Targeted Haplotype Phasing of PCR Products. Homo sapiens

In this Application Note, we demonstrate that the TELL-Seq WGS Library Prep kit can phase PCR products of varying sizes, both as single products and as mixed amplicons. For our tests, we focused on two clinically relevant examples. First, we phased a pair of PIK3CA mutations from 1.8 and 3.4 kb fragments amplified from breast cancer HCC202 cDNA. The cis/trans configuration of these two mutations has prognostic value and predicts susceptibility to treatment. Second, we phased seven genomic positions in the SCN10A locus from 13 kb fragments along with smaller 2.7, 3.9, and 4.1 kb fragments amplified from NA12878 gDNA. The cis/trans configurations at these seven sites are associated with a risk for heart arrythmia and sudden cardiac death. We sequenced PIK3CA and SCN10A libraries on an Illumina MiSeq instrument and processed the read outputs using UST software-Tell-Read and Tell-Sort. Data visualization was based on the Integrative Genomics Viewer assisted by UST software. Taken together, our data show robust phasing of PCR products using the TELL-Seq WGS Library Prep kit with highly accurate and low-cost NGS data collection.