BreakDancer

Overview

BreakDancer is a computational tool for detecting genome-wide structural variation (SV) from paired-end sequencing data. It identifies candidate SVs — including deletions, insertions, inversions, and translocations — by analyzing anomalously mapped read pairs whose insert size, orientation, or mapping location deviate from the expected library distribution. BreakDancer has been widely used in cancer genomics studies as a SV discovery algorithm applied to whole-genome sequencing data.

Used by

• Used alongside BamBam as a structural variant caller in the TCGA GBM 2013 whole-genome sequencing analysis (n=42 tumor/normal pairs); together identified 238 high-confidence somatic rearrangements including 49 interchromosomal, 125 intrachromosomal, and 64 intragenic events, and one case of chromothripsis PMID:24120142
• BreakDancer used for structural-variant detection in the TCGA esophageal/stomach study of 164 oesophageal carcinomas and 359 gastric adenocarcinomas PMID:28052061.

Notes

• BreakDancer is based on anomalously mapped read pairs; it complements soft-clip–based callers (e.g., CREST) and assembly-based approaches.
• False-positive rates can be high in low-coverage WGS; orthogonal validation (e.g., PCR, long-read sequencing) is recommended for candidate SVs.
• Often run in ensemble with other callers (BamBam, DELLY, CREST) to increase specificity.

Sources

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