Determination of <i>cis</i> vs <i>trans</i> orientation using next-generation sequencing (NGS).

<p>The Integrative Genomics Viewer (IGV) graphic report is from a patient with 2 adjacent variants on a single DNA molecule visualized with NGS on the MiSeq/QSAP platform. The <i>cis</i> orientation is clearly visible, as each strand contains either both or neither of the mutations.</p

Alignment of a 64 bp-deletion (41246533-41246596del; c.952_1015del) in a validation sample.

<p>The Integrative Genomics Viewer (IGV) graphic reports show detection of the deletion using MiSeq platform with QSAP (panel A) but not the PGM platform with Torrent Suite variant calling software (panel B).</p

Alignment of a 40-bp deletion in <i>BRCA1</i> (deletion c.1175_1214del40) in a validation sample.

<p>The Integrative Genomics Viewer (IGV) graphic report shows detection of the mutation with the PGM platform with Torrent Suite variant calling (panel A) but not the MiSeq platform with MiSeq Reporter (panel B). Use of QSAP with the MiSeq platform allowed detection of the deletion (panel C).</p

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

<p>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.</p