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

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From: Nature(Vol. 497, Issue 7447)
Publisher: Nature Publishing Group
Document Type: Report
Length: 5,229 words
Lexile Measure: 1510L

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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 noninvasive liquid biopsy (5-7). 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.

Serial sampling of the tumour genome is required to identify the mutational mechanisms underlying drug resistance (2). Serial tumour biopsies are invasive and often unattainable. Tumours are heterogeneous and continuously evolve, and even if several biopsies are obtained, these are limited both spatially and temporally. Analysis of isolated circulating tumour cells (CTCs) has been proposed, but circulating tumour DNA (ctDNA) is more accessible and easier to process (15). Previous studies of tumour mutations in plasma have analysed individual loci, genes or structural variants to quantify tumour burden and to detect previously-characterized resistance-conferring mutations (1,6,16-18). Genome-wide sequencing of plasma samples is used in prenatal diagnostics, demonstrating comprehensive coverage of the genome (19). More recently, genome-wide sequencing of plasma DNA has been demonstrated as a potential tool for detection of disease or analysis of tumour burden in patients with advanced cancers (5,7). These studies established that plasma DNA contains representation of the entire tumour genome (7), mixing together variants originating from multiple independent tumours (5). This suggests that deeper sequencing of plasma DNA, applied to selected samples with high tumour burden in blood, may allow assessment of clonal heterogeneity and selection. In this...

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Gale Document Number: GALE|A328944252