Detection of homozygous deletions in tumor suppressor genes ranging from dozens to hundreds nucleotides

Authors

• LC Chang
• S Vural
• D Sonkin

Abstract

Tumor suppressor genes can be inactivated by several mechanisms and in majority of cases both alleles needs to be affected. One of the mechanisms of inactivation is due to deletions ranging from dozens to hundreds of nucleotides in size and such deletions are often missed by variant callers. HomDelDetect is a method which we developed in order to detect such homozygous deletions in cancer models such as cancer cell lines and patient tumor derived xenografts. This method can be applied to partial exome, whole exome, whole genome and RNA-seq sequencing data. We applied our method across panel of cancer cell lines and detected deletions which have been missed by variant callers, demonstrating the ability of HomDelDetect to improve annotations of tumor suppressor genes in cancer models.

Scientific Focus Area: Computational Biology

This page was last updated on Friday, March 26, 2021