Patent Application
20170009302
The present invention relates to genetic diagnosis field. More specifically, the present invention is directed to a method for detecting Epidermal Growth Factor Receptor (EGFR) gene mutations, as well as a kit for use in the detection of EGFR gene mutations.
EGFR (Epidermal Growth Factor Receptor) is normally embedded in the cell membrane on the cell surface. EGFR gene is 118 kb in length, includes 28 exons, and encodes a 170 kD glycoprotein comprised of 1186 amino acids. It is a membrane protein that plays an important role in regulating proliferation, growth, repair and survival of tumor cells. Currently, targeted therapy has become an important tool in the clinical treatment of Non Small Cell Lung Cancer (NSCLC). Iressa (Gefitinib, AstraZeneca) and Tarceva (Erlotinib, Roche), which function as EGFR tyrosine kinase inhibitors (TKI), are the main drugs approved by FDA for NSCLC targeted therapy. However, clinical experiments showed that Iressa and Tarceva only had significant therapeutic effects on 10-30% NSCLC patients. Further studies indicated that EGFR gene mutations relate to the therapeutic effects of NSCLC targeted therapy, and most of the patients carrying EGFR gene mutations showed significant therapeutic effects. A large number of research documents indicated that EGFR gene mutations are mainly located in the tyrosine kinase coding domain (exons 18-21), wherein deletion in exon 19 (746-753) accounts for about 45% of all mutations, and substitution in exon 21 (mainly L858R) accounts for about 40% of all mutations. At present, it is generally believed that these two hot mutations can enhance the sensitivity of tumor cells against TKI, and can be used as an effective index to predict TKI treatment. Therefore, the detection of EGFR gene mutations has an important reference value for guiding clinical administration in patients with NSCLC. Methods for detecting EGFR currently used in clinical treatment include: 1) traditional sequencing. This method has high accuracy. However, high requirement on the sample source, long sequencing time, the need for sequence analysis, and high cost of this method limit its use in clinic. 2) Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). It is a classical method for detecting gene mutations, and can detect unknown mutations. It has advantages of simple operation and high sensitivity. However, it also has an obvious disadvantage, which is the requirement for parallel standard control. Additionally, this method has a high false positive: the detection rate is 75-95% when the tested PCR product is less than 200 bp, while the detection rate is only about 50% when the tested PCR sample is more than 400 bp. 3) Mutation enriched PCR: a two-step PCR using a restriction endonuclease to selectively digest the wild type EGFR gene. After the first PCR, the wild type EGFR is digested selectively and the mutated EGFR genes are enriched, and then the second PCR is conducted. The PCR product is detected by electrophoresis, and whether EGFR is mutated is determined based on the detection results of PCR product. This method is highly sensitive, and can detect one mutation among 103-104 wild type EGFRs. However, this method needs twice PCR and enzyme digestion, thus is complex and time-consuming. In addition, there are technologies like AMRS and micro digital PCR, but their application in clinic still needs time.
Thus, there is an urgent need for a fast and efficient method for detecting EGFR gene mutations clinically. The inventor found, during the research of fragment DNA detection, a new method for detecting DNA fragments, including cyclizing and then amplifying DNA fragments. Based on this discovery and in combination with the second generation high throughput sequencing technology, the inventor improved the aforementioned method and designed optimized primers specifically based on the EGFR genes, and developed a method and a kit thereof for sequencing and analyzing EGFR gene mutations in plasma DNAs.
In one aspect, the present invention provides a method for non-invasively detecting EGFR gene mutations in subjects, comprising the following steps:
Further, the primers are a pair of primers that are adjacent and backward extended.
Further, primers of the backward extended primer pair are located on 5′ or 3′ end of the EGFR gene exons.
Further, space of the backward extended primer pair is 0-½ of the total base pairs of the fragment DNAs.
Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes.
Further, 5′ end of the backward extended primers contains linker sequences for high throughput sequencing library.
Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes, and sequences of the primers are as follows:
Further, the cyclization is a splint mediated single strand DNA cyclization.
Further, the EGFR genes in plasma DNAs have insertion, deletion, substitution or gene fusion mutations.
Further, the high throughput sequencing technologies are selected from Roche/454 FLX, Illumina/Hiseq/Miseq, Applied Biosystems SOLID and life Technologies/Ion Torrent/Proton.
In another aspect, the present invention provides a kit for non-invasively detecting EGFR gene mutations, comprising: reagents for extracting plasma DNAs, a DNA cyclase, primers and reagents for amplifying target DNAs.
Further, the kit comprises primers and reagents for pre-amplifying regions to be tested in the EGFR genes.
Further, the kit comprises reagents for high throughput sequencing.
Further, the reagents for high throughput sequencing are applicable to the following high throughput sequencing technologies: Roche/454 FLX, Illumina/Hiseq/Miseq, Applied Biosystems SOLID and life Technologies/Ion Torrent/Proton.
Further, the primers for amplifying regions to be tested in the EGFR genes are a pair of primers that are adjacent and backward extended.
Further, primers of the backward extended primer pair are located on 5′ or 3′ end of the sites or regions to be tested in the EGFR genes.
Further, space of the backward extended primer pair is 0-½ of total base pairs of the plasma DNAs.
Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes.
Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes, and sequences of the primers are as follows:
Further, the plasma DNA linkers contain tagging sequences.
Further, the plasma DNAs are pre-amplified before they are cyclised.
Further, the cyclization is a splint mediated single strand DNA cyclization.
Further, the sites or regions to be tested in the EGFR genes have insertion, deletion, substitution or gene fusion mutations.
In yet another aspect, the present invention provides a use of primers against EGFR gene exons in the preparation of diagnosing reagents or kits for non-invasively detecting EGFR gene mutations in subjects, characterized in that the diagnosing reagents or kits are applicable to a method for non-invasively detecting EGFR gene mutations in subjects comprising the following steps:
Further, the primers are a pair of primers that are adjacent and backward extended.
Further, primers of the backward extended primer pair are located on 5′ or 3′ end of the EGFR gene exons.
Further, space of the backward extended primer pair is 0-½ of total base pairs of the fragment DNAs.
Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes.
Further, 5′ end of the backward extended primers contains linker sequences for high throughput sequencing library.
Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes, and sequences of the primers are as follows:
Further, the cyclization is a splint mediated single strand DNA cyclization.
Further, the EGFR genes in the plasma DNAs have insertion, deletion, substitution or gene fusion mutations.
Further, the high throughput sequencing is selected from Roche/454 FLX, Illumina/Hiseq/Miseq, Applied Biosystems SOLID and life Technologies/Ion Torrent/Proton.
With improvements in the sequencing technology, the traditional Sanger sequencing has been unable to fully meet the requirement of research. Thus, the second generation sequencing technology with lower cost, higher throughput, faster speed, and having capability for sequencing the whole genome emerges. The main principle of the second generation sequencing technology is high throughput sequencing by synthesis, namely, determining DNA sequences by capturing newly synthesized end labelling. The available technologic platforms mainly include Roche/454 FLX, Illumina/Genome Analyzer/Hiseq/Miseq, Applied Biosystems SOLID, life Technologies/Ion Torrent, and the like. Taking Illumina product as an example, HiSeq 2000 can reach a sequencing throughput of 30× coverage in 6 human genomes per run, i.e., about 600 G/run, and the operation time is reduced to 30 minutes. Furthermore, with the maturity of the second generation sequencing technology, the investigation on its clinical application has developed quickly. Research shows that fetus genetic health can be judged by sequencing maternal plasma DNAs, and that sequencing plasma DNAs in subjects can be used for early cancer screening, which will have a wide application in the future.
