https://github.com/broadinstitute/ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
https://github.com/broadinstitute/ichorcna

cell-free-dna copy-number low-coverage-sequencing

Last synced: about 1 year ago
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Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

• Host: GitHub
• URL: https://github.com/broadinstitute/ichorcna
• Owner: broadinstitute
• License: gpl-3.0
• Created: 2017-01-06T16:47:46.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2024-03-20T13:29:09.000Z (about 2 years ago)
• Last Synced: 2025-04-02T09:10:26.025Z (about 1 year ago)
• Topics: cell-free-dna, copy-number, low-coverage-sequencing
• Language: R
• Homepage:
• Size: 10.7 MB
• Stars: 180
• Watchers: 20
• Forks: 87
• Open Issues: 96
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
[![Build Status](https://travis-ci.com/broadinstitute/ichorCNA.svg?branch=master)](https://travis-ci.com/broadinstitute/ichorCNA)

# *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](https://github.com/broadinstitute/ichorCNA/wiki)**

## 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](https://doi.org/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  

3. CNA prediction and estimation of tumor fraction of cfDNA

## Contacts

If you have any questions or feedback, please contact us at:  

**Email:**   

**Google Group:** 

## 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 .