ichorCNA

ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing (ULP-WGS, 0.1x coverage). This is a version maintained by the laboratory of Gavin Ha.

How to run ichorCNA

1. WDL pipleine
   • The WDL pipeline uses release ichorCNA:v0.5.0
   • The docker image gavinhalab/ichorcna:1.0.0 can be found at DockerHub
   • Clone WDL pipleine
   • To run the WDL pipeline, please follow instructions here
2. Snakemake pipeline
   • The Snakemake pipeline is part of release ichorCNA:v0.4.0
   • Clone ichorCNA:v0.4.0 or download v0.4.0.tar.gz
   • To run the Snakemake pipeline, please follow instructions here

Description

ichorCNA uses a probabilistic model, implemented as a hidden Markov model (HMM), to simultaneously segment the genome, predict large-scale copy number alterations, and estimate the tumor fraction of a ultra-low-pass whole genome sequencing sample (ULP-WGS).

The methodology and probabilistic model are described in:
Adalsteinsson, Ha, Freeman, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. (2017) Nature Communications Nov 6;8(1):1324. doi: 10.1038/s41467-017-00965-y

The analysis workflow consists of 2 tasks:

1. GC-content bias correction (using HMMcopy)
   a. Computing read coverage from ULP-WGS
   b. Data correction and normalization
2. CNA prediction and estimation of tumor fraction of cfDNA

Contacts

If you have any questions or feedback, please contact us at:
Email: gha@fredhutch.org or pchandra@fredhutch.org

Acknowledgements

ichorCNA is maintained by Gavin Ha, Pooja Chandra, and Michael Yang.

ichorCNA was originally developed in collaboration with

• Blood Biopsy Group, Group Leader Viktor Adalsteinsson, Broad Institute of MIT and Harvard
• Laboratory of Matthew Meyerson, Medical Oncology, Dana-Farber Cancer Institute
• Laboratory of J. Christopher Love, Koch Institute for integrative cancer research at MIT
• Laboratory of Gad Getz, Cancer Program, Broad Institute

Software License

ichorCNA Copyright (C) 2024 Gavin Ha Lab

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.