Mismatch and G-stack modulated probe signals on SNP microarrays.

ABSTRACT:

Background

Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates.

Methodology/principal findings

The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along

SUBMITTER: Binder H 

PROVIDER: S-EPMC2775684 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature