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

Gao, M.; Callari, M.; Beddowes, E.; Sammut, S.-J.; Grzelak, M.; Biggs, H.; Jones, L.; Boumertit, A.; Linn, S. C.; Cortes, J.; Baird, R.; Chin, S.-F.; Caldas, C.

doi:10.1101/366534

bioRxiv · 10.1101/366534

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

Gao, M.·Callari, M.·Beddowes, E.·Sammut, S.-J.·Grzelak, M.·Biggs, H.·Jones, L.·Boumertit, A.·Linn, S. C.·Cortes, J.·Baird, R.·Chin, S.-F.·Caldas, C.

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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.

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Gao, M., Callari, M., Beddowes, E., Sammut, S.-J., Grzelak, M., Biggs, H., Jones, L., Boumertit, A., Linn, S. C., Cortes, J., Baird, R., Chin, S.-F., Caldas, C.. 2018-07-15. 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

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