C
0.33
0.24 (0.07-0.84)
0.0335


rs41348645
4
FGF2/ NUDT6
UTR-3/ Intron
BBS12
SPATA5
G > A
0.41
0.31 (0.11-0.87)
0.0350


rs3950680
11
PIK3C2A
Intron
RPS13
LOC732199
G > A
0.36
2.61 (1.12-6.06)
0.0385


rs6743202
2
TGFA
Intron
LOC100128042
ADD2
A > T
0.32
0.27 (0.08-0.93)
0.0421


rs11644322
16
WWOX
Intron
LOC645947
LOC729251
C > T
0.21
2.66 (1.10-6.42)
0.0431


rs446086
2
TGFA
Intron
LOC100128042
ADD2
C > A
0.23
0.19 (0.04-0.84)
0.0431


rs3804452
6
MAPK14
utr-3
SLC26A8
MAPK13
C > T
0.11
2.86 (1.04-7.84)
0.0439


rs2293348
7
EGFR
Intron
LOC100133256
LOC100130121
G > A
0.36
0.32 (0.11-0.96)
0.0466


rs16947173
16
WWOX
Intron
LOC100131126
LOC645947
A > G
0.20
0.12 (0.02-0.93)
0.0480


rs11644207
16
WWOX
Intron
LOC100131126
LOC645947
T > G
0.24
0.22 (0.05-0.64)
0.0484


rs8193040
6
NA
NA
IL17A
LOC730141
T > G
0.48
0.39 (0.16-0.97)
0.0499









A total of 1,041 patients treated with bevacizumab in the CALGB trials were included in this study. Because neither rs444904 nor rs1346563 were genotyped on the GWAS platforms, rs427554 (G>A, MAF 0.10-0.11 in complete LD R2=1.0 with rs444904) and rs4888628 (A>G, MAF 0.26-0.29, LD R2=0.96 with rs1346563) were used as proxies. Variant rs427554 was associated with an increased risk of hypertension (p=0.008, 13=0.33, OR=1.39, CI 1.09-1.78) (FIG. 10). This result is consistent with the discovery set, where the frequencies of patients without hypertension with the AA and GA genotypes are 2.3% and 20.3%, respectively, versus 25.0% and 16.7% in patients with hypertension (FIG. 9B).


Table 17 provides bioinformatic analyses for both rs444904 and rs427554. There is evidence in GTex that rs444904 and rs427554 are both eQTLs for PIK3R5 in whole blood, with the A allele of both variants associated with decreased gene expression. DNase 1 hypersensitivity peaks indicate that both rs444904 and rs427554 are located in areas of open chromatin, thus permitting selective binding of transcription factors, while ChIP-seq revealed that the two SNPs are potential loci for binding with putative transcription factors. RegulomeDB, utilizing data from the ENCODE-motif database, indicates that rs427554 is located in the binding motif for the SP1 transcription factor. Additional data from the JASPAR database (using atSNP) predicts preferential binding of SP1 to the G allele of rs444904 rather than the A allele (p=0.01 for the G allele, and p=0.30 for the A allele). The majority of non-coding variation scores provided by SNPnexus shows a higher evidence of regulatory function of rs427554 compared to rs444904 (Table 17).









TABLE 17







Bioinformatic analysis of rs444904 and rs427554. The RegulomeDB score represents the evidence that a SNP has a regulatory function


(1-strong evidence, 6-weak evidence). SNPnexus non-coding variation scoring predicts functional impact of non-coding SNPs


using 8 non-coding SNP scoring algorithms. Higher scores in CADD (range 0-99), FitCons (range 0-1), Eigen (range 0-1), FATHMM


(range 0-1), GWAVA (3 scores, range 0-1), funSeq2 (range 0-5) ReMM (range 0-1) mean that the SNP is most likely to be


functional/deleterious, while a lower score in DeepSEA (range 0-1) means that the SNP is most likely to


be functional/deleterious. eQTL: expression quantitative trait loci, NES: normalized effect size












