137838 20240604120453.0 1471-2105 ISSN 10.1186/s12859-015-0521-4 doi pmid:25880419 pmid pmc:PMC4367953 pmc altmetric:3789126 altmetric DZNE-2020-04160 English 610 Lacour, Andre P:(DE-2719)2810305 0 First author dzne Novel genetic matching methods for handling population stratification in genome-wide association studies. Heidelberg 2015 Springer online Crossref Springer Science and Business Media LLC 2015-03-14 print Crossref Springer Science and Business Media LLC 2015-12-01 article DRIVER Output Types/Journal article DataCite Journal Article journal journal PUB:(DE-HGF)16 1717420545_5455 PUB:(DE-HGF) ARTICLE BibTeX JOURNAL_ARTICLE ORCID Journal Article 0 EndNote A usually confronted problem in association studies is the occurrence of population stratification. In this work, we propose a novel framework to consider population matchings in the contexts of genome-wide and sequencing association studies. We employ pairwise and groupwise optimal case-control matchings and present an agglomerative hierarchical clustering, both based on a genetic similarity score matrix. In order to ensure that the resulting matches obtained from the matching algorithm capture correctly the population structure, we propose and discuss two stratum validation methods. We also invent a decisive extension to the Cochran-Armitage Trend test to explicitly take into account the particular population structure.We assess our framework by simulations of genotype data under the null hypothesis, to affirm that it correctly controls for the type-1 error rate. By a power study we evaluate that structured association testing using our framework displays reasonable power. We compare our result with those obtained from a logistic regression model with principal component covariates. Using the principal components approaches we also find a possible false-positive association to Alzheimer's disease, which is neither supported by our new methods, nor by the results of a most recent large meta analysis or by a mixed model approach.Matching methods provide an alternative handling of confounding due to population stratification for statistical tests for which covariates are hard to model. As a benchmark, we show that our matching framework performs equally well to state of the art models on common variants. 345 - Population Studies and Genetics (POF3-345) G:(DE-HGF)POF3-345 POF3-345 POF III 0 344 - Clinical and Health Care Research (POF3-344) G:(DE-HGF)POF3-344 POF3-344 POF III 1 2015-03-14 Crossref http://creativecommons.org/licenses/by/2.0 Dataset connected to CrossRef, PubMed, Alzheimer Disease: genetics MeSH Case-Control Studies MeSH Cluster Analysis MeSH Genetics, Population MeSH Genome-Wide Association Study: methods MeSH Genotype MeSH Humans MeSH Logistic Models MeSH Population Groups MeSH Schüller, Vitalia P:(DE-2719)2810897 1 dzne Drichel, Dmitriy P:(DE-2719)2740473 2 dzne Herold, Christine P:(DE-2719)2802016 3 dzne Jessen, Frank P:(DE-2719)2000032 4 dzne Leber, Markus P:(DE-HGF)0 5 Maier, Wolfgang P:(DE-HGF)0 6 Noethen, Markus M P:(DE-HGF)0 7 Ramirez, Alfredo P:(DE-HGF)0 8 Vaitsiakhovich, Tatsiana P:(DE-HGF)0 9 Becker, Tim P:(DE-2719)2501867 10 Last author dzne 10.1186/s12859-015-0521-4 : Springer Science and Business Media LLC, 2015-03-14 1 84 journal-article Crossref BMC Bioinformatics 16 2015 1471-2105 10.1186/s12859-015-0521-4 Vol. 16, no. 1, p. 84 PERI:(DE-600)2041484-5 1 16:1<84 84 BMC bioinformatics 16 2015 1471-2105 OpenAccess http://pub.dzne.de/record/137838/files/DZNE-2020-04160.pdf OpenAccess pdfa http://pub.dzne.de/record/137838/files/DZNE-2020-04160.pdf?subformat=pdfa Pubmed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367953 oai:pub.dzne.de:137838 openaire open_access VDB driver dnbdelivery Deutsches Zentrum für Neurodegenerative Erkrankungen I:(DE-588)1065079516 DZNE 0 P:(DE-2719)2810305 Deutsches Zentrum für Neurodegenerative Erkrankungen I:(DE-588)1065079516 DZNE 1 P:(DE-2719)2810897 Deutsches Zentrum für Neurodegenerative Erkrankungen I:(DE-588)1065079516 DZNE 2 P:(DE-2719)2740473 Deutsches Zentrum für Neurodegenerative Erkrankungen I:(DE-588)1065079516 DZNE 3 P:(DE-2719)2802016 Deutsches Zentrum für Neurodegenerative Erkrankungen I:(DE-588)1065079516 DZNE 4 P:(DE-2719)2000032 Deutsches Zentrum für Neurodegenerative Erkrankungen I:(DE-588)1065079516 DZNE 10 P:(DE-2719)2501867 DE-HGF Gesundheit Erkrankungen des Nervensystems G:(DE-HGF)POF3-340 G:(DE-HGF)POF3-345 G:(DE-HGF)POF3 G:(DE-HGF)POF3-300 G:(DE-HGF)POF Population Studies and Genetics 0 DE-HGF Gesundheit Erkrankungen des Nervensystems G:(DE-HGF)POF3-340 G:(DE-HGF)POF3-344 G:(DE-HGF)POF3 G:(DE-HGF)POF3-300 G:(DE-HGF)POF Clinical and Health Care Research 1 2015 DBCoverage StatID:(DE-HGF)0200 StatID SCOPUS Creative Commons Attribution CC BY (No Version) LIC:(DE-HGF)CCBYNV V:(DE-HGF) DOAJ DBCoverage StatID:(DE-HGF)1050 StatID BIOSIS Previews DBCoverage StatID:(DE-HGF)0600 StatID Ebsco Academic Search JCR StatID:(DE-HGF)0100 StatID BMC BIOINFORMATICS : 2017 DBCoverage StatID:(DE-HGF)0501 StatID DOAJ Seal DBCoverage StatID:(DE-HGF)0500 StatID DOAJ WoS StatID:(DE-HGF)0111 StatID Science Citation Index Expanded DBCoverage StatID:(DE-HGF)0150 StatID Web of Science Core Collection IF < 5 StatID:(DE-HGF)9900 StatID OpenAccess StatID:(DE-HGF)0510 StatID Peer Review StatID:(DE-HGF)0030 StatID ASC DBCoverage StatID:(DE-HGF)0310 StatID NCBI Molecular Biology Database DBCoverage StatID:(DE-HGF)0300 StatID Medline DBCoverage StatID:(DE-HGF)0320 StatID PubMed Central DBCoverage StatID:(DE-HGF)0199 StatID Clarivate Analytics Master Journal List I:(DE-2719)1013007 GenomMathematik Genomische Mathematik in der Neuroepidemiologie 0 I:(DE-2719)1610003 AG Roes Implementation Science & Person-Centered Dementia Care 1 I:(DE-2719)1011102 AG Jessen Clinical Alzheimer’s Disease Research 2 journal VDB UNRESTRICTED I:(DE-2719)1013007 I:(DE-2719)1610003 I:(DE-2719)1011102 FullTexts -- missing cx lookup -- 10.1038/nrg1521 Crossref 10.1038/nrg1521 -- missing cx lookup -- 10.1371/journal.pcbi.1002822 Crossref 10.1371/journal.pcbi.1002822 -- missing cx lookup -- 10.1038/nature08494 Crossref 10.1038/nature08494 -- missing cx lookup 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