R package falcon (finding somatic allele-specific copy number changes by NGS of tumors with matched normals.

falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models that copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases.

Summary #

Introduction #

정확한 ASCN 추정은 tumor purity와 malignant cell ploidy 추정을 가능하게 한다. 예를 들어 ABSOLUTE는 ASCN을 입력으로 받는다.

Patchwork는 NGS에서 ASCN을 추정하는데, 처음 total coverage으로 segment를 나눈 후, 각 segment에 대해 ASCN을 추정한다. - total copy number의 변화가 없는 gene conversion 같은 것은 못찾는다.

falcon은 segment를 나누는데, allele specific coverage를 이용한다.

Materials and Methods #

Materials #

Bivariate mixed binomial change-point model for ASCNs in tumor and matched normal #

Results #

Clonal analysis of a late-stage colorectal adenocarcinoma #

Sensitivity analysis: performance under varying normal cell contamination studied by in silico spike-in experiments #

Conclusion #

Suggested Pages #

• 0.025 CODEX: a normalization and copy number variation detection method for whole exome sequencing
• 0.025 Programming language
• 0.025 April 18
• 0.025 Python
• 0.025 Briefings in Bioinformatics
• 0.025 April 8
• 0.025 Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control
• 0.025 CNVkit
• 0.025 Frontiers in Genetics
• 0.025 GATK
• More suggestions...