RegulomeDB/ ENCODE













SNP


DNase I

SNPnexus non-coding variation rankings



















(Regulome
eQTL

Sensitivity

CA-
Fit-
EIG-
FAT-
GWA-
Deep-
Fun-
Re-


DB score)
(GTEx)
ChIP-seq
region
Motif
DD
Cons
EN
HMM
VA
SEA
Seq2
MM





rs444904
Whole blood
POLR2A, RELA, EP300,
Yes

0.775
0.102
0.176
0.110
0.38/
0.035
1.560
0.019


(4)
(p =
TCF12, EBF1, IKZF2, IKZF1,






0.48/






2.7 × 10−12,
TAF1, MEF2C, TBL1XR1,






0.44






NES = −0.16)
FOXM1, ZNF687, TARDBP,














NFATC1, MTA3, ZEB1,














MTA2, YY1, CBFB, RUNX3,














GATAD2B, CHD2, ELF1,














BCLAF1, ETS1, ARNT,














EGR1, IRF4, PBX3, TCF7,














NFIC, BHLHE40, POU2F2,














CREM, BCL3, MEF2A, ETV6.












rs427554
Whole blood
POLR2A, GATA1, SPI1,
Yes
SP1
2.641
0.102
0.614
0.141
0.45/
0.118
1.560
0.122


(2c)
(p =
IKZF1, IKZF2, ZBTB40,






0.53/






9.4 × 10−13,
TCF7, MLLT1, EP300, ELF1,






0.41






NES = −0.17)
LEF1, PAX5, BCLAF1, DPF2,














TRIM22, RELB, ARNT, MXI1,














FOXM1, NR2F1, SMARCA5,














ZMYM3, SP1, MEF2A,














RBM25, TARDBP, NBN,














TAF1, BHLHE40, BCL3,














RUNX3, KLF5, BATF, ETV6,














NFATC3, ZFHX2, ZBTB33,














ETS1, IRF4, NKRF, VEZF1,














ZBED1, SKIL, ZNF207,














CREM, ETV1, CBFB, HDGF,














TBX21, ARID3A, BCL11A,














POU2F2, EGR1, COMMD3-














BMI1, BMI1, ATF2, REST,














RFX1, MAZ, EBF1, ZNF143,














EED.









The results of the study identified a common intronic SNP (rs444904) located in PIK3R5 that increased the risk of grade≥2 hypertension in patients treated with the VEGF-pathway inhibitors sorafenib and bevacizumab.


Bioinformatic analyses of rs444904 and rs427554 in PIK3R5 showed that both SNPs are located in a region that binds numerous transcription factors, indicating a potential regulatory role for each SNP in gene expression (Table 17). rs427554 is located within a binding motif for SP1, and rs444904 may alter an SP1 binding motif as described above. Considering that both SNPs are in complete LD with each other, it is plausible to suggest that the G allele of both variants may increase binding of the SP1 transcription factor to DNA.


In embodiments, the data provided herein proposes a novel mechanism through which rs444904 and rs427554 regulate the expression of PIK3R5 and mediate hypertension induced by sorafenib, bevacizumab, or other VEGF pathway inhibitors. The G allele of both SNPs allows the binding of SP1, which, by inhibiting the action of DNMT, activates PIK3R5 transcription (FIG. 12). Conversely, the A allele decreases the binding of the SP1, which allows DNA methylation by DNMT, downregulating PIK3R5 transcription, (FIGS. 11 and 12).


The validation of rs444904 in an external dataset utilizing a different VEGF-pathway inhibitor (such as bevacizumab) provides additional evidence of clinical applicability of biomarkers of hypertension induced by different anti-angiogenic drugs. Taken together, the study provides evidence for rs444904 in PIK3R5 as a biomarker of hypertension induced by sorafenib, bevacizumab, and other VEGF pathway inhibitors. Common genetic variants in PIK3R5, rs444904 and rs427554 in complete LD with each other (R2=1.00), increased the risk of sorafenib and bevacizumab-induced hypertension in two independent datasets, and may be used as predictor biomarkers of hypertension induced by the whole class of VEGF-pathway inhibitors


Example 3

Two SNPs associated with grade≥2 hypertension in Example 1 above, rs2350620 and rs6770663, were evaluated for replication in European ancestry patients from ECOG-ACRIN E5103. A summary of the cohort evaluated is provided as Table 18.









