ASCAT

ASCAT estimates allele-specific copy number across tumor genomes while accounting for normal cell admixture and tumor aneuploidy to produce genome-wide allele-specific copy-number profiles from SNP array data.

Key Features:

• Allele-specific copy number analysis: Provides genome-wide allele-specific copy-number calls enabling identification of gains, losses, copy number-neutral events, and loss of heterozygosity (LOH).
• Adjustment for tumor ploidy and cell admixture: Simultaneously estimates and adjusts for tumor ploidy and nonaberrant (normal) cell admixture to correct copy-number profiles from heterogeneous samples.
• SNP array compatibility: Supports analysis of Illumina and Affymetrix SNP array data and can operate with or without matching germline samples.
• ASCAT profiles: Generates genome-wide allele-specific copy-number profiles ("ASCAT profiles") for each tumor sample.
• Aggregation to frequency distributions: Aggregates ASCAT profiles to derive genomic frequency distributions of gains, losses, LOH, and copy number-neutral events across cohorts.
• Allelic skewness mapping: Enables construction of a genome-wide map of allelic skewness to identify loci with preferential loss or gain of specific alleles.

Scientific Applications:

• Cancer genomics research: Enables investigation of genome-wide copy-number alterations and allelic imbalance in cancers, including breast carcinoma.
• Subtype characterization: Supports comparison of aberrant tumor cell fraction, ploidy, frequencies of gains, losses, LOH, and copy number-neutral events between molecular subtypes.
• Genomic instability studies: Facilitates analysis of aneuploidy and LOH patterns and their role in tumor development and progression.

Methodology:

Processes Illumina or Affymetrix SNP array data (with or without matched germline), simultaneously estimates and adjusts tumor ploidy and nonaberrant cell admixture, produces genome-wide allele-specific copy-number profiles (ASCAT profiles), aggregates profiles into genomic frequency distributions, and constructs genome-wide allelic skewness maps.