A highly accurate platform for clone-specific mutation discovery enables the study of active mutational processes
- University of Oxford, United Kingdom
- Ludwig Maximilian University of Munich, Germany
- University of Birmingham, United Kingdom
Abstract
Bulk whole genome sequencing (WGS) enables the analysis of tumor evolution but, because of depth limitations, can only identify old mutational events. The discovery of current mutational processes for predicting the tumor's evolutionary trajectory requires dense sequencing of individual clones or single cells. Such studies, however, are inherently problematic because of the discovery of excessive false positive mutations when sequencing picogram quantities of DNA. Data pooling to increase the confidence in the discovered mutations, moves the discovery back in the past to a common ancestor. Here we report a robust whole genome sequencing and analysis pipeline (DigiPico/MutLX) that virtually eliminates all false positive results while retaining an excellent proportion of true positives. Using our method, we identified, for the first time, a hyper-mutation (kataegis) event in a group of ∼30 cancer cells from a recurrent ovarian carcinoma. This was unidentifiable from the bulk WGS data. Overall, we propose DigiPico/MutLX method as a powerful framework for the identification of clone-specific variants at an unprecedented accuracy.
Data availability
Sequence data has been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI and the CRG, under accession number EGAS00001003555 (EGAD00001005118). Further information about EGA can be found on https://ega-archive.org "The European Genome-phenome Archive of human data consented for biomedical research"
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DigiPico sequencing data for the study of active mutational processes in HGSOCEuropean Genome-phenome Archive, EGAD00001005118.
Article and author information
Author details
Mohammad KaramiNejadRanjbar
Tatjana Sauka-Spengler
Funding
Ovarian Cancer Action (HER000762)
- Ahmed A Ahmed
National Institute for Health Research (IS-BRC-0211-10025)
- Ahmed A Ahmed
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- C Daniela Robles-Espinoza, International Laboratory for Human Genome Research, Mexico
Ethics
Human subjects: Patients #11152, #11502 and #11513 provided written consent for participation in the prospective biomarker validation study Gynaecological Oncology Targeted Therapy Study 01 (GO-Target-01) under research ethics approval number 11/SC/0014. Patient OP1036 participated in the prospective Oxford Ovarian Cancer Predict Chemotherapy Response Trial (OXO-PCR-01), under research ethics approval number 12/SC/0404. Necessary informed consents from study participants were obtained as appropriate.
Version history
- Received: January 16, 2020
- Accepted: April 7, 2020
- Accepted Manuscript published: April 7, 2020 (version 1)
- Version of Record published: May 15, 2020 (version 2)
- Version of Record updated: June 29, 2020 (version 3)
Copyright
© 2020, KaramiNejadRanjbar et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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A highly accurate platform for clone-specific mutation discovery enables the study of active mutational processes
eLife 9:e55207.
https://doi.org/10.7554/eLife.55207
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