Next Generation-Targeted Amplicon Sequencing (NG-TAS): An optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA
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Authors
Gao, Meiling
Callari, Maurizio
Biggs, Heather
Jones, Linda
Boumertit, Abdelhamid
Linn, Sabine
Cortes, Javier
Oliveira, Mafalda
Publication Date
2018-07-15ISSN
1756-994X
Publisher
Springer Nature
Type
Article
This Version
AM
Metadata
Show full item recordCitation
Gao, M., Callari, M., Beddowes, E., Sammut, S., Grzelak, M., Biggs, H., Jones, L., et al. (2018). Next Generation-Targeted Amplicon Sequencing (NG-TAS): An optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA. https://doi.org/10.1101/366534
Abstract
Circulating tumour DNA (ctDNA) detection and monitoring has enormous potential clinical utility in oncology. We describe here a fast, flexible and cost-effective method to profile multiple genes simultaneously in low input cell-free DNA (cfDNA): Next Generation-Targeted Amplicon Sequencing (NG-TAS). We designed a panel of 377 amplicons spanning 20 cancer genes and tested the NG-TAS pipeline using cell-free DNA from two hapmap lymphoblastoid cell lines. NG-TAS consistently detected
mutations in cfDNA when mutation allele fraction was >1%. We applied NG-TAS to a clinical cohort of metastatic breast cancer patients, demonstrating its potential in monitoring the disease. The computational pipeline is available at: https://github.com/cclab-brca/NGTAS_pipeline.
Keywords
NG-TAS, ctDNA, liquid biopsy, mutation, multiplexing, deep sequencing,
computational pipeline, cancer, heterogeneous
Sponsorship
Cancer Research UK (CB4140)
European Commission Horizon 2020 (H2020) Marie Sk?odowska-Curie actions (660060)
Identifiers
External DOI: https://doi.org/10.1101/366534
This record's URL: https://www.repository.cam.ac.uk/handle/1810/287449
Rights
Licence:
http://www.rioxx.net/licenses/all-rights-reserved