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

PloS One
Hans BinderTorsten Glomb

Abstract

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. 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 the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G) and the particular type of mismatched p...Continue Reading

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Citations

Jan 12, 2013·Nucleic Acids Research·Andrew HarrisonAlexander E Pozhitkov
Jun 12, 2013·Journal of the American Chemical Society·Jeffrey R ViereggNiles A Pierce
Sep 3, 2016·Bioinformatics·Olga V MatveevaSvetlana A Shabalina

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Methods Mentioned

BETA
genotyping
chip
array technology

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