Fig 1. Schematic of the work flow for the next-generation sequencing (NGS) BRCA1/ BRCA2 assay using both the MiSeq and the Personal Gene Machine (PGM) platforms.

For the MiSeq platform, variant calling was performed initially with the vendor-supplied MiSeq Reporter software and then with the Quest Sequencing Analysis Pipeline (QSAP). For the PGM platform, the vendor-supplied Torrent Suite variant-calling software was used.