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Targeted Gene Sequencing in Children with Crohn's Disease and Their Parents: Implications for Missing Heritability. G3-GENES GENOMES GENETICS 2018; 8:2881-2888. [PMID: 30166421 PMCID: PMC6118318 DOI: 10.1534/g3.118.200404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Crohn’s disease is a complex genetic trait characterized by chronic relapsing intestinal inflammation. Genome wide association studies (GWAS) have identified more than 170 loci associated with the disease, accounting for ∼14% of the disease variance. We hypothesized that rare genetic variation in GWAS positional candidates also contribute to disease pathogenesis. We performed targeted, massively-parallel sequencing of 101 genes in 205 children with Crohn’s disease, including 179 parent-child trios and 200 controls, both of European ancestry. We used the gene burden test implemented in VAAST and estimated effect sizes using logistic regression and meta-analyses. We identified three genes with nominally significant p-values: NOD2, RTKN2, and MGAT3. Only NOD2 was significant after correcting for multiple comparisons. We identified eight novel rare variants in NOD2 that are likely disease-associated. Incorporation of rare variation and compound heterozygosity nominally increased the proportion of variance explained from 0.074 to 0.089. We estimated the population attributable risk and total heritability of variation in NOD2 to be 32.9% and 3.4%, respectively, with 3.7% and 0.25% accounted for by rare putatively functional variants. Sequencing probands (as opposed to genotyping) to identify rare variants and incorporating phase by sequencing parents can recover a portion of the missing heritability of Crohn’s disease.
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Xie C, Liu XF, Yang MS. A meta-analysis on the association between three promoter variants of TNF-α and Crohn’s disease. Mol Biol Rep 2011; 39:1575-83. [PMID: 21633892 DOI: 10.1007/s11033-011-0896-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 05/17/2011] [Indexed: 01/22/2023]
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Hsiao PC, Wang PH, Tee YT, Yang SF, Su PH, Chen YC, Lin LY, Tsai HT. Significantly Elevated Concentration of Plasma Monocyte Chemotactic Protein 1 of Patients With Pelvic Inflammatory Disease. Reprod Sci 2010; 17:549-55. [DOI: 10.1177/1933719110362593] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Pei-Ching Hsiao
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan, Institute of Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Po-Hui Wang
- Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yi-Torng Tee
- School of Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan, Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Pen-Hua Su
- School of Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan, Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yi-Chen Chen
- School of Nutrition, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Long-Yau Lin
- School of Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan, Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hsiu-Ting Tsai
- Department of Nursing, Chung Shan Medical University Hospital, Taichung, Taiwan, School of Nursing, Chung Shan Medical University, Taichung, Taiwan,
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