Patent Application
20050130149
The present invention relates to novel genomic polymorphisms located on chromosome 7 and their use in methods for the detection of Williams-Beuren Syndrome or a carrier of Williams-Beuren Syndrome.
Throughout this application, various references are cited in parentheses to describe more fully the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present disclosure.
The Williams-Beuren Syndrome (WBS), also known as Williams Syndrome, occurs in approximately 1 in 20,000 individuals worldwide. The phenotype includes congenital vascular and heart disease, dysmorphic facies, growth deficiency, infantile hypercalcemia, mental retardation, a unique cognitive profile and a characteristic personality (Greenberg, F. (1990); Pober et al., (1996)).
Presently, diagnosis of WBS includes testing for a hemizygous deletion at 7q11.23 by fluorescence in situ hybridization (FISH) using a probe encompassing the elastin gene (ELN) (Ewart et al., (1993)). In over 95% of WBS cases, there is observed a defined hemizygous 1.5 Mb deletion (
Due to the sporadic nature of the microdeletions that occur, there is currently no screening method for testing extended family members who may be predisposed to have a WBS child.
Thus there remains a need for improved diagnostic methods for Williams-Beuren Syndrome and for carriers.
The present invention discloses novel genomic polymorphisms comprising inversions within the WBS region (7q 11.23 region) of chromosome 7 which encompass multiple genes within this region of chromosome 7. These novel genomic polymorphisms can be used in methods for determining individual carriers of the inversions and thus the likelihood of having children with WBS. The methods of the present invention can also be used for the diagnosis of Williams-Beuren Syndrome. Prenatal screening methods are included within the scope of the invention and predictive tests are also provided to determine whether an individual is at risk of having a child with WBS.
With the identification of novel, inversions in the WBS region, nucleic acid probes can be used in a variety of hybridization assays to screen for and detect the presence of the inversions. Kits for such screening and diagnosis are also provided.
In accordance with an aspect of the present invention is a gene region comprising the 7q11.23 WBS region containing an inversion leading to a syndrome or disease profile in an individual.
In accordance with a further aspect of the invention is an inversion comprising a 1.5 Mb gene region of 7q11.23
In accordance with another aspect of the invention is a method for determining the presence or absence of an inversion within the WBS region of chromosome 7 in a subject, the method comprising the steps of: i) analyzing cells from an individual using a genomic hybridization technique; and
ii) detecting the presence or absence of an inversion in the WBS region.
In one embodiment, the genomic hybridization technique used is fluorescent in situ hybridization (FISH).
In accordance with another aspect of the invention is a method for determining whether a subject displaying Williams-Beuren Syndrome (WBS)-associated symptoms suffers from WBS, or an asymptomatic subject is a carrier of WBS, the method comprising:
obtaining a biological sample from the subject; and
conducting an assay on the sample to determine the presence or absence of at least one inversion in the WBS region of chromosome 7, the presence of at least one inversion being indicative that the subject displaying symptoms suffers from WBS or that the asymptomatic subject is a carrier of WBS.
In a preferred embodiment, the method comprises using three colour FISH analysis on lymphocytes which have been synchronized in interphase. Two probes are designed to hybridize with specific sequences within the WBS deletion region and a third probe hybridizes to a region which flanks the WBS region. The relative positioning of the probes determines the presence of an inversion.
According to another aspect of the invention is a method for determining the presence of a Williams-Beuren Syndrome (WBS)-associated inversion, the method comprising the steps of:
i) digesting DNA from an individual with a restriction enzyme to obtain restriction fragments;
ii) size fractionating said fragments; and
iii) determining the presence or absence of novel restriction fragments, indicating the presence of a WBS inversion mutation.
In a preferred embodiment, the DNA is digested with Not1 enzyme. It is well known to one skilled in the art that other restriction enzymes which provide a restriction map which differs from that seen in the normal can also be used in the above method.
According to a further aspect of the invention is a method for the detection of a WBS-associated inversion comprising the steps of:
i) subjecting DNA or RNA from a subject to amplification using oligonucleotide primers, wherein at least one primer is complementary to a nucleic acid sequence upstream of a breakpoint and at least one primer is complementary to a nucleic acid sequence downstream of said breakpoint and wherein said primers are complementary to opposite strands of nucleic acid;
ii) amplifying the genetic region between the primers using a polymerization chain reaction technique and obtaining an amplification product;
iii) determining the sequence of the amplification product; and
iv) comparing the sequence of the amplified region with the sequence from a control individual to determine the presence of an inversion.
