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While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been optimized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3\u2009K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be advisable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author.<\/jats:p>","DOI":"10.1016\/s1672-0229(08)60014-5","type":"journal-article","created":{"date-parts":[[2008,2,11]],"date-time":"2008-02-11T12:15:33Z","timestamp":1202732133000},"page":"256-259","source":"Crossref","is-referenced-by-count":5,"title":["Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays"],"prefix":"10.1093","volume":"5","author":[{"given":"Edward M.","family":"Smith","sequence":"first","affiliation":[{"name":"Human and Molecular Genetics Center, Medical College of Wisconsin , Milwaukee, WI, 53226 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jack","family":"Littrell","sequence":"additional","affiliation":[{"name":"Human and Molecular Genetics Center, Medical College of Wisconsin , Milwaukee, WI, 53226 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Olivier","sequence":"additional","affiliation":[{"name":"Human and Molecular Genetics Center, Medical College of Wisconsin , Milwaukee, WI, 53226 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,2,8]]},"reference":[{"key":"2024051008235408200_bib1","doi-asserted-by":"crossref","first-page":"2397","DOI":"10.1093\/bioinformatics\/btg332","article-title":"Algorithms for large-scale genotyping microarrays","volume":"19","author":"Liu","year":"2003","journal-title":"Bioinformatics"},{"key":"2024051008235408200_bib2","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/1471-2164-6-149","article-title":"SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data","volume":"6","author":"Huentelman","year":"2005","journal-title":"BMC Genomics"},{"key":"2024051008235408200_bib3","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkl475","article-title":"Genotyping and annotation of Affymetrix SNP arrays","volume":"34","author":"Lamy","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2024051008235408200_bib4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1093\/bioinformatics\/btl536","article-title":"SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays","volume":"23","author":"Hua","year":"2007","journal-title":"Bioinformatics"},{"key":"2024051008235408200_bib5","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/bioinformatics\/bti741","article-title":"A genotype calling algorithm for Affymetrix SNP arrays","volume":"22","author":"Rabbee","year":"2006","journal-title":"Bioinformatics"},{"key":"2024051008235408200_bib6","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1093\/bioinformatics\/btm131","article-title":"A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays","volume":"23","author":"Xiao","year":"2007","journal-title":"Bioinformatics"},{"key":"2024051008235408200_bib7","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/nbt821","article-title":"Multiplexed genotyping with sequence-tagged molecular inversion probes","volume":"21","author":"Hardenbol","year":"2003","journal-title":"Nat. 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