SNP array design. (A) Design for querying a locus. Target sequences (lowercase) for both A and B alleles are identical except for the polymorphic base (uppercase). Five positions at or near the polymorphic locus, indicated by −4, −1, 0, +1 and +4, are queried. (Solid line) Probe sequences on the SNP array that are complementary to the targets; (squares) set of four probes (each probe 20 bases in length), referred to as a tiling, identical except for the single base that is either A, C, G, or T; (closed squares) perfect match (PM) probes for the target sample; (open squares) mismatch (MM) probes for the target sample. (B) Block design for genotyping of two alleles. The A-allele (A) and B-allele (B) probes are arranged adjacent to each other at each position (−4, −1, 0, +1 and +4). The A- and B-allele tiles at position −1, −4, +1, or +4 define a miniblock, whereas for the polymorphic base (position 0) the single tile defines a miniblock. One strand of a marker is represented by these five miniblocks, defining a block.
