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Next Generation-Targeted Amplicon Sequencing (NG-TAS): An optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Gao, Meiling 
Callari, Maurizio 
Sammut, Stephen-John 
Grzelak, Marta 

Abstract

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 .

Description

Keywords

31 Biological Sciences, 32 Biomedical and Clinical Sciences, 3211 Oncology and Carcinogenesis, Cancer, Human Genome, Breast Cancer, Genetics, Clinical Research, Genetic Testing, 4 Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Cancer, 3 Good Health and Well Being

Journal Title

Genome Medicine

Conference Name

Journal ISSN

1756-994X

Volume Title

Publisher

Springer Nature
Sponsorship
Cancer Research UK (CB4140)
European Commission Horizon 2020 (H2020) Marie Sk?odowska-Curie actions (660060)