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. 2007 Mar 14;2(3):e287. doi: 10.1371/journal.pone.0000287

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Smemo, Borevitz.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Probe set layout for Affymetrix 100K chip. Each SNP is assayed with 20 perfect match 25-mer oligonucleotides. The additional 20 mismatch oligonucleotides are not shown. Both sense and antisense strands are interrogated with 5 features for each allele that differ only at the SNP nucleotide, denoted A and B. The position of the SNP within the 25mer features is shifted from the central nucleotide (boxed, “0”) by 1 or 2 nucleotides in either direction. For this SNP (rs836702), and sample (NA11994) allele B has a stronger normalized hybridization signal, as indicated by the lighter color and higher hybridization values for most probes. Generally the central base and a particular strand have more discrimination specificity. The genotype for this individual was called as BB with full and all reduced probesets. This is clear when many other samples are tested such that the range of intensity categories is known.