An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population

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An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population. / Lu, Timothy Tehua; Lao, Oscar; Nothnagel, Michael; Junge, Olaf; Freitag-Wolf, Sandra; Caliebe, Amke; Balascakova, Miroslava; Bertranpetit, Jaume; Bindoff, Laurence Albert; Comas, David; Holmlund, Gunilla; Kouvatsi, Anastasia; Macek, Milan; Mollet, Isabelle; Nielsen, Finn; Parson, Walther; Palo, Jukka; Ploski, Rafal; Sajantila, Antti; Tagliabracci, Adriano; Gether, Ulrik; Werge, Thomas; Rivadeneira, Fernando; Hofman, Albert; Uitterlinden, André Gerardus; Gieger, Christian; Wichmann, Heinz-Erich; Ruether, Andreas; Schreiber, Stefan; Becker, Christian; Nürnberg, Peter; Nelson, Matthew Roberts; Kayser, Manfred; Krawczak, Michael.

In: European Journal of Human Genetics, Vol. 17, No. 7, 2009, p. 967-75.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Lu, TT, Lao, O, Nothnagel, M, Junge, O, Freitag-Wolf, S, Caliebe, A, Balascakova, M, Bertranpetit, J, Bindoff, LA, Comas, D, Holmlund, G, Kouvatsi, A, Macek, M, Mollet, I, Nielsen, F, Parson, W, Palo, J, Ploski, R, Sajantila, A, Tagliabracci, A, Gether, U, Werge, T, Rivadeneira, F, Hofman, A, Uitterlinden, AG, Gieger, C, Wichmann, H-E, Ruether, A, Schreiber, S, Becker, C, Nürnberg, P, Nelson, MR, Kayser, M & Krawczak, M 2009, 'An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population', European Journal of Human Genetics, vol. 17, no. 7, pp. 967-75. https://doi.org/10.1038/ejhg.2008.266

APA

Lu, T. T., Lao, O., Nothnagel, M., Junge, O., Freitag-Wolf, S., Caliebe, A., ... Krawczak, M. (2009). An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population. European Journal of Human Genetics, 17(7), 967-75. https://doi.org/10.1038/ejhg.2008.266

Vancouver

Lu TT, Lao O, Nothnagel M, Junge O, Freitag-Wolf S, Caliebe A et al. An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population. European Journal of Human Genetics. 2009;17(7):967-75. https://doi.org/10.1038/ejhg.2008.266

Author

Lu, Timothy Tehua ; Lao, Oscar ; Nothnagel, Michael ; Junge, Olaf ; Freitag-Wolf, Sandra ; Caliebe, Amke ; Balascakova, Miroslava ; Bertranpetit, Jaume ; Bindoff, Laurence Albert ; Comas, David ; Holmlund, Gunilla ; Kouvatsi, Anastasia ; Macek, Milan ; Mollet, Isabelle ; Nielsen, Finn ; Parson, Walther ; Palo, Jukka ; Ploski, Rafal ; Sajantila, Antti ; Tagliabracci, Adriano ; Gether, Ulrik ; Werge, Thomas ; Rivadeneira, Fernando ; Hofman, Albert ; Uitterlinden, André Gerardus ; Gieger, Christian ; Wichmann, Heinz-Erich ; Ruether, Andreas ; Schreiber, Stefan ; Becker, Christian ; Nürnberg, Peter ; Nelson, Matthew Roberts ; Kayser, Manfred ; Krawczak, Michael. / An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population. In: European Journal of Human Genetics. 2009 ; Vol. 17, No. 7. pp. 967-75.

Bibtex

@article{06570550a5ee11df928f000ea68e967b,
title = "An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population",
abstract = "Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309,790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0{\%}), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.",
keywords = "Faculty of Health and Medical Sciences, DNA, Europe, Female, Genetic Markers, Genetic Variation, Genome, Genome-Wide Association Study, Matched-Pair Analysis, Polymorphism, Single Nucleotide, Population Groups, Research Design, Sequence Analysis",
author = "Lu, {Timothy Tehua} and Oscar Lao and Michael Nothnagel and Olaf Junge and Sandra Freitag-Wolf and Amke Caliebe and Miroslava Balascakova and Jaume Bertranpetit and Bindoff, {Laurence Albert} and David Comas and Gunilla Holmlund and Anastasia Kouvatsi and Milan Macek and Isabelle Mollet and Finn Nielsen and Walther Parson and Jukka Palo and Rafal Ploski and Antti Sajantila and Adriano Tagliabracci and Ulrik Gether and Thomas Werge and Fernando Rivadeneira and Albert Hofman and Uitterlinden, {Andr{\'e} Gerardus} and Christian Gieger and Heinz-Erich Wichmann and Andreas Ruether and Stefan Schreiber and Christian Becker and Peter N{\"u}rnberg and Nelson, {Matthew Roberts} and Manfred Kayser and Michael Krawczak",
year = "2009",
doi = "10.1038/ejhg.2008.266",
language = "English",
volume = "17",
pages = "967--75",
journal = "European Journal of Human Genetics",
issn = "1018-4813",
publisher = "nature publishing group",
number = "7",

}

RIS

TY - JOUR

T1 - An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population

AU - Lu, Timothy Tehua

AU - Lao, Oscar

AU - Nothnagel, Michael

AU - Junge, Olaf

AU - Freitag-Wolf, Sandra

AU - Caliebe, Amke

AU - Balascakova, Miroslava

AU - Bertranpetit, Jaume

AU - Bindoff, Laurence Albert

AU - Comas, David

AU - Holmlund, Gunilla

AU - Kouvatsi, Anastasia

AU - Macek, Milan

AU - Mollet, Isabelle

AU - Nielsen, Finn

AU - Parson, Walther

AU - Palo, Jukka

AU - Ploski, Rafal

AU - Sajantila, Antti

AU - Tagliabracci, Adriano

AU - Gether, Ulrik

AU - Werge, Thomas

AU - Rivadeneira, Fernando

AU - Hofman, Albert

AU - Uitterlinden, André Gerardus

AU - Gieger, Christian

AU - Wichmann, Heinz-Erich

AU - Ruether, Andreas

AU - Schreiber, Stefan

AU - Becker, Christian

AU - Nürnberg, Peter

AU - Nelson, Matthew Roberts

AU - Kayser, Manfred

AU - Krawczak, Michael

PY - 2009

Y1 - 2009

N2 - Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309,790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.

AB - Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309,790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.

KW - Faculty of Health and Medical Sciences

KW - DNA

KW - Europe

KW - Female

KW - Genetic Markers

KW - Genetic Variation

KW - Genome

KW - Genome-Wide Association Study

KW - Matched-Pair Analysis

KW - Polymorphism

KW - Single Nucleotide

KW - Population Groups

KW - Research Design

KW - Sequence Analysis

U2 - 10.1038/ejhg.2008.266

DO - 10.1038/ejhg.2008.266

M3 - Journal article

VL - 17

SP - 967

EP - 975

JO - European Journal of Human Genetics

JF - European Journal of Human Genetics

SN - 1018-4813

IS - 7

ER -

ID: 21336103