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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. 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 |
|---|---|
| Subjects: | Q Science > QH Natural history > QH426 Genetics Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software |
| Divisions: | Faculty of 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 |
| Date: | 2007 |
| Volume: | Vol.5 |
| Number: | No.3-4 |
| Page Range: | pp. 256-259 |
| Identification Number: | 10.1016/S1672-0229(08)60014-5 |
| Status: | Peer Reviewed |
| Access rights to Published version: | Open Access |
| Funder: | National Institutes of Health (U.S.) (NIH) |
| Grant number: | 1RO1HL74168 (NIH) |
| References: | 1. Liu WM, et al. Algorithms for large-scale genotyping microarrays. Bioinformatics 2003;19:2397– 2403. [PubMed: 14668223] 2. Huentelman MJ, et al. SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data. BMC Genomics 2005;6:149. [PubMed: 16262895] 3. Lamy P, et al. Genotyping and annotation of Affymetrix SNP arrays. Nucleic Acids Res 2006;34:e100. [PubMed: 16899450] 4. Hua J, et al. SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. Bioinformatics 2007;23:57–63. [PubMed: 17062589] 5. Rabbee N, Speed TP. A genotype calling algorithm for Affymetrix SNP arrays. Bioinformatics 2006;22:7–12. [PubMed: 16267090] 6. Xiao Y, et al. A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. Bioinformatics 2007;23:1459–1467. [PubMed: 17459966] 7. Hardenbol P, et al. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol 2003;21:673–678. [PubMed: 12730666] 8. Hardenbol P, et al. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res 2005;15:269–275. [PubMed: 15687290] 9. Kissebah AH, et al. Quantitative trait loci on chromosomes 3 and 17 influence phenotypes of the metabolic syndrome. Proc. Natl. Acad. Sci. USA 2000;97:14478–14483. [PubMed: 11121050] 10. Sonnenberg GE, et al. Genetic determinants of obesity-related lipid traits. J. Lipid Res 2004;45:610– 615. [PubMed: 14754912] 11. Smith EM, et al. Comparison of linkage disequilibrium patterns between the HapMap CEPH samples and a family-based cohort of Northern European descent. Genomics 2006;88:407–414. [PubMed: 16713172] 12. Olivier M, et al. High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. Nucleic Acids Res 2002;30:e53. [PubMed: 12060691] 13. McPeek MS, et al. Best linear unbiased allele-frequency estimation in complex pedigrees. Biometrics 2004;60:359–367. [PubMed: 15180661] |
| URI: | http://wrap.warwick.ac.uk/id/eprint/3629 |
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