Efficient Detection of Copy Number Mutations in PMS2 Exons with Close Homologs: Detection of copy number variants in 3 ’ PMS2 exons

Detection of 3 ’ PMS2 copy number mutations that cause Lynch syndrome is difficult, because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequence reads using PMS2 targets, maps sequences randomly amongst regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ra nges.

Source: Journal of Molecular Diagnostics - May 21, 2018 Category: Pathology Authors: Daniel S. Herman, Christina Smith, Chang Liu, Cecily P. Vaughn, Selvi Palaniappan, Colin C. Pritchard, Brian H. Shirts Tags: Regular Article Source Type: research