Breakway

Breakway detects structural variation breakpoints from aligned genomic data to characterize genome architecture and mutations.

Key Features:

• Structural Variation Detection: Detects interchromosomal translocations, large deletions, insertions, small indels, and reports SV breakpoints from aligned sequencing data.
• High-Resolution Genomic Analysis: Leverages high-throughput sequencing to identify a comprehensive set of genetic alterations and was demonstrated to detect over 1,300 structural variations and numerous indels and SNVs in the U87MG glioma cell line.
• Integration with Alignment Tools: Utilizes the BFAST aligner and processes both mate-end and single-end reads to support accurate mapping and variant identification.

Scientific Applications:

• Cancer Genome Sequencing: Applied to tumor genomes to reveal the extent and nature of mutations, exemplified by the highly mutated U87MG glioma genome with disruptions in protein-coding sequences.
• Mutation Characterization: Identifies novel mutations including the 8 SNVs and 99 indels reported in the U87MG study.
• Comparative Genomic Analysis: Compares detected variants with known polymorphisms such as Illumina genotyping array data, achieving over 93% SNP detection accuracy at stringent thresholds.

Methodology:

Sequencing at greater than 30x genomic coverage using a 50-base mate-paired approach with a mean insert library size of 1.4 kb; alignment and variant analysis performed using BFAST on mate-end and single-end reads.