SNiPer 500K: A Novel SNP Genotype Calling Algorithm
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abstract
The fast development in high-throughput single nucleotide polymorphism (SNP) genotyping technology provides unprecedented power for genome-wide SNP association studies. However, inaccurate genotyping can lead to false association between markers and phenotype. We introduce a new SNP genotyping scheme, SNiPer 500K, for Affymetrix 500K GeneChip. SNiPer 500K designs a parametric classifier for each SNP, by using expectation-maximization algorithm to estimate the parameters. A quality index provided by SNiPer 500K shows that it can reliably genotype about 65% of all SNPs, with superior call rate, better Hardy-Weinberg Equilibrium and reproducibility. SNiPer 500K provides a good balance between coverage and accuracy for high-throughput SNP genotyping and would prove to be an invaluable tool for genome-wide association study. 2006 IEEE.
name of conference
2006 IEEE/NLM Life Science Systems and Applications Workshop
2006 IEEE/NLM Life Science Systems and Applications Workshop
author list (cited authors)
Hua, J., Craig, D. W., Brun, M., Webster, J., Zismann, V., Joshipura, K., ... Stephan, D. A.
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Hua, Jianping||Craig, David W||Brun, Marcel||Webster, Jennifer||Zismann, Victoria||Joshipura, Keta||Huentelman, Matthew||Dougherty, Edward R||Stephan, Dietrich A