In yet another aspect of the invention, there is provided a method for determining the risk of having a child with WBS or other syndromes associated with an inversion polymorphism in the WBS region. The method comprises screening family members for the presence or absence of an inversion polymorphism in the 7q11.23 gene region
In yet another aspect of the invention, there is provided a kit for determining the Williams-Beuren genotype of an individual, said kit comprising at least one internal probe labeled with a fluorophore, said internal probe being able to hybridize to a sequence within the WBS region of chromosome 7 and at least one external probe labeled with a different fluorophore, said external probe being able to hybridize to a region flanking said WBS region.
Other features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from said detailed description.
The invention is described in more detail herein with reference to the accompanying drawings, in which:
Genes are depicted as arrows where the transcriptional orientation (5′ to 3′) is known, and as blocks where it is not known. DNA sequence scaffolds from Celera (component 3 assembly) and the public genome project are shown. Repetitive gene sequences within the duplicons are identified by degree of shading in the legend below left and the duplicons themselves are presented as large vertical shaded boxes. The minimal regions within which the inversion breakpoints could be localized are depicted by diagonal hatched boxes.
The present invention discloses previously undescribed inversions of a portion of chromosome 7 in a number of atypical WBS patients and in asymptomatic relatives of these patients. The first group of inversions detected involves an approximately 1.5 Mb region of 7q11.23. The patients either did not show all the typical symptoms of WBS or they did not exhibit the previously identified WBS deletion. The clinical features of the WBS families studied are outlined in Table 1.
The intrachromosomal segmental DNA duplications flanking the WBS region (often called duplicons) were analysed and determined to be approximately 400 kb in size (
To test for the presence of chromosomal inversion or duplication at 7q11.23, interphase FISH analysis was initially performed on 11 atypical WBS individuals and their parents (when available). The atypical individuals were divided into two groups, (i) 3 patients having an inversion or translocation on chromosome 7 and (ii) 8 patients with no detectable cytogenetic chromosomal rearrangement (Table 1).
An inversion of the 7q11.23 WBS region on the rearranged chromosome was identified in atypical individuals 11719 and 15441, who carried a balanced translocation and a paracentric inversion, respectively (Table 1). The inversion was also detected in an atypical WBS patient (12503) who, upon extensive FISH analysis, did not appear to have any other chromosomal anomaly. The father of individual 11719 and the mother of individual 15441, both phenotypically normal, also carried a hemizygous inversion of the WBS region. No rearrangement was found in the other atypical WBS patients as indicated in Table 1.
The unexpected observation of an inversion being present in parents of two unrelated atypical WBS individuals carrying more complex chromosome rearrangements, suggested that it would be beneficial to examine parents of typical WBS patients who carry the microdeletion. A diagnostic test of probability can be developed based on the rationale that, in a parent carrying an inversion on one chromosome, there may be difficulties in chromosome pairing at meiosis leading to the WBS deletion. Using the same interphase FISH assay, a heterozygous inversion was found in 4 of 12 (33%) families examined. These results are shown in Table 1.
In addition to the data shown in Table 1, this inversion was found in three further WBS patients in three separate new families.
Breakpoints for the observed inversions occurred between the position of probes RP11-815K3 and CTA-208H19 on the centromeric side and between probes RP5-1186P10 and RP11-229D13 on the telomeric side.
As discussed above, the presence of the inversion was detected by FISH analysis. Combinations of probes in three-color FISH experiments (with two probes from within the common deletion and one from the outside) were used to determine the orientation of the 1.5 Mb WBS region relative to flanking DNA as described in the following Examples. Changes in copy number due to duplications or smaller deletions can also be detected and the boundaries of chromosome rearrangement can also be defined.
Using combinations of FISH probes to examine interphase and metaphase chromosome preparations, it was consistently demonstrated that the inversion breakpoints in each individual studied occurred within the duplicon region. For example, by examining metaphase chromosomes of a patient, the proximal and distal parts of the WBS region could be studied in isolation since they resided on different derivative chromosomes. The results of one such analysis is shown in
The presence of the inversion may be detected by any suitable method known to those of skill in the art, including, for example, genomic hybridization techniques, PCR analysis and restriction fragment analysis.
