Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays.

ABSTRACT:

Background

Microarray measurements are susceptible to a variety of experimental artifacts, some of which give rise to systematic biases that are spatially dependent in a unique way on each chip. It is likely that such artifacts affect many SNP arrays, but the normalization methods used in currently available genotyping algorithms make no attempt at spatial bias correction. Here, we propose an effective single-chip spatial bias removal procedure for Affymetrix 6.0 SNP arrays or platforms with similar design features. This procedure deals with both extreme and subtle biases and is intended to be applied before standard genotype calling algorithms.

Results

Application of the spatial bias adjustments on HapMap samples resulted in higher genotype call rates with equal or even bet

SUBMITTER: Chai HS 

PROVIDER: S-EPMC2910027 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature