19629167

Source:http://linkedlifedata.com/resource/pubmed/id/19629167

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0004083, umls-concept:C0022885, umls-concept:C0034378, umls-concept:C0039593, umls-concept:C0079809, umls-concept:C0185125, umls-concept:C0237401, umls-concept:C0332306, umls-concept:C0702111, umls-concept:C1285573, umls-concept:C1511726, umls-concept:C1516048, umls-concept:C2350277, umls-concept:C2603343
pubmed:issue	7
pubmed:dateCreated	2009-7-24
pubmed:abstractText	Allele transmissions in pedigrees provide a natural way of evaluating the genotyping quality of a particular proband in a family-based, genome-wide association study. We propose a transmission test that is based on this feature and that can be used for quality control filtering of genome-wide genotype data for individual probands. The test has one degree of freedom and assesses the average genotyping error rate of the genotyped SNPs for a particular proband. As we show in simulation studies, the test is sufficiently powerful to identify probands with an unreliable genotyping quality that cannot be detected with standard quality control filters. This feature of the test is further exemplified by an application to the third release of the HapMap data. The test is ideally suited as the final layer of quality control filters in the cleaning process of genome-wide association studies. It identifies probands with insufficient genotyping quality that were not removed by standard quality control filtering.
pubmed:grant	http://linkedlifedata.com/resource/pubmed/grant/P01 HL083069, http://linkedlifedata.com/resource/pubmed/grant/R01 MH09532-08, http://linkedlifedata.com/resource/pubmed/grant/T32 HL07427, http://linkedlifedata.com/resource/pubmed/grant/U01 HL089856
pubmed:commentsCorrections	http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-10782012, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-10825280, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-11055368, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-11443542, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-11791214, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-11791215, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-12446984, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-12587097, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-14748013, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-15716906, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-15761122, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-16614226, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-16715096, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-16715099, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17068223, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17293876, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17401363, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17401366, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17435756, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17463246, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17463248, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17463249, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17476111, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17529967, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17529973, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17554300, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17562002, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17728769, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-17943122, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-18388693, http://linkedlifedata.com/resource/pubmed/commentcorrection/19629167-8447318
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/101239074
pubmed:citationSubset	IM
pubmed:status	MEDLINE
pubmed:month	Jul
pubmed:issn	1553-7404
pubmed:author	pubmed-author:FardoDavid WDW, pubmed-author:Ionita-LazaIulianaI, pubmed-author:LangeChristophC
pubmed:issnType	Electronic
pubmed:volume	5
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	e1000572
pubmed:dateRevised	2009-11-18
pubmed:meshHeading	pubmed-meshheading:19629167-Genome-Wide Association Study, pubmed-meshheading:19629167-Genotype, pubmed-meshheading:19629167-Humans, pubmed-meshheading:19629167-Linkage Disequilibrium, pubmed-meshheading:19629167-Pedigree, pubmed-meshheading:19629167-Polymorphism, Single Nucleotide, pubmed-meshheading:19629167-Software
pubmed:year	2009
pubmed:articleTitle	On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.
pubmed:affiliation	Department of Biostatistics, University of Kentucky College of Public Health, Lexington, Kentucky, United States of America.
pubmed:publicationType	Journal Article, Research Support, N.I.H., Extramural