title: Distinct subclonal tumour responses to therapy revealed by circulating cell-free DNA.
abstract: The application of precision medicine in oncology requires in-depth characterisation of a patient's tumours and the dynamics of their responses to treatment.
  
  
  
  We used next-generation sequencing of circulating cell-free DNA (cfDNA) to monitor the response of a KIT p.L576P-mutant metastatic vaginal mucosal melanoma to sequential targeted, immuno- and chemotherapy.
  
  
  
  Despite a KIT mutation, the response to imatinib was mixed. Unfortunately, tumours were not accessible for molecular analysis. To study the mechanism underlying the mixed clinical response, we carried out whole-exome sequencing and targeted longitudinal analysis of cfDNA. This revealed two tumour subclones; one with a KIT mutation that responded to imatinib and a second KIT-wild-type subclone that did not respond to imatinib. Notably, the subclones also responded differently to immunotherapy. However, both subclones responded to carboplatin/paclitaxel, and although the KIT-wild-type subclone progressed after chemotherapy, it responded to subsequent re-administration of paclitaxel.
  
  
  
  We show that cfDNA can reveal tumour evolution and subclonal responses to therapy even when biopsies are not available.
authors: Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester.
authors: G
authors: G
authors: Gremel
authors: Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester.
authors: R J
authors: RJ
authors: Lee
authors: Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester.
authors: M R
authors: MR
authors: Girotti
authors: Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester.
authors: A K
authors: AK
authors: Mandal
authors: The University of Manchester, The Christie NHS Foundation Trust, Manchester.
authors: S
authors: S
authors: Valpione
authors: Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester.
authors: G
authors: G
authors: Garner
authors: Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester.
authors: M
authors: M
authors: Ayub
authors: Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester.
authors: S
authors: S
authors: Wood
authors: Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester.
authors: D G
authors: DG
authors: Rothwell
authors: The University of Manchester, The Christie NHS Foundation Trust, Manchester.
authors: A
authors: A
authors: Fusi
authors: Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester NHS Foundation Trust, Manchester, UK.
authors: A
authors: A
authors: Wallace
authors: Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester.
authors: G
authors: G
authors: Brady
authors: Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester.
authors: C
authors: C
authors: Dive
authors: Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester.
authors: N
authors: N
authors: Dhomen
authors: The University of Manchester, The Christie NHS Foundation Trust, Manchester.
authors: P
authors: P
authors: Lorigan
authors: Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester richard.marais@cruk.manchester.ac.uk.
authors: R
authors: R
authors: Marais
mesh_terms: D000328:Adult; D000368:Aged; D054316:Biomarkers, Pharmacological; D016190:Carboplatin / Q000008:administration & dosage; D000073888:Cell-Free Nucleic Acids / Q000187:drug effects / Q000235:genetics*; D004273:DNA, Neoplasm / Q000187:drug effects / Q000235:genetics; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D000068877:Imatinib Mesylate / Q000008:administration & dosage; D008545:Melanoma / Q000188:drug therapy* / Q000235:genetics / Q000473:pathology; D008875:Middle Aged; D009154:Mutation; D017239:Paclitaxel / Q000008:administration & dosage; D057285:Precision Medicine; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics*; D014625:Vaginal Neoplasms / Q000188:drug therapy* / Q000235:genetics / Q000473:pathology; D000073359:Exome Sequencing
chemical_list: D054316:Biomarkers, Pharmacological; D000073888:Cell-Free Nucleic Acids; D004273:DNA, Neoplasm; D000068877:Imatinib Mesylate; D016190:Carboplatin; D019009:Proto-Oncogene Proteins c-kit; D017239:Paclitaxel
keywords: circulating cell-free DNA; clonal response to therapy; next-generation sequencing; vaginal mucosal melanoma