GavinHaLab / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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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
  2. Snakemake pipeline

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

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/.