title: Validation and utilisation of high-coverage next-generation sequencing to deliver the pharmacological audit trail.
abstract: BACKGROUND
  Predictive biomarker development is a key challenge for novel cancer therapeutics. We explored the feasibility of next-generation sequencing (NGS) to validate exploratory genomic biomarkers that impact phase I trial selection.
  
  
  METHODS
  We prospectively enrolled 158 patients with advanced solid tumours referred for phase I clinical trials at the Royal Marsden Hospital (October 2012 to March 2013). After fresh and/or archived tumour tissue were obtained, 93 patients remained candidates for phase I trials. Results from tumour sequencing on the Illumina MiSeq were cross-validated in 27 out of 93 patients on the Ion Torrent Personal Genome Machine (IT-PGM) blinded to results. MiSeq validation with Sequenom MassARRAY OncoCarta 1.0 (Sequenom Inc., San Diego, CA, USA) was performed in a separate cohort.
  
  
  RESULTS
  We found 97% concordance of mutation calls by MiSeq and IT-PGM at a variant allele frequency ⩾13% and ⩾500 × depth coverage, and 91% concordance between MiSeq and Sequenom. Common 'actionable' mutations involved deoxyribonucleic acid (DNA) repair (51%), RAS-RAF-MEK (35%), Wnt (26%), and PI3K-AKT-mTOR (24%) signalling. Out of 53, 29 (55%) patients participating in phase I trials were recommended based on identified actionable mutations.
  
  
  CONCLUSIONS
  Targeted high-coverage NGS panels are a highly feasible single-centre technology well-suited to cross-platform validation, enrichment of trials with molecularly defined populations and hypothesis testing early in drug development.
authors.affiliation: 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK.
authors.forename: M
authors.initials: M
authors.lastname: Ong
authors.affiliation: 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK.
authors.forename: S
authors.initials: S
authors.lastname: Carreira
authors.affiliation: 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK.
authors.forename: J
authors.initials: J
authors.lastname: Goodall
authors.affiliation: 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK.
authors.forename: J
authors.initials: J
authors.lastname: Mateo
authors.affiliation: Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.
authors.forename: I
authors.initials: I
authors.lastname: Figueiredo
authors.affiliation: Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.
authors.forename: D N
authors.initials: DN
authors.lastname: Rodrigues
authors.affiliation: Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.
authors.forename: G
authors.initials: G
authors.lastname: Perkins
authors.affiliation: Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.
authors.forename: G
authors.initials: G
authors.lastname: Seed
authors.affiliation: 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK.
authors.forename: T A
authors.initials: TA
authors.lastname: Yap
authors.affiliation: 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK.
authors.forename: G
authors.initials: G
authors.lastname: Attard
authors.affiliation: 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK.
authors.forename: J S
authors.initials: JS
authors.lastname: de Bono
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics*; D005260:Female; D005787:Gene Frequency / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation / Q000235:genetics; D009369:Neoplasms / Q000235:genetics*; D011446:Prospective Studies; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods; D055815:Young Adult
chemical_list: D014408:Biomarkers, Tumor