IchorCNA

Overview

IchorCNA is a tool for estimating tumor fraction and large-scale copy-number alterations from ultra-low-coverage whole-genome sequencing data (as low as 0.1×). It uses a probabilistic model (hidden Markov model) that jointly estimates tumor purity and copy-number states, making it particularly useful for cell-free DNA (liquid biopsy) applications and for tracking tumor evolution in cell-line experiments.

Used by

• Applied to low-coverage MiSeq WGS data from AALE chr_3p-deleted cell clones alongside HMMCopy to monitor subclonal copy-number evolution during in vitro passaging; detected emergence of chromosome-3 duplication subclones that rescued the chr_3p-deletion proliferation defect PMID:29622463

Notes

• Originally developed for cell-free DNA liquid biopsy; also applicable to low-coverage cell-line WGS.
• Jointly estimates tumor/aberrant-cell fraction and copy-number states without a matched normal.
• Minimum input: ~0.1× coverage; higher coverage improves resolution of focal events.

Sources

This page was processed by entity-page-writer on 2026-05-15.