TABLE 18







GWAS patients of European ancestry treated with bevacizumab from ECOG-


ACRIN E5103. ECOG Eastern Cooperative Oncology Group, ACRIN American College of


Radiology Imaging Network, SBP systolic blood pressure, SD standard deviation.









Validation set ECOG-5103










SBP ≥ 160 mm Hg
Grade ≥3



n = 582
n = 564












Hypertension* (n, %)
195 (33.5)
177 (37.8)


Age-Mean (SD)
55.3
55.1










Gender
Male
0
0



Female
582
564








Cancer type
Breast cancer


Treatment
Doxorubicin (60 mg/m2) and cyclophosphamide (600 mg/m2) for



four cycles, followed by 12 weeks (4 cycles) of weekly paclitaxel.



Concurrently to chemotherapy, patients received either placebo (arm



A) or bevacizumab 10-15 mg/kg (arms B and C). Patients in arm



C continued bevacizuma monotherapy (15 mg/kg every 3 weeks)



for an additional 10 cycles.


Genotype platform
Illumina Human Omni1-Quad and Illumina Human OmniExpress









Variants rs2350620 and rs6770663 were selected because they were among the top ten SNPs that also had a concordant effect in three out of four studies (p-value<0.05 for each study) (Table 5). FIG. 13 shows the cumulative incidence of grade≥2 hypertension for rs2350620 and rs6770663. Table 19 shows the results of the SNPs tested for replication. The G allele of rs6770663 (A>G, MAF 0.08-0.09) was associated with a higher risk of SBP>160 mm Hg (odds ratio, OR=1.76, p-value=0.005) in ECOG-ACRIN E5103 (Table 20), similar to the increased risk of grade≥2 hypertension in our study (β=0.57, p-value=4.79×10−6) (Table 5).









TABLE 19







Top two SNPs ranked by unadjusted p-value with a concordant effect


in three out of four studies for grade ≥2 hypertension in the CALGB trials tested for replication


in the ECOG-ACRIN E5103 GWAS. ECOG Eastern Cooperative Oncology Group,


ACRIN American College of Radiology Imaging Network, MAF minor allele frequency,


SBP systolic blood pressure, OR odds ratio. The row in bold is the one SNP that replicated


in ECOG-ACRIN E5103.













MAF






ECOG-





Risk
ACRIN
OR
p-value


SNP
allele
E5103
(SBP ≥ 160 mm Hg)
(SBP ≥ 160 mm Hg)





Grade ≥2






rs2350620
T
0.33
1.14
0.235



rs6770663


G


0.10


1.76


0.005

















TABLE 20







Frequency of rs6770663 AA, GA, and GG genotypes associated with


bevacizumab-induced hypertension in ECOG-ACRIN E5103. ECOG Eastern


Cooperative Oncology Group, ACRIN American College of Radiology Imaging Network,


SBP systolic blood pressure.









rs6770663











AA
GA
GG





SBP ≥ 160
147 (75.4%)
45 (23.1%)
3 (1.5%)


(cases, n = 195)





No hypertension
327 (84.5%)
59 (15.2%)
1 (0.3%)


(controls, n = 387)









Table 21 shows published studies that reported associations between 37 SNPs and bevacizumab-induced hypertension with p-value<0.05. Out of 37 SNPs, 26 of them had either the same SNP or a proxy for it. Three out of the 26 SNPs were associated with composite toxicity (but with neither hypertension nor proteinuria) with the same direction of the effect (either reduced or increased risk) in the herein provided study (Table 22).









