Detection of homozygous deletions in tumor-suppressor genes ranging from dozen to hundreds nucleotides in cancer models.
Tumor-suppressor genes can be inactivated by several mechanisms and, in a majority of cases, both alleles need to be affected. One of the mechanisms of inactivation is due to deletions ranging from dozen to hundreds of nucleotides; such deletions are often missed by variant callers. HomDelDetect is a method to detect such homozygous deletions in cancer models, such as cancer cell lines and potentially patient tumor-derived xenografts. This method can be applied to partial exome, whole-exome sequencing, whole-genome sequencing, and RNA-seq data. We applied our method across a panel of CCLE cancer cell lines and observed good concordance with SNP array-based analysis and also detected deletions that have been missed by variant callers and by SNP arrays, demonstrating the ability of HomDelDetect to improve the annotations of tumor-suppressor genes in cancer models.
['Chang|Lun-Ching|LC|', 'Vural|Suleyman|S|', 'Sonkin|Dmitriy|D|0000-0002-1649-0652']
D045744:Cell Line, Tumor D059472:Exome D015870:Gene Expression D020868:Gene Silencing D016153:Genes, Suppressor D023281:Genomics D005838:Genotype D006720:Homozygote D006801:Humans D008954:Models, Biological D009369:Neoplasms D020411:Oligonucleotide Array Sequence Analysis D017384:Sequence Deletion D000073359:Whole Exome Sequencing
homozygous deletions tumor-suppressor genes cancer models cancer cell lines CCLE