Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
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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).

ichorCNA Wiki Page

For more details on usage/pipelines, outputs, and FAQs, please visit the GitHub Wiki page for ichorCNA

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: ichorcna@broadinstitute.org
Google Group: https://groups.google.com/a/broadinstitute.org/forum/?fromgroups&hl=en#!forum/ichorcna

Acknowledgements

ichorCNA is developed and maintained by Gavin Ha, Justin Rhoades, and Sam Freeman.

This work was done 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) 2017 Broad Institute

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/.