TABLE 21







SNPs previously associated with bevacizumab-induced hypertension in the


literature. VEGF vascular endothelial growth factor, NO nitric oxide, CTCAE Common


Toxicity Criteria for Adverse Events, FOLFIRI 5-fluorouracil (5-FU) + irinotecan,


FOLFOX 5-FU + oxaliplatin, XELOX capecitabine + oxaliplatin, SBP systolic blood


pressure. Not on platform means that either the reported SNP or SNPs in high LD


(R2 > 0.8) were not on the genotype platforms in our study.


















Number of




SNP



bevacizumab




selection
Genes
Hypertension
Concomitant
treated
Clinical trial


Reference
method
associated
phenotype
treatment
patients
discovery set





Li et al.
Sequencing
HSP90AB1
Grade ≥3
FOLFIRI or
61
Discovery:


(2018)
of
PRKCA
(CTCAE
FOLFOX6

CALGB



174
CACNA1C
v3.0)


80405



candidate
HSP90AB1



Validation:



genes
CCL2



CALGB



(VEGF
PDE3B



40502,



signaling,
NOSIP



CALGB



endothelial
FLT4



90401, and



cell biology,




ECOG-5103



NO








signaling or








essential








hypertension








genes)







Frey et al.
103 SNPs in
GRK4
Grade ≥1
Cisplatin and
114
6 clinical


(2017)
11 genes
KLKB1
(CTCAE
taxotere/

trials at



(VEGF and
VEGF
v3.0)
doxorubicin, and

Memorial



essential
WNK1

cyclophosphamide/

Sloan-



hypertension


paclitaxel and

Kettering



associated


cisplatin/ erlotinib/

Cancer



genes)


letrozole/ S-1 and

Center






oxaliplatin




Berger et al.
12 SNPs in
FIP200
Grade ≥2
FOLFIRI
219
TRIBE


(2017)
8
ATG13
(CTCAE






autophagy-

v3.0)






related








genes







Gampenrieder
10 SNPs in
VEGFA
Grade ≥3
Capecitabine or
163
Retrospective


et al. (2017)
VEGFA,


taxane

selection of



FLT1,




patients from



STK39,




hospital



EDN1, and




records



UMOD







Sibertin-
10 SNPs in
VEGFA
Grade ≥1
5-FU based
89
Retrospective


Blanc et al.
VEGFA,

(CTCAE
chemotherapy (the

selection of


(2015)
FLT1, KDR,

v3.0)
majority FOLFIRI)

patients from



and HIF1A




hospital








records


Lambrechts et
236 SNPs in
EGLN3
Grade ≥1
XELOX or
807
NO16966,


al. (2014)
14 genes
KDR
(CTCAE
FOLFOX4/

AViTA,



(VEGF and
EPAS1
v3.0)
gemcitabine and

AVAiL,



essential
FLT1

erlotinib/ cisplatin

AVOREN,



hypertension
FLT4

and gemcitabine/

AVADO,



associated
EGF

interferon α-2a/

AVAGAST



genes).
WNK1

docetaxel/








capecitabine and








cisplatin




Morita et al.
5 SNPs in
VEGFA
Grade ≥2
FOLFIRI or
60
Retrospective


(2013)
VEGFA

(CTCAE
FOLFOX6 or

selection of





v4.0)
5-FU or

patients from






XELOX

hospital








records


Etienne-
5 SNPs in
VEGFA
Grade ≥1
Paclitaxel or
137
ATHENA


Grimaldi et
VEGFA

(CTCAE
docetaxel or




al. (2011)


v3.0)
navelbine




Schneider et
7 SNPs in
VEGFA
Grade ≥3
Paclitaxel
180
ECOG-2100


al. (2008)
VEGF and

(CTCAE






KDR

v2.0)
















TABLE 22







Previously reported variants associated with bevacizumab-induced


hypertension. The associations with a p-value <0.05 and same direction of effect for grade


≥2 composite toxicity in our study are shown. Proxy rs9900205 was genotyped only in


CALGB 90401, and proxy rs833070 was genotyped only in CALGB 40503.











