The Illumina SNP detection assay [16,17] utilizes allele-specific extension and ligation chemistries. Total genomic DNA is bound to paramagnetic beads. For each SNP, three oligonucleotides are used to interrogate the locus. Two allele-specific oligonucleotides (ASO) each incorporate one of the two possible nucleotides. The third locus-specific oligonucleotide (LSO) anneals 1 to 20 bases downstream of the SNP. This LSO contains a locus-specific address that binds to a complementary address on beads contained in a Sentrix Array Matrix. Specific extension of the complementary ASO occurs joining to the LSO by ligation. Three universal PCR primers are used to amplify the ligated product and incorporate allele-specific fluorescent dyes. Up to 1,536 loci may be multiplexed in one reaction. The Linkage III Panel contains over 4,600 SNP markers distributed evenly across the human genome.
