CNAHap

CNAHap estimates allele-specific copy numbers in tumor genomes and phases germline variants across copy-number-imbalanced segments to resolve long germline phasing blocks using allele imbalance in cancer samples.

Key Features:

• Allele-specific copy number estimation: Estimates allele-specific copy numbers in tumor samples.
• Germline haplotyping along imbalanced segments: Performs germline haplotyping (phasing) along segments with allelic imbalance.
• Use of large CNV segments from solid tumors: Leverages large copy number variant (CNV) segments prevalent in solid tumors to extend germline phasing blocks.
• Phasing via allele imbalance analysis: Resolves long germline phasing blocks by analyzing allele imbalance within tumor data.
• Phasing block metrics: Generates extensive phasing blocks with reported in silico N50 = 25M and N90 = 7M.
• Improved allele-specific calling accuracy: Demonstrates higher accuracy in allele-specific copy number calling compared to benchmark tools.

Scientific Applications:

• Tumor copy-number and haplotype analysis: Enables allele-specific copy number and haplotype characterization in cancer genomics studies.
• Germline phasing using tumor data: Facilitates reconstruction of long germline phasing blocks for human genetics by exploiting tumor allele imbalance.
• Discovery of recurrent amplifications and case studies: Applicable to studies such as Hepatocellular carcinoma, where it identified significant phase blocks and recurrent amplifications in the Olfactory receptor family.

Methodology:

Estimation of allele-specific copy numbers and phasing of germline variants is performed by analyzing allele imbalance within large CNV segments in tumor data.