SNP

Base




(literature)
Region
change
Risk (literature)
Risk (our study)





rs59189065
PRKCA
G > A
Increased grade ≥3
Proxy rs9900205 (R2 = 0.82)



intronic

hypertension in CALGB
Increased grade ≥2 composite





80405
toxicity in CALGB 90401






(β = 0.49, p = 0.02)


rs9381299
3 kb 5′ from
T > C
Increased grade ≥3
Increased grade ≥2 composite



HSP90AB1

hypertension in CALGB
toxicity in CALGB 80303, 40503,



and 10 kb 3′

80405 (discovery set),
and 90401 (β = 0.39, p = 0.02)



from of

and in CALGB 40502




SLC29A1

and ECOG 5103






(validation sets), but not






in CALGB 90401



rs833061
5′ of VEGFA
C ≥ T
Decreased grade ≥2 (7)
Proxy rs833070 (R2 = 0.98)





and grade ≥3 (6)
Decreased grade ≥2 composite





hypertension
toxicity in CALGB 40503






(β = 0.44, p = 0.03)









Taken together, the studies provided herein were the largest genome-wide analysis of bevacizumab-induced hypertension and proteinuria, which included 1,041 cancer patients from four randomized phase III clinical trials. The large sample size, randomized design, and standardized collection of the phenotypic and genotypic data facilitated the testing of genetic associations of drug response in patients. The use of genomic data from different studies allowed the evaluation of concordance of the effect, increasing the validity of these associations. For the first time, a variant in KCNAB1 for bevacizumab-induced hypertension was identified from an independent, external dataset provided and provided evidence of clinical actionability. Accordingly, the results of the study provide a critical identification of SNPs and gene variants that can be used to provide improved and safer methods for treating patients with bevacizumab or other VEGF pathway inhibitor drugs. For example, patients indicated for or being treated with an inhibitor of the VEGF pathway (e.g., bevacizumab) can be assessed for the presence of rs6770663, and treatment modified accordingly (e.g., pre-treatment with anti-hypertensive supportive therapy and/or dose modification and/or delivery of an alternative to the VEGF pathway inhibitor).


Importantly, the study established replication of the effect of rs6770663 (A>G), intronic in KCNAB1, as a variant for the risk of hypertension. Similar to the CALGB studies where it increased the risk of grade≥2 hypertension, rs6770663 was also associated with a higher risk of SBP≥160 mm Hg in ECOG-ACRIN E5103 (Table 14, FIG. 13).


In addition to KCNAB1, the studies provided herein identified other new candidate genes associated with VEGF pathway inhibitor-induced toxicity. This selection was based upon the strength and probability of the associations, the biological plausibility of gene, and the bioinformatic prediction of the SNP effect on the gene function or expression. Under this set of evaluations, ASPH was also identified as a new gene for VEGF pathway inhibitor-induced hypertension, based upon the signal of intronic rs2350620 (FIG. 13). Variant rs2350620 (A>G) reduced the risk of bevacizumab-induced hypertension and has SNPs in complete LD located in regulatory regions in HUVEC, aorta and the heart (Table 14). Also, rs2350620 is in complete LD with a deletion in ASPH (rs35026059, T>−), and CTCF can act as an insulator of the expression of ASPH because of binding in the presence the T allele (Table 14).


Despite many years of use of bevacizumab, hypertension and proteinuria still represent an obstacle to full delivery of effective therapy and pose a threat for patients and their quality of life. The studies provided herein identified rs6770663 in KCNAB1 as a novel marker of bevacizumab-induced hypertension that can be used to guide decisions on the risk assessment of patients treated with any VEGF pathway inhibitor. Other novel candidate genes are ASPH for hypertension, and TRIO and DNAH5 for proteinuria. Because these toxicities are also shared by many other antiangiogenesis drugs, the availability of these results in the public domain will expedite their translation into clinical application for other drugs with a similar mechanism of action.


