Equalizer reduces SNP bias in Affymetrix microarrays.

ABSTRACT:

Background

Gene expression microarrays measure the levels of messenger ribonucleic acid (mRNA) in a sample using probe sequences that hybridize with transcribed regions. These probe sequences are designed using a reference genome for the relevant species. However, most model organisms and all humans have genomes that deviate from their reference. These variations, which include single nucleotide polymorphisms, insertions of additional nucleotides, and nucleotide deletions, can affect the microarray's performance. Genetic experiments comparing individuals bearing different population-associated single nucleotide polymorphisms that intersect microarray probes are therefore subject to systemic bias, as the reduction in binding efficiency due to a technical artifact is confounded with

SUBMITTER: Quigley D 

PROVIDER: S-EPMC4518889 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature