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Automated SNP genotype clustering algorithm to improve data completeness in high-throughput SNP genotyping datasets from custom arrays
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Smith, Edward M., Littrell, Jack and Olivier, M. (Michael) (2007) Automated SNP genotype clustering algorithm to improve data completeness in high-throughput SNP genotyping datasets from custom arrays. Genomics Proteomics & Bioinformatics, Vol.5 (No.3-4). pp. 256-259. doi:10.1016/S1672-0229(08)60014-5 ISSN 1672-0229.
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Official URL: http://dx.doi.org/10.1016/S1672-0229(08)60014-5
Abstract
High-throughput SNP genotyping platforms use automated genotype calling algorithms to assign genotypes. 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 3K 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.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) > Biological Sciences ( -2010) | ||||
Library of Congress Subject Headings (LCSH): | Genetics -- Computer programs, Genetic algorithms, Genetic polymorphisms | ||||
Journal or Publication Title: | Genomics Proteomics & Bioinformatics | ||||
Publisher: | Elsevier Ltd | ||||
ISSN: | 1672-0229 | ||||
Official Date: | 2007 | ||||
Dates: |
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Volume: | Vol.5 | ||||
Number: | No.3-4 | ||||
Page Range: | pp. 256-259 | ||||
DOI: | 10.1016/S1672-0229(08)60014-5 | ||||
Status: | Peer Reviewed | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Funder: | National Institutes of Health (U.S.) (NIH) | ||||
Grant number: | 1RO1HL74168 (NIH) |
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