Fastanova: an efficient algorithm for genome-wide association study
Proceedings of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
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Motivation: Typical high-throughput genotyping techniques produce numerous missing calls that confound subsequent analyses, such as disease association studies. Common remedies for this problem include removing affected markers and/or samples or, otherwise, imputing the missing data. On small marker sets imputation is frequently based on a vote of the K-nearest-neighbor (KNN) haplotypes, but this technique is neither practical nor justifiable for large datasets. Results: We describe a data structure that supports efficient KNN queries over arbitrarily sized, sliding haplotype windows, and evaluate its use for genotype imputation. The performance of our method enables exhaustive exploration over all window sizes and known sites in large (150K, 8.3M) SNP panels. We also compare the accuracy and performance of our methods with competing imputation approaches. Availability: A free open source software package, NPUTE, is available at http://compgen.unc.edu/software, for non-commercial uses. Contact: mcmillan@cs.unc.edu