SNP genotyping to screen for a common deletion in CHARGE Syndrome
eScholarship@McGill
View Archive Info| Field | Value | |
| Title |
SNP genotyping to screen for a common deletion in CHARGE Syndrome
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| Creator |
Lalani, Seema
Safiullah, Arsalan Fernbach, Susan Phillips, Michael Bacino, Carlos Molinari, Laura Glass, Nancy Towbin, Jeffrey Craigen, William Belmont, John |
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| Description |
BACKGROUND:CHARGE syndrome is a complex of birth defects including coloboma, choanal atresia, ear malformations and deafness, cardiac defects, and growth delay. We have previously hypothesized that CHARGE syndrome could be caused by unidentified genomic microdeletion, but no such deletion was detected using short tandem repeat (STR) markers spaced an average of 5 cM apart. Recently, microdeletion at 8q12 locus was reported in two patients with CHARGE, although point mutation in CHD7 on chromosome 8 was the underlying etiology in most of the affected patients.METHODS:We have extended our previous study by employing a much higher density of SNP markers (3258) with an average spacing of approximately 800 kb. These SNP markers are diallelic and, therefore, have much different properties for detection of deletions than STRs.RESULTS:A global error rate estimate was produced based on Mendelian inconsistency. One marker, rs431722 exceeded the expected frequency of inconsistencies, but no deletion could be demonstrated after retesting the 4 inconsistent pedigrees with local flanking markers or by FISH with the corresponding BAC clone. Expected deletion detection (EDD) was used to assess the coverage of specific intervals over the genome by deriving the probability of detecting a common loss of heterozygosity event over each genomic interval. This analysis estimated the fraction of unobserved deletions, taking into account the allele frequencies at the SNPs, the known marker spacing and sample size.CONCLUSIONS:The results of our genotyping indicate that more than 35% of the genome is included in regions with very low probability of a deletion of at least 2 Mb.
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| Publisher |
BioMed Central
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| Date |
2005
2006-05-06 |
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| Type |
article
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| Format |
application/pdf
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| Identifier |
DOI:10.1186/1471-2350-6-8
http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=14162 |
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| Source |
BMC Medical Genetics Vol. 6, no. 1 (2005)
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| Language |
eng
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| Rights |
All items in eScholarship@McGill are protected by copyright with all rights reserved unless otherwise indicated.
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