Journal Article

Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA

Wong, Alvin S. C., Humphray, Sean, Piskorz, Anna M., Kingsbury, Zoya, Rosenfeld, Nitzan, Gale, Davina, Bentley, David, Parkinson, Christine, Chin, Suet-Feung, Brenton, James D., Tsui, Dana W. Y., Dawson, Sarah-Jane, Chin, Tan Min, Murtaza, Muhammed, Caldas, Carlos, Forshew, Tim, Marass, Francesco, Hadfield, James

2013

Overview

A proof of principle study shows that by exome sequencing of cell-free circulating DNA from cancer patient plasma samples, the genomic evolution of metastatic cancers and the acquisition of resistance in response to therapy can be tracked over time. Plasma screening tracks tumour evolution This proof-of-principle study shows that by sequencing cancer exomes from patient plasma samples, it is possible to track genomic evolution of metastatic cancers and acquisition of resistance in response to therapy. In six patients with advanced breast, lung and ovarian cancers, sequences were derived from two to five plasma samples taken during multiple courses of treatment. Mutations associated with the emergence of resistance to drugs including cisplatin, tamoxifen and gefitinib were identified. Cancers acquire resistance to systemic treatment as a result of clonal evolution and selection 1 , 2 . Repeat biopsies to study genomic evolution as a result of therapy are difficult, invasive and may be confounded by intra-tumour heterogeneity 3 , 4 . Recent studies have shown that genomic alterations in solid cancers can be characterized by massively parallel sequencing of circulating cell-free tumour DNA released from cancer cells into plasma, representing a non-invasive liquid biopsy 5 , 6 , 7 . Here we report sequencing of cancer exomes in serial plasma samples to track genomic evolution of metastatic cancers in response to therapy. Six patients with advanced breast, ovarian and lung cancers were followed over 1–2 years. For each case, exome sequencing was performed on 2–5 plasma samples (19 in total) spanning multiple courses of treatment, at selected time points when the allele fraction of tumour mutations in plasma was high, allowing improved sensitivity. For two cases, synchronous biopsies were also analysed, confirming genome-wide representation of the tumour genome in plasma. Quantification of allele fractions in plasma identified increased representation of mutant alleles in association with emergence of therapy resistance. These included an activating mutation in PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) following treatment with paclitaxel 8 ; a truncating mutation in RB1 (retinoblastoma 1) following treatment with cisplatin 9 ; a truncating mutation in MED1 (mediator complex subunit 1) following treatment with tamoxifen and trastuzumab 10 , 11 , and following subsequent treatment with lapatinib 12 , 13 , a splicing mutation in GAS6 (growth arrest-specific 6) in the same patient; and a resistance-conferring mutation in EGFR (epidermal growth factor receptor; T790M) following treatment with gefitinib 14 . These results establish proof of principle that exome-wide analysis of circulating tumour DNA could complement current invasive biopsy approaches to identify mutations associated with acquired drug resistance in advanced cancers. Serial analysis of cancer genomes in plasma constitutes a new paradigm for the study of clonal evolution in human cancers.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/208/514/2254 / 631/61/212/2304 / 631/67/69 / 692/308/575 / Alleles / Antineoplastic Agents - pharmacology / Antineoplastic Agents - therapeutic use / Biopsy / Breast cancer / Breast Neoplasms - drug therapy / Breast Neoplasms - genetics / Breast Neoplasms - pathology / Carcinoma, Non-Small-Cell Lung - drug therapy / Carcinoma, Non-Small-Cell Lung - genetics / Carcinoma, Non-Small-Cell Lung - pathology / Class I Phosphatidylinositol 3-Kinases / Deoxyribonucleic acid / DNA / DNA Mutational Analysis / DNA, Neoplasm - analysis / DNA, Neoplasm - genetics / Drug resistance / Drug Resistance, Neoplasm - drug effects / Drug Resistance, Neoplasm - genetics / ErbB Receptors - genetics / Evolution, Molecular / Exome - genetics / Female / Genome, Human - genetics / Genomes / Genomics / Heterogeneity / Humanities and Social Sciences / Humans / Intercellular Signaling Peptides and Proteins - genetics / letter / Lung Neoplasms - drug therapy / Lung Neoplasms - genetics / Lung Neoplasms - pathology / Mediator Complex Subunit 1 - genetics / multidisciplinary / Mutation / Neoplasms - drug therapy / Neoplasms - genetics / Neoplasms - pathology / Ovarian Neoplasms - drug therapy / Ovarian Neoplasms - genetics / Ovarian Neoplasms - pathology / Patients / Phosphatidylinositol 3-Kinases - genetics / Plasma / Plasma - chemistry / Retinoblastoma Protein - genetics / Science / Tumors