In summary, the results of the studies provided herein showed that variant rs6770663 in KCNAB1 was associated with an increased the risk of hypertension (p=4.79×10−6). This was validated in ECOG-ACRIN E5103 (p=0.005). Variant rs2350620 in APSH was associated with a decreased risk of hypertension (p=1.44×10−6) and rs339947 (between DNAH5 and TRIO) was associated with an increased risk of proteinuria (p=7.66×10−8). Three variants previously associated with bevacizumab-induced hypertension were associated with composite toxicity (but not hypertension) with the same direction of effect in our study. To the knowledge of the inventors, this was the largest GWAS of bevacizumab-treated patients from randomized trials. The study has identified new genes involved in bevacizumab-induced hypertension and proteinuria. Genetic variation in KCNAB1 can be regarded to as a new validated biomarker to predict the risk of bevacizumab-induced hypertension.


All literature and similar materials cited in this application, including but not limited to, patents, patent applications, articles, books, treatises, and internet web pages are expressly incorporated by reference in their entirety for any purpose. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art to which the various embodiments described herein belongs. When definitions of terms in incorporated references appear to differ from the definitions provided in the present teachings, the definition provided in the present teachings shall control.


Various modifications and variations of the described compositions, methods, and uses of the technology will be apparent to those skilled in the art without departing from the scope and spirit of the technology as described. Although the technology has been described in connection with specific exemplary embodiments, it should be understood that the disclosure as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the disclosure that are obvious to those skilled in pharmacology, biochemistry, medical science, or related fields are intended to be within the scope of the following claims.


