title: Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma.
abstract: 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.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Catarina D
authors.initials: CD
authors.lastname: Campbell
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Kiana
authors.initials: K
authors.lastname: Mohajeri
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Maika
authors.initials: M
authors.lastname: Malig
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Fereydoun
authors.initials: F
authors.lastname: Hormozdiari
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Nelson
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Gaixin
authors.initials: G
authors.lastname: Du
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Kristen M
authors.initials: KM
authors.lastname: Patterson
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Celeste
authors.initials: C
authors.lastname: Eng
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Dara G
authors.initials: DG
authors.lastname: Torgerson
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Donglei
authors.initials: D
authors.lastname: Hu
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Catherine
authors.initials: C
authors.lastname: Herman
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Jessica X
authors.initials: JX
authors.lastname: Chong
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Arthur
authors.initials: A
authors.lastname: Ko
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: O'Roak
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Niklas
authors.initials: N
authors.lastname: Krumm
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Laura
authors.initials: L
authors.lastname: Vives
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Choli
authors.initials: C
authors.lastname: Lee
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Lindsey A
authors.initials: LA
authors.lastname: Roth
authors.affiliation: Veterans Caribbean Health Care System, San Juan, Puerto Rico, United States of America.
authors.forename: William
authors.initials: W
authors.lastname: Rodriguez-Cintron
authors.affiliation: Centro de Neumología Pediátrica, San Juan, Puerto Rico, United States of America.
authors.forename: Jose
authors.initials: J
authors.lastname: Rodriguez-Santana
authors.affiliation: Department of Allergy & Immunology, Kaiser Permanente-Vallejo Medical Center, Vallejo, California, United States of America.
authors.forename: Emerita
authors.initials: E
authors.lastname: Brigino-Buenaventura
authors.affiliation: Children's Hospital and Research Center Oakland, Oakland, California, United States of America.
authors.forename: Adam
authors.initials: A
authors.lastname: Davis
authors.affiliation: Children's Hospital and Research Center Oakland, Oakland, California, United States of America.
authors.forename: Kelley
authors.initials: K
authors.lastname: Meade
authors.affiliation: Bay Area Pediatrics, Oakland, California, United States of America.
authors.forename: Michael A
authors.initials: MA
authors.lastname: LeNoir
authors.affiliation: San Francisco General Hospital, San Francisco, California, and the Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Shannon
authors.initials: S
authors.lastname: Thyne
authors.affiliation: Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Jackson
authors.affiliation: Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America.
authors.forename: James E
authors.initials: JE
authors.lastname: Gern
authors.affiliation: Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America; Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America.
authors.forename: Robert F
authors.initials: RF
authors.lastname: Lemanske
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Abney
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California, United States of America; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Esteban G
authors.initials: EG
authors.lastname: Burchard
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Carole
authors.initials: C
authors.lastname: Ober
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America; Howard Hughes Medical Institute, Seattle, Washington, United States of America.
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
mesh_terms: D000483:Alleles; D001249:Asthma / Q000235:genetics*; D002874:Chromosome Mapping; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D056827:Endosomal Sorting Complexes Required for Transport / Q000235:genetics; D005260:Female; D018703:Founder Effect; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns; D008297:Male; D000075702:Nedd4 Ubiquitin Protein Ligases; D020641:Polymorphism, Single Nucleotide; D044382:Population Groups / Q000235:genetics; D017384:Sequence Deletion; D044767:Ubiquitin-Protein Ligases / Q000235:genetics
chemical_list: D056827:Endosomal Sorting Complexes Required for Transport; D000075702:Nedd4 Ubiquitin Protein Ligases; C000618485:Nedd4L protein, human; C000618461:Nedd4l protein, mouse; D044767:Ubiquitin-Protein Ligases