Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays

(整期优先)网络出版时间:2007-03-13
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High-throughputSNPgenotypingplatformsuseautomatedgenotypecallingalgo-rithmstoassigngenotypes.Whilethesealgorithmsworkefficientlyforinpidualplatforms,theyarenotcompatiblewithotherplatforms,andhaveinpidualbiasesthatresultinmissedgenotypecalls.HerewepresentdataontheuseofasecondcomplementarySNPgenotypeclusteringalgorithm.ThealgorithmwasoriginallydesignedforinpidualfluorescentSNPgenotypingassays,andhasbeenopti-mizedtopermittheclusteringoflargedatasetsgeneratedfromcustom-designedAffymetrixSNPpanels.Inananalysisofdatafroma3Karraygenotypedon1,560samples,theadditionalanalysisincreasedtheoverallnumberofgenotypesbyover45,000,significantlyimprovingthecompletenessoftheexperimentaldata.Thisanalysissuggeststhattheuseofmultiplegenotypecallingalgorithmsmaybead-visableinhigh-throughputSNPgenotypingexperiments.ThesoftwareiswritteninPerlandisavailablefromthecorrespondingauthor.