Campbell Catarina D, Mohajeri Kiana, Malig Maika, Hormozdiari Fereydoun, Nelson Benjamin, Du Gaixin, Patterson Kristen M, Eng Celeste, Torgerson Dara G, Hu Donglei, Herman Catherine, Chong Jessica X, Ko Arthur, O'Roak Brian J, Krumm Niklas, Vives Laura, Lee Choli, Roth Lindsey A, Rodriguez-Cintron William, Rodriguez-Santana Jose, Brigino-Buenaventura Emerita, Davis Adam, Meade Kelley, LeNoir Michael A, Thyne Shannon, Jackson Daniel J, Gern James E, Lemanske Robert F, Shendure Jay, Abney Mark, Burchard Esteban G, Ober Carole, Eichler Evan E
Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
PLoS One. 2014 Aug 12;9(8):e104396. doi: 10.1371/journal.pone.0104396. eCollection 2014.
Asthma is a complex genetic disease caused by a combination of genetic and environmental risk factors. We sought to test classes of genetic variants largely missed by genome-wide association studies (GWAS), including copy number variants (CNVs) and low-frequency variants, by performing whole-genome sequencing (WGS) on 16 individuals from asthma-enriched and asthma-depleted families. The samples were obtained from an extended 13-generation Hutterite pedigree with reduced genetic heterogeneity due to a small founding gene pool and reduced environmental heterogeneity as a result of a communal lifestyle. We sequenced each individual to an average depth of 13-fold, generated a comprehensive catalog of genetic variants, and tested the most severe mutations for association with asthma. We identified and validated 1960 CNVs, 19 nonsense or splice-site single nucleotide variants (SNVs), and 18 insertions or deletions that were out of frame. As follow-up, we performed targeted sequencing of 16 genes in 837 cases and 540 controls of Puerto Rican ancestry and found that controls carry a significantly higher burden of mutations in IL27RA (2.0% of controls; 0.23% of cases; nominal p = 0.004; Bonferroni p = 0.21). We also genotyped 593 CNVs in 1199 Hutterite individuals. We identified a nominally significant association (p = 0.03; Odds ratio (OR) = 3.13) between a 6 kbp deletion in an intron of NEDD4L and increased risk of asthma. We genotyped this deletion in an additional 4787 non-Hutterite individuals (nominal p = 0.056; OR = 1.69). NEDD4L is expressed in bronchial epithelial cells, and conditional knockout of this gene in the lung in mice leads to severe inflammation and mucus accumulation. Our study represents one of the early instances of applying WGS to complex disease with a large environmental component and demonstrates how WGS can identify risk variants, including CNVs and low-frequency variants, largely untested in GWAS.
哮喘是一种由遗传和环境风险因素共同导致的复杂遗传疾病。我们试图通过对来自哮喘富集家庭和哮喘贫集家庭的16名个体进行全基因组测序（WGS），来检测全基因组关联研究（GWAS）基本遗漏的几类遗传变异，包括拷贝数变异（CNV）和低频变异。这些样本取自一个延续13代的哈特派谱系，由于创始基因库较小，其遗传异质性降低，又因集体生活方式，环境异质性也降低。我们将每个个体测序至平均13倍深度，生成了一份全面的遗传变异目录，并测试了最严重的突变与哮喘的关联性。我们鉴定并验证了1960个CNV、19个无义或剪接位点单核苷酸变异（SNV）以及18个移码插入或缺失。作为后续研究，我们对837例波多黎各裔病例和540例对照中的16个基因进行了靶向测序，发现对照中IL27RA基因的突变负担显著更高（对照的2.0%；病例的0.23%；名义p = 0.004；经邦费罗尼校正p = 0.21）。我们还对1199名哈特派个体中的593个CNV进行了基因分型。我们在NEDD4L基因内含子中的一个6千碱基缺失与哮喘风险增加之间发现了名义上显著的关联（p = 0.03；优势比（OR）= 3.13）。我们在另外4787名非哈特派个体中对该缺失进行了基因分型（名义p = 0.056；OR = 1.69）。NEDD4L在支气管上皮细胞中表达，在小鼠肺部对该基因进行条件性敲除会导致严重炎症和黏液积聚。我们的研究是将WGS应用于具有大量环境因素的复杂疾病的早期实例之一，并展示了WGS如何能够识别在GWAS中基本未被检测的风险变异，包括CNV和低频变异。
