Multiplexing PCR and subsequent amplicon fragmentation results, prior to APEX reaction on HapMap Chip. (a) Standard multiplex PCR from a single Coriell DNA sample using optimally-designed primers [Additional files 1 &2] within seven unique multiplex groups (lanes 1–7; lane M shows 100 bp DNA ladder markers), showing wide range of amplicon sizes across the 50 SNP loci. (b) Purification, concentration and fragmentation of standard PCR amplicons. Lane 1 represents an aliquot of concentrated mixture of all seven multiplex products shown in Fig. 1a. Lane 2 shows the fragmentation result, generating single-stranded nucleic acid of 30–100 base length. (c) Multiplex PCR amplification of all 50 SNP loci in a single reaction tube using new PCR primer set [Additional file 6], showing 50-plex PCR products (individual SNP loci amplicons are unresolvable by agarose gel electrophoresis) from two Coriell DNA samples (lanes 1 & 2), plus a negative PCR control (lane 3). (d) Fragmentation of 50-plex PCR amplicons from aliquots of lane 1 & lane 2 samples shown in Fig. 1c.