A genome-wide association analysis of chromosomal aberrations and Hirschsprung disease

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• 作者：Joon Seol Bae^a ; ¹ ; InSong Koh^b ; ¹ ; Hyun Sub Cheong^c ; Jeong-Meen Seo^d ; Dae-Yeon Kim^e ; Jung-Tak Oh^f ; Hyun-Young Kim^g ; Kyuwhan Jung^h ; Jae Hoon Sulⁱ ; ^j ; Woong-Yang Park^a ; Jeong-Hyun Kim^k ; ^{soykm@sogang.ac.kr" class="auth_mail" title="E-mail the corresponding author} ; Hyoung Doo Shin^k ; ^l ; ^{hdshin@sogang.ac.kr" class="auth_mail" title="E-mail the corresponding author}
• 关键词：HSCR ; Hirschsprung disease ; CNV ; copy number variation ; LOH ; loss of heterozygosity ; qPCR ; quantitative polymerase chain reaction ; S-HSCR ; short-segment Hirschsprung disease ; L-HSCR ; long-segment Hirschsprung disease ; TCA ; total colonic aganglionosis ; SNP ; single nucleotide polymorphism ; PCA ; principal component analysis ; GWAS ; genome-wide association study ; LRR ; log R ratio ; BAF ; B allele frequency ; FDR ; False Discovery Rate ; DGV ; Database of Genomic Variants ; CNVR ; CNV region ; CGH ; comparative
• 刊名：Translational Research
• 出版年：2016
• 出版时间：November 2016
• 年：2016
• 卷：177
• 期：Complete
• 页码：31-40.e6
• 全文大小：1181 K

文摘

Hirschsprung disease (HSCR) is a neurocristopathy characterized by the absence of intramural ganglion cells along variable lengths of the gastrointestinal tract. Although the RET proto-oncogene is considered to be the main risk factor for HSCR, only about 30% of the HSCR cases can be explained by variations in previously known genes including RET. Recently, copy number variation (CNV) and loss of heterozygosity (LOH) have emerged as new ways to understand human genomic variation. The goal of this present study is to identify new HSCR genetic factors related to CNV in Korean patients. In the genome-wide genotyping, using Illumina's HumanOmni1-Quad BeadChip (1,140,419 markers), of 123 HSCR patients and 432 unaffected subjects (total n = 555), a total of 8,188 CNVs (1 kb ∼ 1 mb) were identified by CNVpartition. As a result, 16 CNV regions and 13 LOH regions were identified as associated with HSCR (minimum P = 0.0005). Two top CNV regions (deletions at chr6:32675155-32680480 and chr22:20733495-21607293) were successfully validated by additional real-time quantitative polymerase chain reaction analysis. In addition, 2 CNV regions (6p21.32 and 22q11.21) and 2 LOH regions (3p22.2 and 14q23.3) were discovered to be unique to the HSCR patients group. Regarding the large-scale chromosomal aberrations (>1 mb), 11 large aberrations in the HSCR patients group were identified, which suggests that they may be a risk factor for HSCR. Although further replication in a larger cohort is needed, our findings may contribute to the understanding of the etiology of HSCR.