The presence of the described inversion may also be detected by PCR analysis, by amplification of a portion of chromosome 7 spanning an inversion breakpoint, using suitable primers and sequencing of the amplified portion. The presence of an abnormal junction sequence, resulting from inclusion of an inverted sequence within the amplified portion, indicates the presence of the inversion.
The present invention provides the unexpected demonstration that the WBS region can undergo two relatively large genomic rearrangements, deletion and inversion, both apparently mediated by the repetitive units flanking the interval. The presence of the above-described inversion in parents of WBS children suggests that this genomic variant may lead to disturbances in meiosis predisposing to chromosome rearrangements in future generations. In WBS, since the number of reported families with more than one affected individual is small, this would be a rare event. Most inversion carriers do not exhibit any obvious phenotypic features although in at least two individuals (12503 and 15441) the inversion seems to be associated with many WBS symptoms (Table 1). The data indicates that the inversion breakpoints in these 2 individuals reside within the duplicons, just as in each of the other phenotypically normal WBS inversion cases studied. It appears from PFGE experiments that the site of the breakpoint(s), or extent of rearrangement, in individual 12503 could be different. It may be that breakpoint(s) in 12503 and 15441 interrupt or affect the expression of functional gene(s) located within or near the duplicon or there may be another mutation or rearrangement. GTF2I is one such gene that could be affected since it is located partially inside the telomeric duplicon. Moreover, GTF2I was found deleted in atypical WBS patients carrying sub-WBS deletions having a similar phenotype to individuals 12503 and 15441.
The majority (˜67%) of WBS interstitial deletions have been shown to be due to unbalanced recombination during meiosis (interchromosomal rearrangement) while less (˜33%) appear to arise due to intrachromosomal recombination3. To determine if the inversion polymorphism is associated with one or both events and to provide better estimates of recurrence risk to siblings, the analysis can be expanded to include grandparents and siblings. The finding of the present invention that ˜30% of transmitting chromosomes in WBS families carry a genomic inversion provides new insight into the mechanism underlying the disease. The FISH and PFGE tests described for detection of the inversion are valuable in assisting in clinical diagnosis of WBS and for screening methods involved in family planning.
Further studies were carried out on patients or family members who, from the studies described above, did not appear to have either a deletion or the inversion described above. A new inversion at a different location in the WBS region of chromosome 7 (second inversion) was detected in one of these patients and in a parent of that patient. In the second inversion, breakpoints occurred between the position of probes CTA-208H19 and RP5-1186P10 on the centromeric side and between probes CTB-139P11 and RP11-275G11 on the telomeric side.
Four WBS patients in different families have been identified who have both the first described and second inversions and in some instances a parent was also shown to have both inversions.
The methods of the invention may be used for the diagnosis of patients presenting with classical WBS symptoms but showing no deletion of chromosome 7 or of patients presenting with some WBS-associated symptoms but lacking the full array of classical symptoms. WBS-associated symptoms include congenital vascular disease, congenital heart disease, dysmorphic facies, growth deficiency, infantile hypercalcemia and mental retardation.
The methods may also be used to screen members of a family with a history of WBS, as a basis for genetic counselling, as the finding of a WBS-associated inversion will indicate a possibility of bearing a child with WBS.
The methods may also be used for in utero testing to determine if a fetus carries a WBS-associated inversion.
The examples are described for the purposes of illustration and are not intended to limit the scope of the invention.
Methods of molecular biology, molecular hybridization, protein and peptide biochemistry, histology and genetics referred to but not explicitly described in this disclosure and examples are reported in the scientific literature and are well known to those skilled in the art.
Patient Samples and Controls.
