title: Serial Next-Generation Sequencing of Circulating Cell-Free DNA Evaluating Tumor Clone Response To Molecularly Targeted Drug Administration.
abstract: OBJECTIVE
  We evaluated whether next-generation sequencing (NGS) of circulating cell-free DNA (cfDNA) could be used for patient selection and as a tumor clone response biomarker in patients with advanced cancers participating in early-phase clinical trials of targeted drugs.
  
  
  METHODS
  Plasma samples from patients with known tumor mutations who completed at least two courses of investigational targeted therapy were collected monthly, until disease progression. NGS was performed sequentially on the Ion Torrent PGM platform.
  
  
  RESULTS
  cfDNA was extracted from 39 patients with various tumor types. Treatments administered targeted mainly the PI3K-AKT-mTOR pathway (n = 28) or MEK (n = 7). Overall, 159 plasma samples were sequenced with a mean sequencing coverage achieved of 1,685X across experiments. At trial initiation (C1D1), 23 of 39 (59%) patients had at least one mutation identified in cfDNA (mean 2, range 1-5). Out of the 44 mutations identified at C1D1, TP53, PIK3CA and KRAS were the top 3 mutated genes identified, with 18 (41%), 9 (20%), 8 (18%) different mutations, respectively. Out of these 23 patients, 13 received a targeted drug matching their tumor profile. For the 23 patients with cfDNA mutation at C1D1, the monitoring of mutation allele frequency (AF) in consecutive plasma samples during treatment with targeted drugs demonstrated potential treatment associated clonal responses. Longitudinal monitoring of cfDNA samples with multiple mutations indicated the presence of separate clones behaving discordantly. Molecular changes at cfDNA mutation level were associated with time to disease progression by RECIST criteria.
  
  
  CONCLUSIONS
  Targeted NGS of cfDNA has potential clinical utility to monitor the delivery of targeted therapies.
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom. Institut de Cancerologie de l'Ouest, Nantes-Saint Herblain, France.
authors.forename: Jean Sebastien
authors.initials: JS
authors.lastname: Frenel
authors.affiliation: The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Carreira
authors.affiliation: The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom.
authors.forename: Jane
authors.initials: J
authors.lastname: Goodall
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Desam
authors.initials: D
authors.lastname: Roda
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Raquel
authors.initials: R
authors.lastname: Perez-Lopez
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Nina
authors.initials: N
authors.lastname: Tunariu
authors.affiliation: The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom.
authors.forename: Ruth
authors.initials: R
authors.lastname: Riisnaes
authors.affiliation: The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom.
authors.forename: Susana
authors.initials: S
authors.lastname: Miranda
authors.affiliation: The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom.
authors.forename: Ines
authors.initials: I
authors.lastname: Figueiredo
authors.affiliation: The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom.
authors.forename: Daniel
authors.initials: D
authors.lastname: Nava-Rodrigues
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Alan
authors.initials: A
authors.lastname: Smith
authors.affiliation: Département de Santé Publique, CHU de Nantes, Nantes Cedex 1, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Leux
authors.affiliation: The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom.
authors.forename: Isaac
authors.initials: I
authors.lastname: Garcia-Murillas
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Roberta
authors.initials: R
authors.lastname: Ferraldeschi
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Lorente
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Joaquin
authors.initials: J
authors.lastname: Mateo
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Michael
authors.initials: M
authors.lastname: Ong
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Yap
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Udai
authors.initials: U
authors.lastname: Banerji
authors.affiliation: The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom.
authors.forename: Delila
authors.initials: D
authors.lastname: Gasi Tandefelt
authors.affiliation: The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom.
authors.forename: Nick
authors.initials: N
authors.lastname: Turner
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
authors.forename: Gerhardt
authors.initials: G
authors.lastname: Attard
authors.affiliation: The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom. Johann.de-Bono@icr.ac.uk.
authors.forename: Johann S
authors.initials: JS
authors.lastname: de Bono
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics*; D018450:Disease Progression; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation / Q000235:genetics; D009360:Neoplastic Cells, Circulating / Q000473:pathology*; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D051057:Proto-Oncogene Proteins c-akt / Q000235:genetics; D058570:TOR Serine-Threonine Kinases / Q000235:genetics; D018631:ras Proteins / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; D018076:DNA, Complementary; D004273:DNA, Neoplasm; D019869:Phosphatidylinositol 3-Kinases; D051057:Proto-Oncogene Proteins c-akt; D058570:TOR Serine-Threonine Kinases; D018631:ras Proteins; C546842:MTOR protein, human