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Identification of SNP markers for common CNV regions and association analysis of risk of subarachnoid aneurysmal hemorrhage in Japanese population

Authors
Bae, Joon SeolCheong, Hyun SubKim, Ji-OnLee, Soo OkKim, Eun MiLee, Hye WonKim, SangsooKim, Ji-WoongCui, TailinInoue, IturoShin, Hyoung Doo
Issue Date
5-Sep-2008
Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
Keywords
copy number variation (CNV); single-nucleotide polymorphism (SNP); multi-allelic CNV genotype; whole genome association study; subarachnoid aneurismal hemorrhage (SAH)
Citation
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, v.373, no.4, pp.593 - 596
Journal Title
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Volume
373
Number
4
Start Page
593
End Page
596
URI
http://scholarworks.bwise.kr/ssu/handle/2018.sw.ssu/16806
DOI
10.1016/j.bbrc.2008.06.083
ISSN
0006-291X
Abstract
Copy number variation (CNV) is emerging as a new tool for understanding human genomic variation, but its relationship with human disease is not yet fully understood. The data for a total of 317,503 genotypes were collected for a genome-wide association study of subarachnoid aneurismal hemorrhage (SAH) in a Japanese population (cases and controls, n = 497) using Illumina HumanHap300 BeadChip (R). To identify multi-allelic CNV markers, we visually inspected all genotype clusters of 317,503 SNP markers covering the whole genome using Illumina's BeadStudio 3.0 (R) software. As a result, we identified 597 multi-allelic CNV markers for common (copy loss frequency > 0.05) CNV regions in a Japanese population (n = 497). The identified CNV markers shared the following characteristics: enrichment of Hardy-Weinberg disequilibria, Mendelian inconsistency among families, and high missing genotype rate. All annotated information for those markers is summarized in our database (http://www.snp-genetics.com/user/srch.htm). In addition, we performed case-control association analyses of identified multi-allelic CNV markers with the risk of subarachnoid aneurysmal hemorrhage. One SNP marker (rs1242541) within a CNV region neighboring the Sel-1 suppressor of lin-12-like protein (SEL1L) was significantly associated with a risk of SAH (P = 0.0006). We also validated the CNV around rs1242541 using real-time quantitative polymerase chain reaction (PCR). Information and methods used in this study would be helpful for accurate genotyping of SNPs on CNV regions, which could be used for association analysis of SNP markers within CNV regions. (c) 2008 Elsevier Inc. All rights reserved.
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