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Genet Epidemiol. 2017 Jan;41(1):61-69. doi: 10.1002/gepi.22010. Epub 2016 Dec 1.

Whole exome association of rare deletions in multiplex oral cleft families.

Author information

1
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA.
2
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA.
3
Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore MD, USA.
4
Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore MD, USA.
5
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
6
Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA.
7
Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA, USA.
8
Institute of Human Genetics, University of Bonn, Bonn, Germany.
9
Dr. Hejazi Clinic, Damascus, Syrian Arab Republic.
10
Department of Pediatrics, School of Medicine, University of Iowa, IA, USA.
11
Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec and Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada.
12
Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.

Abstract

By sequencing the exomes of distantly related individuals in multiplex families, rare mutational and structural changes to coding DNA can be characterized and their relationship to disease risk can be assessed. Recently, several rare single nucleotide variants (SNVs) were associated with an increased risk of nonsyndromic oral cleft, highlighting the importance of rare sequence variants in oral clefts and illustrating the strength of family-based study designs. However, the extent to which rare deletions in coding regions of the genome occur and contribute to risk of nonsyndromic clefts is not well understood. To identify putative structural variants underlying risk, we developed a pipeline for rare hemizygous deletions in families from whole exome sequencing and statistical inference based on rare variant sharing. Among 56 multiplex families with 115 individuals, we identified 53 regions with one or more rare hemizygous deletions. We found 45 of the 53 regions contained rare deletions occurring in only one family member. Members of the same family shared a rare deletion in only eight regions. We also devised a scalable global test for enrichment of shared rare deletions.

KEYWORDS:

copy number; multiplex families; oral clefts; rare variants; structural variants

PMID:
27910131
PMCID:
PMC5154821
DOI:
10.1002/gepi.22010
[Indexed for MEDLINE]
Free PMC Article

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