Patchwork

Patchwork performs allele-specific copy number analysis and loss-of-heterozygosity characterization from whole-genome sequencing (WGS) BAM data to profile cancer genomes.

Key Features:

• Input Flexibility: Accepts WGS BAM files and processes sequencing datasets without requiring prior knowledge of average ploidy or tumor cell content.
• Aneuploid Sample Analysis: Determines copy numbers in aneuploid samples and tolerates moderate sequence coverage and tumor cell content.
• Allele-specific Analysis: Focuses on allele-specific copy number changes and loss-of-heterozygosity events.
• Comprehensive Genomic Characterization: Analyzes homologous sequences across the genome to provide insights into genomic alterations ranging from point mutations to large-scale chromosomal changes.

Scientific Applications:

• Tumor Genomic Profiling: Provides copy number variation and LOH information to construct comprehensive genomic profiles of tumor samples.
• Research on Aneuploidy: Enables analysis of cancers characterized by complex chromosomal rearrangements and aneuploid genomes.
• Precision Oncology: Supplies detailed genomic alteration data that can inform personalized treatment strategies and investigations of drug resistance.

Methodology:

Operates on whole-genome sequencing BAM input using algorithms that infer allele-specific copy number and loss-of-heterozygosity without prior knowledge of average ploidy or tumor cell content, and that function with low or moderate coverage and low tumor purity.