WBS probands were identified through the University of Arizona Genetics Program (15441), Virginia Commonwealth University (12503), Yale University School of Medicine (4 atypical individuals), McMaster University Medical Centre (1 atypical individual), and The Hospital for Sick Children, Toronto (remaining atypical and all classic WBS individuals). WBS was diagnosed using recognized diagnostic criteria. Local guidelines for human subject experimentation were followed. Proband 11719 was a neonate with severe supravalvular aortic stenosis and hydrops fetalis (von Dadelszen et al., (2000)), who died shortly after birth. Proband 12503 is an 18 year old female with WBS-like facial features, developmental delay, hypersensitivity to sound, malocclusion, strabismus, joint tightness, and WBS-like behaviour. Proband 15441 is a 16 year old female with ectrodactyly of the feet, WBS-like facial features, strabismus, musculoskeletal abnormalities, mild developmental delay, recurrent otitis media resulting in hearing loss, hyperactivity and WBS-like behaviour. In addition to the WBS inversion, she was also shown to have a larger inversion on chromosome 7 with breakpoints at 7q11.2 (over 1 Mb proximal to the WBS deletion, near D7S726) and at 7q21.3 (within the SHFM1 critical region). As controls for the WBS families (which were of different ethnic backgrounds), 26 randomly selected non-WBS cell lines and blood samples from ethnically diverse sources were used (52 chromosomes).
Mapping, DNA Sequence Analysis, DNA Markers, and Microsatellite Experiments.
An integrated genetic, physical, DNA sequence, and gene map spanning the WBS region was assembled for this study using new mapping data, published data (Osborne et at., (1997); Peoples et al., (2000); Valero et al., (2000)) and by annotating all available DNA sequence (
The intrachromosomal segmental DNA duplications flanking the WBS region (often called duplicons) were analyzed and determined to be approximately 400 kb in size (
Percent Identity Plot (PIP) analysis was performed on the completed sequence of clones CTA-350L10, CTA-269P13, RP11-313P13 and RP5-953A4 using the automated analysis server PipMaker (Schwartz et al., (2000). Additional genetic markers for the studies were generated, including WS13 (D7S3197)(
Fluorescence in situ Hybridization.
The protocols for FISH analysis were based on previously described techniques (Heng et al., (1992 & 1993)). Briefly, for metaphase analysis, lymphocytes were cultured for 68-72 hr, synchronized with BrdU (0.18 μg/ml, Sigma), washed and then re-cultured for 6 hr in α-MEM with thymidine (2.5 μg/ml, Sigma). Cells were harvested and slides were prepared by hypotonic treatment, fixed, and air-dried. For interphase analysis, slides from cell lines or peripheral blood were dried at room temperature for 3 days. Before hybridization, all slides were denatured in 70% formamide/2×SSC for 30 seconds at 70° C., and dehydrated with ethanol. Genomic DNA was isolated from clones using standard methods (e.g. Heng et al. 1992) and labeled with either biotin (green) or digoxigenin (red) to generate 500 bp fragments. For the dual color signal (yellow), DNA was labeled separately with biotin and digoxigenin and then mixed. Standard labeling techniques were used (Heng et al. 1992, 1993).
Probes were denatured for 5 min at 75° C. and hybridized to slides overnight (37° C. in 50% formamide with CotI DNA). The slides were washed, a detection solution was added and following DAPI staining, the slides were examined under a fluorescence microscope. Any standard labeled antibody solution can be used as the detection solution to detect the tag (e.g. biotin) on the probe. The detection efficiency on metaphase chromosomes was 90-99%, enabling assessment of the position of the hybridization signal relative to the rearrangement breakpoint. The WBS patients, family members, and controls were randomized so there was no bias of interpretation of results. Approximately 100 mitotic figures were examined for each probe tested. For assessment of interphase cells, only those chromosomes where all three probes could be visualized in close alignment with each other were scored (at least 25 chromosomes were scored for each individual).
Pulsed-field Gel Electrophoresis
Patient lymphoblast cell lines were embedded in low melting-point agarose at a concentration of ˜107 cells/ml. High molecular weight DNA was prepared by incubation with sodium sarkosyl and Proteinase K. The DNA blocks were digested with NotI restriction endonuclease (New England Biolabs) and size fractionated through 1% agarose using a CHEF-II apparatus. Multiple gels under different conditions were run. Undigested Saccharomyces cerevisiae chromosomes were used as a size marker. The gels were transferred to nylon membranes and hybridized in Ambion hybridization buffer at 50° C., followed by washing at 55° C.
Accession Numbers
The DNA sequences generated in the present invention were submitted to GenBank. The GenBank accession numbers are G68164 (WS10), G68161 (WS11), G68162 (WS12), G68163 (WS13), AF020782 (pMD24), AZ757825/AZ757826 (cos24g11).
