Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows.

Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Research Abstract Details 

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Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Abstract Text:

Adam Roberts,Leonard McMillan,Wei Wang,Joel Parker,Ivan Rusyn,David Threadgill,

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.

Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Publishing Authors By Initials

A Roberts,L McMillan,W Wang,J Parker,I Rusyn,D Threadgill,

For similar genetic phenomena: variation (genetics) research abstracts see: genetic phenomena: variation (genetics) research

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Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Bioinformatics (Oxford, England)

VOLUME: 23

Page Numbers: i401-7

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 1

MONTH: Jul

YEAR: 2007

Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Information

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LANGUAGE: eng

NlmUniqueID: 9808944

Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Keywords Mesh Terms:

KEYWORDS: Variation (Genetics)

MESH TERMS: genetics

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Grant and Affiliation Information for Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows.

AFFILIATION: Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA.

Country: England

AGENCY: United States NCI

GRANT: U01CA105417

ACRONYM: CA

MEDLINETA: Bioinformatics

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