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

Craig E. Pennell; Felipe Vadillo-Ortega; David M. Olson; Eun Hee Ha; Scott Williams; Tim M. Frayling; Siobhan Dolan; Michael Katz; Mario Merialdi; George Davey-Smith; Eunyoung Ha; Ramkumar Menon; Jeffrey C. Murray; Poul Thorsen; Calvin Hobel; Bonnie Petrauskas; Scott M. Williams; Marshall Lindheimer; Stephen Fortunato; Bo Jacobsson; Steven S. Witkin; Siobhan M. Dolan; Carole Ober; Kenneth Ward; Martha Karen Campbell; Michael Kramer; Jason H. Moore; Nils Halvdan Morken; Caroline Relton; Mehmet R. Genc; Errol R. Norwitz; S. Vanderpoel; Stephen Lye

doi:10.1515/jpm-2012-0145

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

Craig E. Pennell, Felipe Vadillo-Ortega, David M. Olson, Eun Hee Ha, Scott Williams, Tim M. Frayling, Siobhan Dolan, Michael Katz, Mario Merialdi, George Davey-Smith, Eunyoung Ha, Ramkumar Menon, Jeffrey C. Murray, Poul Thorsen, Calvin Hobel, Bonnie Petrauskas, Scott M. Williams, Marshall Lindheimer, Stephen Fortunato, Bo JacobssonSteven S. Witkin, Siobhan M. Dolan, Carole Ober, Kenneth Ward, Martha Karen Campbell, Michael Kramer, Jason H. Moore, Nils Halvdan Morken, Caroline Relton, Mehmet R. Genc, Errol R. Norwitz, S. Vanderpoel, Stephen Lye

Obstetrics & Gynecology and Women's Health

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

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.

Original language	English (US)
Pages (from-to)	45-49
Number of pages	5
Journal	Journal of Perinatal Medicine
Volume	41
Issue number	1
DOIs	https://doi.org/10.1515/jpm-2012-0145
State	Published - Jan 2013

Keywords

DNA
Genetic analysis
Prematurity
Samples
Single nucleotide polymorphisms (SNPs)

ASJC Scopus subject areas

Pediatrics, Perinatology, and Child Health
Obstetrics and Gynecology

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10.1515/jpm-2012-0145

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Pennell, C. E., Vadillo-Ortega, F., Olson, D. M., Ha, E. H., Williams, S., Frayling, T. M., Dolan, S., Katz, M., Merialdi, M., Davey-Smith, G., Ha, E., Menon, R., Murray, J. C., Thorsen, P., Hobel, C., Petrauskas, B., Williams, S. M., Lindheimer, M., Fortunato, S., ... Lye, S. (2013). Preterm Birth Genome Project (PGP) - Validation of resources for preterm birth genome-wide studies. Journal of Perinatal Medicine, 41(1), 45-49. https://doi.org/10.1515/jpm-2012-0145

Pennell, CE, Vadillo-Ortega, F, Olson, DM, Ha, EH, Williams, S, Frayling, TM, Dolan, S, Katz, M, Merialdi, M, Davey-Smith, G, Ha, E, Menon, R, Murray, JC, Thorsen, P, Hobel, C, Petrauskas, B, Williams, SM, Lindheimer, M, Fortunato, S, Jacobsson, B, Witkin, SS, Dolan, SM, Ober, C, Ward, K, Campbell, MK, Kramer, M, Moore, JH, Morken, NH, Relton, C, Genc, MR, Norwitz, ER, Vanderpoel, S & Lye, S 2013, 'Preterm Birth Genome Project (PGP) - Validation of resources for preterm birth genome-wide studies', Journal of Perinatal Medicine, vol. 41, no. 1, pp. 45-49. https://doi.org/10.1515/jpm-2012-0145

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title = "Preterm Birth Genome Project (PGP) - Validation of resources for preterm birth genome-wide studies",

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)",

author = "Pennell, {Craig E.} and Felipe Vadillo-Ortega and Olson, {David M.} and Ha, {Eun Hee} and Scott Williams and Frayling, {Tim M.} and Siobhan Dolan and Michael Katz and Mario Merialdi and George Davey-Smith and Eunyoung Ha and Ramkumar Menon and Murray, {Jeffrey C.} and Poul Thorsen and Calvin Hobel and Bonnie Petrauskas and Williams, {Scott M.} and Marshall Lindheimer and Stephen Fortunato and Bo Jacobsson and Witkin, {Steven S.} and Dolan, {Siobhan M.} and Carole Ober and Kenneth Ward and Campbell, {Martha Karen} and Michael Kramer and Moore, {Jason H.} and Morken, {Nils Halvdan} and Caroline Relton and Genc, {Mehmet R.} and Norwitz, {Errol R.} and S. Vanderpoel and Stephen Lye",

note = "Funding Information: The Preterm Birth Genome Project has been generously funded by the World Health Organization, the March of Dimes Foundation, the Alberta Health and Medical Research Foundation, Telethon (Western Australia), the Women and Infant Research Foundation and the Government of Mexico.",

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doi = "10.1515/jpm-2012-0145",

language = "English (US)",

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T1 - Preterm Birth Genome Project (PGP) - Validation of resources for preterm birth genome-wide studies

AU - Pennell, Craig E.

AU - Vadillo-Ortega, Felipe

AU - Olson, David M.

AU - Ha, Eun Hee

AU - Williams, Scott

AU - Frayling, Tim M.

AU - Dolan, Siobhan

AU - Katz, Michael

AU - Merialdi, Mario

AU - Davey-Smith, George

AU - Ha, Eunyoung

AU - Menon, Ramkumar

AU - Murray, Jeffrey C.

AU - Thorsen, Poul

AU - Hobel, Calvin

AU - Petrauskas, Bonnie

AU - Williams, Scott M.

AU - Lindheimer, Marshall

AU - Fortunato, Stephen

AU - Jacobsson, Bo

AU - Witkin, Steven S.

AU - Dolan, Siobhan M.

AU - Ober, Carole

AU - Ward, Kenneth

AU - Campbell, Martha Karen

AU - Kramer, Michael

AU - Moore, Jason H.

AU - Morken, Nils Halvdan

AU - Relton, Caroline

AU - Genc, Mehmet R.

AU - Norwitz, Errol R.

AU - Vanderpoel, S.

AU - Lye, Stephen

N1 - Funding Information: The Preterm Birth Genome Project has been generously funded by the World Health Organization, the March of Dimes Foundation, the Alberta Health and Medical Research Foundation, Telethon (Western Australia), the Women and Infant Research Foundation and the Government of Mexico.

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N2 - 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.

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

Abstract

Keywords

ASJC Scopus subject areas

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