Plasma DNAs, also known as circulating DNAs, are extracellular DNAs in the blood and is tens to hundreds of nucleotides in length (a main peak of about 167 bp). It presents in a form of DNA-protein complex, or as free DNA fragments. Normally, plasma DNAs are derived from DNA release of a small amount of senescent and dead cells. Under healthy condition, the generation and removal of the circulating DNAs are in a dynamic equilibrium and are maintained at a relatively steady low level. 1 mL plasma from a normal person contains about 2000 genomic DNAs. The circulating DNAs can reflect the metabolic condition of cells in human body, thus is an important index for judging health. The change of quantity and quality of circulating DNAs in peripheral blood is closely related to several diseases (including tumour, complex severe traumata, organ transplantation, pregnancy-related diseases, infectious diseases, organ failure, and the like). As a non-invasive detection index, it is expected to be an important molecular marker for early diagnosing some diseases, monitoring the conditions, and evaluating the therapeutic effects and prognosis of the diseases. For example, researches show that EGFR regulates the cell cycle progress, repair and survival of tumor cells, and at the same time relates to tumor metastasis. Recently, molecular targeted therapy using EGFR as the therapy target has received widespread attention from cancer communities both at home and abroad, and an EGFR tyrosine kinase inhibitor, Iressa (Genfitinib), has been approved by America Food and Drug Administration (FDA) for treating advanced NSCLC. The prominent feature of molecular targeted drugs is that its therapeutic effect strongly depends on the target: the therapeutic effect is significant strong in patients with the “target”, while the therapeutic effect is weak or none in patients without the “target”, which thus delays other treatments and makes the conditions worse. Therefore, blind administrations without target detection not only may result in high economic loss, but also may delay the valuable timing for treatment, or even aggravate the conditions. It is curtail to judge quickly and accurately whether the patient has the specific target for the targeted drug treatment. The traditional EGFR detection mainly detects the lesion tissue section by FISHor qPCR. However, it is found that there are more free DNAs in the plasma of NSCLC patients, about 10 times of those of normal people. A large quantity of free DNAs in plasma derives from DNAs release of senescent and dead tumor cells. They are similar to tumor genomic DNAs in genetic characteristics, and mutations thereof include deletion, point mutation, and increased copy number. EGFR gene mutations can be detected by examining plasma DNAs in NSCLC patients, and thus make it possible to detect EGFR expression non-invasively. The present invention detects EGFR expressions and mutations in plasma DNAs by the second generation sequencing technology quickly, accurately, non-invasively and with high sensitivity, and thus provides various diagnosis basis for patients.
In view of the clinical significance of non-invasive detection by plasma DNAs sequencing and the rapid development of the second generation high throughput sequencing, the inventor found that sequencing plasma DNAs in large-scale can detect EGFR gene expressions and mutations more quickly, accurately, and non-invasively. It is applicable to a variety of second generation high throughput sequencing platforms, including but not limited to, Roche/454 FLX, Illumina/Genome Analyzer/Hiseq/Miseq, Applied Biosystems SOLID, life Technologies/Ion Torrent, and the like.
The present invention is based on the following two facts: 1) plasma free DNAs in patients are similar to genomic DNAs in genetic characteristics. The plasma free DNAs of patients are higher in content than those of normal people, and often contain lots of mutations, while each mutation may be of low frequency; 2)The second generation high throughput sequencing can obtain the information of plasma free DNAs quickly, accurately, and with high throughput. Combining these two facts enables the non-invasive large scale application of the detection in genome specific regions. Researches show that plasma DNAs exist as fragments with low amount (1 mL plasma contains about 2000 genomes) and short length (mainly about 167 bp), which make it difficult for the traditional PCR to enrich mutations effectively using plasma DNAs as templates, resulting in rapid decrease in detection sensitivity. The present invention differs from the traditional methods in that the DNA fragments connected with sequence tagging linkers are amplified and single strand cyclized, then by means of back-to-back primer amplification, the templates are used maximally and the library is sequenced by high throughput paired-end sequencing. The original amplified templates are assembled based on the original sequencing analysis, and the tagging sequences are recorded. Sequences with the same position on the genome and the same tagging sequences are calculated as one template. The number of templates amplified by every primer pair is calculated and the number of mutated template is counted and recorded. The present invention improves the cyclization method and optimizes primers for the EGFR genes. The unique design of tagging sequences reduces background and prevents contamination effectively. The unique template set is counted by restoring templates in systems accurately, and thus a single molecule detection with high accuracy is finally achieved.
