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Journal of Perinatal Medicine

Official Journal of the World Association of Perinatal Medicine

Editor-in-Chief: Dudenhausen, MD, FRCOG, Joachim W.

Ed. by Bancalari, Eduardo / Chappelle, Joseph / Chervenak, Frank A. / D'Addario , Vincenzo / Genc, Mehmet R. / Greenough, Anne / Grunebaum, Amos / Konje, Justin C. / Kurjak M.D., Asim / Romero, Roberto / Zalud, MD PhD, Ivica


IMPACT FACTOR 2018: 1.361
5-year IMPACT FACTOR: 1.578

CiteScore 2018: 1.29

SCImago Journal Rank (SJR) 2018: 0.522
Source Normalized Impact per Paper (SNIP) 2018: 0.602

Online
ISSN
1619-3997
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Volume 41, Issue 1

Issues

Preterm Birth Genome Project (PGP) – validation of resources for preterm birth genome-wide studies

Craig E. Pennell
  • School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Felipe Vadillo-Ortega / David M. Olson / Eun-Hee Ha / Scott Williams
  • Center for Human Genetics Research, Division of Human Genomics, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Tim M. Frayling / Siobhan Dolan / Michael Katz / Mario Merialdi
  • Department of Reproductive Health and Research, World Health Organization, Geneva, Switzerland
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/ Ramkumar Menon
  • Corresponding author
  • School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
  • Complete list of collaborators at the end of the article
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2012-08-18 | DOI: https://doi.org/10.1515/jpm-2012-0145

Abstract

We determined a series of quality control (QC) analyses to assess the usability of DNA collected and processed from different countries utilizing different DNA extraction techniques prior to genome-wide association studies (GWAS). The quality of DNA collected utilizing four different DNA extraction techniques and the impact of shipping DNA at different temperatures on array performance were evaluated. Fifteen maternal-fetal pairs were used from four countries. DNA was extracted using four approaches: whole blood, blood spots with whole genome amplification (WGA), saliva and buccal swab. Samples were sent to a genotyping facility, either on dry ice or at room temperature and genotyped using Affymetrix SNP array 6.0. QC measured included extraction techniques, effect of shipping temperatures, accuracy and Mendelian concordance. Significantly fewer (50%) single nucleotide polymorphisms (SNPs) passed QC metrics for buccal swab DNA (P<0.0001) due to missing genotype data (P<0.0001). Whole blood or saliva DNA had the highest call rates (99.2 0.4% and 99.3 0.2%, respectively) and Mendelian concordance. Shipment temperature had no effect. DNA from blood or saliva had the highest call rate accuracy, and buccal swabs had the lowest. DNA extracted from blood, saliva and blood spots were found suitable for GWAS in our study.

Keywords: DNA; genetic analysis; prematurity; samples; single nucleotide polymorphisms (SNPs)

About the article

Corresponding author: Ramkumar Menon, UTMB – Ob Gyn 301 University Blxd Galrestion 77555 Germany


Received: 2012-06-19

Revised: 2012-07-16

Accepted: 2012-07-19

Published Online: 2012-08-18

Published in Print: 2013-01-01


Citation Information: Journal of Perinatal Medicine, Volume 41, Issue 1, Pages 45–49, ISSN (Online) 1619-3997, ISSN (Print) 0300-5577, DOI: https://doi.org/10.1515/jpm-2012-0145.

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