Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data

Mary M Jenkins; Lynn M Almli; Faith Pangilinan; Jessica X Chong; Elizabeth E Blue; Stuart K Shapira; Janson White; Daniel McGoldrick; Joshua D Smith; Christopher J Bean; Wendy N Nembhard; Xiang‐Yang Lou; Gary M Shaw; Paul A Romitti; Kim Keppler‐Noreuil; Mahsa M Yazdy; Denise M Kay; Tonia C Carter; Andrew F Olshan; Kristin J Moore; Nanette Nascone‐Yoder; Richard H Finnell; Philip J Lupo; Marcia L Feldkamp; Deborah A Nickerson; Michael J Bamshad; Lawrence C Brody; Jennita Reefhuis; National Birth Defects Prevention Study

doi:10.1002/bdr2.1554

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Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data

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Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data

Mary M Jenkins, Lynn M Almli, Faith Pangilinan, Jessica X Chong, Elizabeth E Blue, Stuart K Shapira, Janson White, Daniel McGoldrick, Joshua D Smith, Christopher J Bean, …

Birth defects research, Vol.111(20), pp.1618-1632

12/01/2019

DOI: 10.1002/bdr2.1554

PMCID: PMC6889076

PMID: 31328417

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Abstract

Background The National Birth Defects Prevention Study (NBDPS) is a multisite, population‐based, case–control study of genetic and nongenetic risk factors for major structural birth defects. Eligible women had a pregnancy affected by a birth defect or a liveborn child without a birth defect between 1997 and 2011. They were invited to complete a telephone interview to collect pregnancy exposure data and were mailed buccal cell collection kits to collect specimens from themselves, their child (if living), and their child's father. Over 23,000 families representing more than 30 major structural birth defects provided DNA specimens. Methods To evaluate their utility for exome sequencing (ES), specimens from 20 children with colonic atresia were studied. Evaluations were conducted on specimens collected using cytobrushes stored and transported in open versus closed packaging, on native genomic DNA (gDNA) versus whole genome amplified (WGA) products and on a library preparation protocol adapted to low amounts of DNA. Results The DNA extracted from brushes in open packaging yielded higher quality sequence data than DNA from brushes in closed packaging. Quality metrics of sequenced gDNA were consistently higher than metrics from corresponding WGA products and were consistently high when using a low input protocol. Conclusions This proof‐of‐principle study established conditions under which ES can be applied to NBDPS specimens. Successful sequencing of exomes from well‐characterized NBDPS families indicated that this unique collection can be used to investigate the roles of genetic variation and gene–environment interaction effects in birth defect etiologies, providing a valuable resource for birth defect researchers.

Genetics

birth defects

gene–environment interaction

intestinal atresia

sequence analysis

Details

Title: Subtitle: Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data
Creators: Mary M Jenkins - Centers for Disease Control and Prevention
Lynn M Almli - Carter Consulting Incorporated
Faith Pangilinan - National Institutes of Health
Jessica X Chong - University of Washington
Elizabeth E Blue - Department of Medicine, University of Washington
Stuart K Shapira - Centers for Disease Control and Prevention
Janson White - University of Washington
Daniel McGoldrick - University of Washington
Joshua D Smith - University of Washington
Christopher J Bean - Centers for Disease Control and Prevention
Wendy N Nembhard - University of Arkansas for Medical Sciences
Xiang‐Yang Lou - College of Medicine, University of Arkansas for Medical Sciences
Gary M Shaw - Stanford University School of Medicine, Department of Pediatrics
Paul A Romitti - University of Iowa
Kim Keppler‐Noreuil - Children's National Medical Center, George Washington University
Mahsa M Yazdy - Massachusetts Department of Public Health
Denise M Kay - Division of Genetics, Wadsworth Center
Tonia C Carter - Marshfield Clinic Research Institute
Andrew F Olshan - Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina
Kristin J Moore - Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina
Nanette Nascone‐Yoder - Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University
Richard H Finnell - Center for Precision Environmental Health, Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine
Philip J Lupo - Section of Hematology‐Oncology, Baylor College of Medicine
Marcia L Feldkamp - University of Utah School of Medicine
Deborah A Nickerson - University of Washington
Michael J Bamshad - University of Washington
Lawrence C Brody - National Institutes of Health
Jennita Reefhuis - Centers for Disease Control and Prevention
National Birth Defects Prevention Study
Resource Type: Journal article
Publication Details: Birth defects research, Vol.111(20), pp.1618-1632
DOI: 10.1002/bdr2.1554
PMID: 31328417
PMCID: PMC6889076
NLM abbreviation: Birth Defects Res
ISSN: 2472-1727
eISSN: 2472-1727
Publisher: Wiley
Number of pages: 15
Grant note: National Human Genome Research Institute (U24 HG008956; UM1 HG006493) National Heart, Lung, and Blood Institute Centers for Disease Control and Prevention (PA 96043; PA 02081; FOA DD09‐001; FOA DD13‐003; NOFO DD18‐001) NIH‘s Division of Intramural Research of the NHGRI
Language: English
Date published: 12/01/2019
Academic Unit: Epidemiology; Biostatistics
Record Identifier: 9984214829602771

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