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Assessment of global phase uncertainty in case-control studies

BACKGROUND: In haplotype-based candidate gene studies a problem is that the genotype data are unphased, which results in haplotype ambiguity. The [Image: see text] measure [1] quantifies haplotype predictability from genotype data. It is computed for each individual haplotype, and for a measure of g...

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Autores principales: Uh, Hae-Won, Houwing-Duistermaat, Jeanine J, Putter, Hein, van Houwelingen, Hans C
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760579/
https://www.ncbi.nlm.nih.gov/pubmed/19751505
http://dx.doi.org/10.1186/1471-2156-10-54
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author Uh, Hae-Won
Houwing-Duistermaat, Jeanine J
Putter, Hein
van Houwelingen, Hans C
author_facet Uh, Hae-Won
Houwing-Duistermaat, Jeanine J
Putter, Hein
van Houwelingen, Hans C
author_sort Uh, Hae-Won
collection PubMed
description BACKGROUND: In haplotype-based candidate gene studies a problem is that the genotype data are unphased, which results in haplotype ambiguity. The [Image: see text] measure [1] quantifies haplotype predictability from genotype data. It is computed for each individual haplotype, and for a measure of global relative efficiency a minimum [Image: see text] value is suggested. Alternatively, we developed methods directly based on the information content of haplotype frequency estimates to obtain global relative efficiency measures: [Image: see text] and [Image: see text] based on A- and D-optimality, respectively. All three methods are designed for single populations; they can be applied in cases only, controls only or the whole data. Therefore they are not necessarily optimal for haplotype testing in case-control studies. RESULTS: A new global relative efficiency measure [Image: see text] was derived to maximize power of a simple test statistic that compares haplotype frequencies in cases and controls. Application to real data showed that our proposed method [Image: see text] gave a clear and summarizing measure for the case-control study conducted. Additionally this measure might be used for selection of individuals, who have the highest potential for improving power by resolving phase ambiguity. CONCLUSION: Instead of using relative efficiency measure for cases only, controls only or their combined data, we link uncertainty measure to case-control studies directly. Hence, our global efficiency measure might be useful to assess whether data are informative or have enough power for estimation of a specific haplotype risk.
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spelling pubmed-27605792009-10-13 Assessment of global phase uncertainty in case-control studies Uh, Hae-Won Houwing-Duistermaat, Jeanine J Putter, Hein van Houwelingen, Hans C BMC Genet Methodology Article BACKGROUND: In haplotype-based candidate gene studies a problem is that the genotype data are unphased, which results in haplotype ambiguity. The [Image: see text] measure [1] quantifies haplotype predictability from genotype data. It is computed for each individual haplotype, and for a measure of global relative efficiency a minimum [Image: see text] value is suggested. Alternatively, we developed methods directly based on the information content of haplotype frequency estimates to obtain global relative efficiency measures: [Image: see text] and [Image: see text] based on A- and D-optimality, respectively. All three methods are designed for single populations; they can be applied in cases only, controls only or the whole data. Therefore they are not necessarily optimal for haplotype testing in case-control studies. RESULTS: A new global relative efficiency measure [Image: see text] was derived to maximize power of a simple test statistic that compares haplotype frequencies in cases and controls. Application to real data showed that our proposed method [Image: see text] gave a clear and summarizing measure for the case-control study conducted. Additionally this measure might be used for selection of individuals, who have the highest potential for improving power by resolving phase ambiguity. CONCLUSION: Instead of using relative efficiency measure for cases only, controls only or their combined data, we link uncertainty measure to case-control studies directly. Hence, our global efficiency measure might be useful to assess whether data are informative or have enough power for estimation of a specific haplotype risk. BioMed Central 2009-09-14 /pmc/articles/PMC2760579/ /pubmed/19751505 http://dx.doi.org/10.1186/1471-2156-10-54 Text en Copyright © 2009 Uh et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Uh, Hae-Won
Houwing-Duistermaat, Jeanine J
Putter, Hein
van Houwelingen, Hans C
Assessment of global phase uncertainty in case-control studies
title Assessment of global phase uncertainty in case-control studies
title_full Assessment of global phase uncertainty in case-control studies
title_fullStr Assessment of global phase uncertainty in case-control studies
title_full_unstemmed Assessment of global phase uncertainty in case-control studies
title_short Assessment of global phase uncertainty in case-control studies
title_sort assessment of global phase uncertainty in case-control studies
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760579/
https://www.ncbi.nlm.nih.gov/pubmed/19751505
http://dx.doi.org/10.1186/1471-2156-10-54
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