Detection and Characterisation of WBS-associated Inversion
Interphase FISH analysis of 11 atypical WBS individuals and available parents was performed as described above. Table 1 indicates the karyotype and phenotype of the subjects in the study.
Two different clone sets were used for FISH, both with two probes, 208419 and 1186P10, from within the common WBS deletion interval, but with the third either telomeric (A) or centromeric (B) to the region. The order of probes along a normal chromosome 7 are depicted in
The probes, from centromere to telomere, are CTA-208H19 (green), RP5-1186P10 (yellow) and CTB-139P11 (red)(
The probes are, from centromere to telomere, RP11-815K3 (red), CTA-208H19 (green), and RP5-1186P10 (yellow). On an inverted chromosome, the yellow signal appears between the red and green, indicating an inversion of the region. From the combined data, as well as using additional probes, it was demonstrated that the inversion breakpoints resided within the duplicon region (
An inversion of the 7q11.23 WBS region on the rearranged chromosome was identified in atypical individuals 11719 and 15441, who carried both a balanced translocation and a paracentric inversion (Table 1). A control probe on chromosome 7p22 (RP11-13N3 containing LFNG, red) was used to identify the derivative chromosome 7. Multiple test probes (green) were used to determine the site of the translocation and extent of the inversion in patient 11719. Based on the presence or absence of signals on the derivative chromosomes, the translocation breakpoint was mapped to the immediate 5′ end of the ELN gene (see
It was observed that probes cos34b3 and cos82c2 had the same pattern of hybridization to the translocation chromosomes as HSC7E610 (ie. hybridizing to the derivative chromosome 7), while cos16g10 hybridized to the derivative chromosome 6. This suggests a probe order of HSC7E610 (D7S672)-[cos34b3 (3′-ELN)-cos82c2 (5′-ELN)]-cos16g10 (STX1A). However, on a normal chromosome the known order of probes is: 7cen-HSC7E610 (D7S672)-duplicon-cos16g10 (STX1A)-cos82c2 (5′-ELN)-cos34b3 (3′-ELN)-duplicon-7qter (
The inversion was also detected in an atypical WBS patient (12503), who upon extensive FISH analysis, did not appear to have any other chromosomal anomaly.
The father of individual 11719 and the mother of individual 15441, both phenotypically normal, also carried a hemizygous inversion of the WBS region. No rearrangement was found in the eight other atypical WBS patients, as indicated in Table 1.
Using the same interphase FISH assay, twelve parents of WBS probands with the common WBS deletion were examined. As shown in Table 2, a heterozygous inversion was found in four of the twelve families examined (33%).
Polymorphic DNA marker analysis was carried out using standard techniques in several WBS families. Polymorphic marker analysis throughout the WBS deletion region at 7q11.23 and the rest of chromosome 7 identified the microdeletion-containing chromosome in WBS probands to be inherited from the parent carrying the inversion. Representative results for three families with WS13 (D7S3197), a polymorphic (TAGA)n repeat marker that resides within the unique 5′ end of GTF2I and, therefore, within the WBS microdeletion, are shown in
NotI-digested genomic DNA from WBS families was fractionated by PFGE and examined by blot-hybridization analysis using a GTF2I-specific probe (corresponding to the 3′ UTR of GTF2I; nucleotides 2134-2638 of GenBank NM—032999). A representative result with resolution of fragments in the 450 kb to 1.6 Mb size range is shown. A novel NotI junction fragment was found in only those individuals (eg. 8580, 11107, 9912, 12503) shown by FISH to carry the WBS inversion. In normal individuals, the GTF2I probe should detect NotI fragments of 3 Mb and 1 Mb in size on the centromeric and telomeric side of the WBS region, respectively (GTF2I is present at each end of the WBS region and therefore hybridizes to two NotI fragments as seen in
Although preferred embodiments of the invention have been described herein in detail, it will be understood by those skilled in the art that variations may be made thereto without departing from the spirit of the invention.
aINV, WBS region inverted; not INV, WBS region not inverted.
bThe site of the 7q11.23 inversion breakpoint is indicated in
cP = 0.0038
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA02/01611 | 10/25/2002 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 60330571 | Oct 2001 | US |
