https://github.com/broadinstitute/ichorcna
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
Science Score: 36.0%
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Low similarity (11.9%) to scientific vocabulary
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Repository
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
Basic Info
Statistics
- Stars: 182
- Watchers: 20
- Forks: 87
- Open Issues: 96
- Releases: 2
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Metadata Files
README.md
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
3. 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/.
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
GitHub Events
Total
- Issues event: 3
- Watch event: 21
- Issue comment event: 4
- Fork event: 5
Last Year
- Issues event: 3
- Watch event: 21
- Issue comment event: 4
- Fork event: 5
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 98
- Total pull requests: 6
- Average time to close issues: about 2 months
- Average time to close pull requests: about 1 year
- Total issue authors: 66
- Total pull request authors: 5
- Average comments per issue: 2.65
- Average comments per pull request: 0.67
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 3
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
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- rahulram70 (5)
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- CuriusScientist (3)
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- yuanzhao0502 (3)
- hw538 (3)
- Jingjiao-ma (3)
- ury (2)
- gavinha (2)
- samhitapn (2)
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- mpierrejean (2)
Pull Request Authors
- mjko1210 (2)
- abcoxyzide (2)
- ZKai0801 (2)
- hw538 (1)
- ryanrichholt (1)
- awchrist (1)
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Dependencies
- R >= 3.6.0 depends
- GenomeInfoDb >= 1.20.0 imports
- GenomicRanges >= 1.36.0 imports
- HMMcopy >= 1.14.0 imports
- plyr >= 1.8.4 imports