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

Genome Medicine

Linda Jones¹  Abdelhamid Boumertit¹  Heather Biggs¹  Richard Baird¹  Suet-Feung Chin²  Meiling Gao²  Carlos Caldas²  Emma Beddowes²  Maurizio Callari²  Stephen-John Sammut²  Marta Grzelak²  Sabine C. Linn³  Javier Cortes⁴  Mafalda Oliveira⁵ 

[1] Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust;Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge;Netherland Cancer Institute;Ramon y Cajal University Hospital;Vall d’Hebron Institute of Oncology;

关键词: NG-TAS;    ctDNA;    Liquid biopsy;    Mutation;    Multiplexing;    Deep sequencing;   

DOI  :  10.1186/s13073-018-0611-9

来源: DOAJ

【 摘 要 】

Abstract Circulating tumour DNA (ctDNA) detection and monitoring have 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.

【 授权许可】

Unknown