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Claims
  • 1. A method of treating a subject, the method comprising the steps of: a. determining the risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject based upon the presence or absence of a mutation in one or more nucleic acids in a sample obtained from a subject, wherein the subject is undergoing therapy or is a candidate for therapy with a VEGF-pathway inhibitor; andb. modulating therapy with a VEGF-pathway inhibitor and/or providing the subject with one or more supportive therapies based upon the determined risk of developing one or more VEGF-pathway inhibitor-induced toxicities in the subject.
  • 2. The method of claim 1, wherein the method further comprises detecting the mutation in the one or more nucleic acids in a sample obtained from the subject.
  • 3. The method of claim 1, wherein the detecting of the mutation in one or more nucleic acids in the sample comprises detecting a single nucleotide polymorphism (SNP) in the one or more nucleic acids in the sample.
  • 4. The method of claim 3, wherein the SNP is located in a gene provided in Table 8 or Table 9.
  • 5. The method of claim 4, wherein the gene is KCNAB1, PIK3R5, DNAH5 TRIO, or TTMA.
  • 6. The method of claim 4, wherein the mutation in the gene is a mutation that lowers expression of KCNAB1 relative to wildtype.
  • 7. The method of claim 3, wherein the SNP is selected from the SNPs provided in Table 4, Table 5, Table 6, Table 7, Table 10, Table 11, Table 12, Table 13, rs444904, and rs427554.
  • 8. The method of claim 3, wherein the SNP is selected from the group consisting of rs339947, rs12482855, rs13135230, rs2350620, rs11662763, rs6770663, rs408130, rs418173, rs12482855, rs444904, and rs427554.
  • 9. The method of claim 8, wherein a. the mutation is SNP rs6770663 and wherein the base identified at rs6770663 is a guanine,b. the mutation is SNP rs444904 and wherein the base identified at rs444904 is a an adenine,c. the mutation is rs427554 and wherein the base identified at rs427554 is an adenine,d. the mutation is SNP rs339947 and wherein the base identified at rs339947 is an adenine, and/ore. the mutation is SNP rs11662763 and the base identified at rs11662763 is an adenine.
  • 10. The method of claim 1, wherein the one or more VEGF-pathway inhibitor-induced toxicities are selected from proteinuria, hypertension, or both.
  • 11. The method of claim 10, comprising providing the subject with one or more supportive therapies when the subject is determined to have a high risk of developing proteinuria, hypertension, or both.
  • 12. The method of claim 11, wherein the one or more supportive therapies include one or more anti-hypertensive agents, one or more proteinuria medications, or a combination thereof.
  • 13. The method of claim 12, wherein the anti-hypertensive agent or proteinuria medication is in a class of drug selected from the group consisting of diuretics, beta blockers, alpha and beta blockers, calcium channel blockers, Angiotensin-converting enzyme (ACE) inhibitors, angiotensin II receptor antagonists (ARBs), adrenergic receptor antagonists, vasodilators, renin inhibitors, aldosterone receptor antagonists, alpha-2 adrenergic receptor agonists, central alpha-2 agonists and other centrally acting drugs, and endothelin receptor blockers.
  • 14. (canceled)
  • 15. The method of claim 11, wherein the supportive therapy comprises blood pressure monitoring and/or monitoring for proteinuria.
  • 16. The method of claim 11, wherein the subject is treated with the supportive therapy prior to or concurrently with the VEGF pathway inhibitor.
  • 17. (canceled)
  • 18. (canceled)
  • 19. (canceled)
  • 20. (canceled)
  • 21. The method of claim 1, wherein modulating therapy with the VEGF pathway inhibitor comprises reducing the total number of doses of the VEGF inhibitor.
  • 22. The method of claim 1, wherein modulating therapy with the VEGF pathway inhibitor comprises reducing the dosing frequency of the VEGF inhibitor.
  • 23. (canceled)
  • 24. (canceled)
  • 25. (canceled)
  • 26. The method of claim 1, wherein the VEGF-pathway inhibitor is selected from the group consisting of bevacizumab, bevacizumab-awwb, bevacizumab-bvzr, ranibizumab, aflibercept, ziv-aflibercept, lenalidomide, lenvatinib, ramucirumab, cabozantinib, pazopanib, sunitinib malate, regorafenib, axitinib, tipiracil and trifluridine, ponatinib, vandetanib, sorafenib, everolimus, thalidomide, temsirolimus, interferon alfa, interferon alfa-2B, interferon alfa-N3, peginterferon alfa-2B, peginterferon alfa-2A, rhEndostatin, cediranib, semaxanib, pomalidomide, alitretinoin, imiquimod, sinecatechins, vismodegib, sonidegib, pegaptanib sodium, dexamethasone intravitreal implant, fluocinolone acetonide, conbercept, brolucizumab-dbll, selpercatinib, nintedanib, apatinib, and motesanib.
  • 27. (canceled)
  • 28. A method for treating or preventing a VEGF pathway inhibitor-induced toxicity in a subject in need of treatment with a VEGF pathway inhibitor, the method comprising (i) identifying the subject as having a mutation in the gene KCNAB1 and(ii) treating the subject with one or more prophylactic therapies for the toxicity.
  • 29. A method for treating a subject having a disease or disorder associated with neovascularization or angiogenesis, the method comprising (i) identifying the subject as having a mutation in the gene KCNAB1;(ii) treating the subject with an anti-hypertensive agent; and(iii) treating the subject with a VEGF pathway inhibitor.
  • 30. (canceled)
CROSS REFERENCE TO RELATED APPLICATION

This application is a continuation of U.S. application Ser. No. 16/932,002, filed Jul. 17, 2020, which claims priority to U.S. Provisional Application No. 62/903,442, filed Sep. 20, 2019, which are hereby incorporated by reference in its entirety.

STATEMENT OF GOVERNMENTAL INTEREST

This invention was made with government support under Grant Numbers CA180821, CA180882, CA196171, CA233327, CA233253, CA233373, CA139280 and CA140390 awarded by the National Institutes of Health. The government has certain rights in the invention.

Provisional Applications (1)
Number Date Country
62903442 Sep 2019 US
Continuations (1)
Number Date Country
Parent 16932002 Jul 2020 US
Child 17313742 US