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PLOS ONE  2012 

Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays

DOI: 10.1371/journal.pone.0007862

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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.

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