According to one specific embodiment of the present invention, it provides a method for non-invasively detecting EGFR gene mutations in subjects, comprising the following steps: (1) designing primers according to EGFR gene exons; (2) extracting plasma DNAs from the subjects; (3) connecting the extracted plasma DNAs with tagging linkers; (4) PCR pre-amplifying the tagging linkers connected plasma DNA; (5) cyclizing the amplified DNAs to obtain cyclised DNAs; (6) PCR amplifying the cyclised DNAs using the designed primers; and (7) high throughput sequencing the PCR amplified product and analyzing the EGFR gene mutations. “Non-invasive detection” in the present invention means that in comparison with that routine histology detection methods such as surgery, tissue biopsy and the like, which are directly against cancer tissues, will result in body damages in subjects, the present invention only detects blood sample from the subjects. Traditional methods for detecting DNAs or gene fragments require PCR amplification of the regions to be tested before detection, and thus the DNAs or gene fragments to be tested should be complete. However, most of the plasma DNA fragments are incomplete, and thus the DNA fragments that can be used as templates in PCR amplification is few in number and is difficult to be detected by a routine PCR. Therefore, PCR amplification in the present invention adopts DNA cycllization technology to transform fragment DNAs into cyclic DNAs using linker sequences and enzymes. Primers based on the regions to be tested are designed; sequencing library is amplified and constructed, and then is sequenced by a high throughput sequencing technology; and the EGFR gene mutations are analyzed.
According to another further specific embodiment of the present invention, primers of the backward extended primer pair are located on 5′ or 3′ end of the EGFR gene exons. Further, space of the backward extended primer pair is 0-½ of total base pairs of the fragment DNAs. Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes. Further, 5′ end of the backward extended primers contains linker sequences for high throughput sequencing library. Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of EGFR genes, and sequences of the primers are as follows:
Further, the cyclization is a splint mediated single strand DNA cyclization.
Further, the high throughput sequencing technologies are selected from Roche/454 FLX, Illumina/Hiseq/Miseq, Applied Biosystems SOLID and life Technologies/Ion Torrent/Proton. Illumina technology is used in the present invention.
According to another specific embodiment of the present invention, it provides a kit for non-invasively detecting EGFR gene mutations, comprising: reagents for extracting plasma DNAs, a DNA cyclase, primers and reagents for amplifying target DNAs. Conventional reagents or commercially available kits can be used in the extraction of plasma DNAs. Further, the amplification primers of the regions to be tested in the EGFR genes are a pair of primers that are adjacent and backward extended. Further, primers of the backward extended primer pair are located on 5′ or 3′ end of the sites or regions to be tested in the EGFR genes. Further, space of the backward extended primer pair is 0-½of total base pairs of the plasma DNAs. Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes. Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes, and sequences of the primers are as follows:
Further, the kit comprises primers and reagents for pre-amplifying the regions to be tested in the EGFR genes. Specifically, the reagents and primers for pre-amplification include Taq DNA polymerase and its buffer, and primers for pre-amplification that are complementary to the Y-shape linkers.
Further, the kit comprises reagents for high throughput sequencing. Further, the reagents for high throughput sequencing are applicable to the following high throughput sequencing technologies: Roche/454 FLX, Illumina/Hiseq/Miseq, Applied Biosystems SOLID and life Technologies/Ion Torrent/Proton. Further, the plasma DNA connection linkers contain tagging sequences. Further, the plasma DNAs are pre-amplified before they are cyclised. Further, the cyclization is a splint mediated single strand DNA cyclization.
According to yet another specific embodiment of the present invention, it provides a use of primers according to EGFR gene exons in the preparation of diagnosing reagents or kits for non-invasively detecting EGFR gene mutations in subjects, characterized in that the diagnosing reagents or kits are applicable to a method for non-invasively detecting EGFR gene mutations in subjects comprising the following steps:
Further, the primers are a pair of primers that are adjacent and backward extended. Further, primers of the backward extended primer pair are located on 5′ or 3′ end of the EGFR gene exons. Further, space of the backward extended primer pair is 0-½ of total base pairs of the fragment DNAs. Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes. Further, 5′ end of the backward extended primers contains linker sequences for high throughput sequencing library. Further, the backward extended primers aim at exon 18, exon 19, exon 20, or exon 21 of the EGFR genes, and sequences of the primers are as follows:
Further, the cyclization is a splint mediated single strand DNA cyclization. Further, the high throughput sequencing technologies are selected from Roche/454 FLX, Illumina/Hiseq/Miseq, Applied Biosystems SOLID and life Technologies/Ion Torrent/Proton.
The plasma DNA template was amplified using self-designed linkers and according to a method for constructing a plasma DNA high throughput sequencing library (that is, PCR pre-amplification using phosphorylated primers after linker connection). The PCR product was purified by a gel cutting and cyclised by a splint connection. The cyclised product was digested by Exo III, purified, and screened by multiplex PCR with 8 pairs of back-to-back primers (the primers contain universal sequences for constructing a sequencing library). The mutation sites should be close to the forward primer or the reverse primer. The library was finally obtained by purifying the amplification product amplified by the universal primers.
1. Linker design. It is annealed to a double strand, wherein X is a tagging sequence:
The structure of connection product:
Primers:
The library structure after pre-amplification:
Back-to-back primers for amplification in target zones:
TCTCTTGAGGATCTTGAAGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTGCGTTCGGCACGGTGTATAAG
GTAAGGTC
CCTGGCACAGGCCTCTGGGCTGGGCCGCAGGGCCTCTCATGGTCTGGTGGGGAGCCCAGAGTCCTTGCAAGCTGTATATTTCCATCA
GTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTT
GCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTCTAGACCCTGCTCATCTCCA
CGAAGCCACACTGACGTGCCTCTCCCTCCCTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGG
GCATCTGCCTCACCTCCACCGTGCAGCTCATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTATGTCCGGGAACACAAAGACA
ATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGTAATCAGGGAAGGGAGATACGGGGAGGGGAGATAAGGAG
CCAGGATCCTCACATGCGGTCTGCGCTCCTGGGATAGCAAGAGTTTGCCATGGGGATATG
CCCATGATGATCTGTCCCTCACAGCAGGGTCTTCTCTGTTTCAGGGCATGAACTACTTGGAGGACCGTCGCTTGGTGCACCGCGACC
TGGCAGCCAGGAACGTACTGGTGAAAACACCGCAGCATGTCAAGATCACAGATTTTGGGCTGGCCAAACTGCTGGGTGCGGAAGAGA
AAGAATACCATGCAGAAGGAGGCAAAGTAAGGAGGTGGCTTTAGGTCAGCCAGCATTTTCCTGACACCAGGGACCAGGCTGCCTTCC
2. Plasma free DNAs were extracted from 2 mL plasma.
3. End-filling:
The reaction mixture was prepared as follows:
The mixture was placed in a 20° C. warm bath for 30 min. The DNA sample was purified on a purification column and eluted by 42 μl sterile dH2O or an elution buffer.
