Multipoint identity-by-descent computations for single-point polymorphism and microsatellite maps

Anthony L. Hinrichs, Sarah Bertelsen, Laura J. Bierut, Gerald Dunn, Carol H. Jin, John S. Kauwe, Brian K. Suarez

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Abstract

We used the LOKI software to generate multipoint identity-by-descent matrices for a microsatellite map (with 31 markers) and two single-nucleotide polymorphism (SNP) maps to examine information content across chromosome 7 in the Collaborative Study on the Genetics of Alcoholism dataset. Despite the lower information provided by a single SNP, SNP maps overall had higher and more uniform information content across the chromosome. The Affymetrix map (578 SNPs) and the Illumina map (271 SNPs) provided almost identical information. However, increased information has a computational cost: SNP maps require 100 times as many iterations as microsatellites to produce stable estimates.

Original languageEnglish
Article numberS34
JournalBMC genetics
Volume6
Issue numberSUPPL.1
DOIs
StatePublished - Dec 30 2005

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    Hinrichs, A. L., Bertelsen, S., Bierut, L. J., Dunn, G., Jin, C. H., Kauwe, J. S., & Suarez, B. K. (2005). Multipoint identity-by-descent computations for single-point polymorphism and microsatellite maps. BMC genetics, 6(SUPPL.1), [S34]. https://doi.org/10.1186/1471-2156-6-S1-S34