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Title:
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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
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Author:
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Gao, Meiling; Callari, Maurizio; Beddowes, Emma; Sammut, Stephen-John; Grzelak, Marta; Biggs, Heather; Cortés Castan, Javier; Antunes de Melo Oliveira, Ana Mafalda
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Other authors:
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Institut Català de la Salut; [Gao M, Callari M] Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK. [Beddowes E] Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK. Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK. [Sammut SJ, Grzelak M] Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK. [Biggs H] Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK. [Cortes J] Ramon y Cajal University Hospital, Madrid, Spain. Vall d'Hebron Institut d'Oncologia, Barcelona, Spain. [Oliveira M] Vall d'Hebron Institut d'Oncologia, Barcelona, Spain.; Hospital Universitari Vall d'Hebron |
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Abstract:
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Cancer; Computational pipeline; Deep sequencing |
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Abstract:
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Càncer; Segmentació computacional; Seqüenciació |
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Abstract:
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Cáncer; Segmentación computacional; Secuenciación |
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Abstract:
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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 |
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Subject(s):
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-ADN - Anàlisi
-Biologia computacional
-Càncer
-ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES AND EQUIPMENT::Investigative Techniques::Genetic Techniques::Sequence Analysis::Sequence Analysis, DNA
-Other subheadings::Other subheadings::/methods
-DISEASES::Neoplasms
-INFORMATION SCIENCE::Information Science::Computing Methodologies
-TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::técnicas de investigación::técnicas genéticas::análisis de secuencias::análisis de secuencias de ADN
-Otros calificadores::Otros calificadores::/métodos
-ENFERMEDADES::Neoplasias
-CIENCIA DE LA INFORMACIÓN::Ciencias de la información::metodologías computacionales |
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Rights:
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Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/
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Document type:
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Article
Article - Published version |
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Published by:
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BMC
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