4. Adding poly-adenine tail on the 3′ end of the DNA fragments:
The reaction mixture was prepared as follows:
The mixture was placed in a 37° C. warm bath for 30 min. The DNA sample was purified on a column and eluted by 25 μl sterile dH2O or an elution buffer.
5. Connecting linkers to the DNA fragments
The reaction mixture was prepared as follows:
The mixture was placed in a 20° C. warm bath for 15 min. The DNA sample was purified on a Qiagen column and eluted by 25 μl sterile dH2O or an elution buffer.
6. Enriching the linker-modified DNA fragments by PCR pre-amplification
The PCR reaction mixture was prepared as follows:
PCR programs:
Amplification using the following PCR programs:
a. 98° C. 30 s;
b. 18 cycles as follows:
98° C. 10s, 65° C. 30 s, 72° C. 30 s;
c. 72° C. 5 min;
d. maintained at 4° C.
6. PCR product was analyzed by electrophoresis on 2% agarose gel, and the results were shown in
7. Cyclization
The cyclization system was prepared as follows (Table 5)
Reaction conditions
8. Enzyme digestion:
All the cyclization products were digested by Exo III, and the digestion system was
The digestion system was placed in a PCR machine, and reacted for 30 min at 37° C.
The digested product was purified on a purification column and dissolved in 30 ul EB buffer. The concentration was measured by Qubit, and the results were as follows:
Examples of the present invention used a splint-mediated cyclization, which has a high rate of cyclization. Detailed tracking and detecting results of every step during the cyclization process were shown in
9. Reverse PCR screening of the target zone using back-to-back primers
PCR reaction system was prepared as follows
PCR reaction conditions
10. The second round PCR
The second round PCR was performed using products of the reverse PCR as templates. System
Programs:
10 uL PCR product from the second round PCR was analyzed by electrophoresis on 2% agarose gel, and the results were shown in
11. The remaining 40 uL PCR product from the second round PCR was purified on a QIAGEN column, and dissolved in 20 uL EB buffer to generate the final library.
12. After quality control, the generated library was 250 bp double-end sequenced by IlluminaMiseq.
13. Every high throughput sequenced double-end sequences were assembled to one sequence based on repeated regions. Linkers were removed, and the sequence was restored to the original template sequence, which was then compared to the human genome (hg19). The unique template sequence set was counted by comparing the start and terminal coordinates and tagging sequences of the template sequence on the genome. Using the unique template sequence, genome coverage was then calculated, which can be used for evaluating the specificity of the library and calculating the somatic cell mutations in the EGFR region.
The results were compared with an EGFR gene mutation detection kit from AmoyDx (directed to the same cancer tissue) and a digital PCR. The comparison results were:
5 samples tested by the method of the present invention showed highly consistent results with those tested by other methods. AMRS-PCR (amplification refractory mutation system) Taq DNA polymerase lacks 3′-5′ exonuclease activity. Under certain conditions, effective amplification occurs only when the last base on 3′ end of PCR primers is complementary to the template DNA. Mutated genes and wild type genes can be directly distinguished by PCR using suitable primers directed to different known mutations. This method is mainly for biopsy and FFPE samples. 5 mL peripheral blood before surgery and FFPE samples after surgery from the same patient were provided. The mutation type of FFPE samples on the known sites was detected by ARMS-PCR, and then plasma DNA was detected by digital PCR and the method of the present invention, respectively.
Reliability of the present method was verified by detecting known cancer mutation sites. The method was the same as that disclosed in Example 1.
Cancer cell line DNA: cell DNAs containing hybrid c.2235_2249de115 (exon 19) mutation were broken by ultrasonication, 166±10 bp fragments were recycled and mixed with plasma DNAs from a normal person at certain ratio. The sensitivity and stability of the method were examined.
The detection results of c.2235_2249del15 were as follows:
| Number | Date | Country | Kind |
|---|---|---|---|
| 201310756037.2 | Dec 2013 | CN | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2014/093940 | 12/16/2014 | WO | 00 |
