title: Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity.
abstract: BACKGROUND
  Most personalized cancer care strategies involving DNA sequencing are highly reliant on acquiring sufficient fresh or frozen tissue. It has been challenging to comprehensively evaluate the genome of advanced prostate cancer (PCa) because of limited access to metastatic tissue.
  
  
  OBJECTIVE
  To demonstrate the feasibility of a novel next-generation sequencing (NGS)-based platform that can be used with archival formalin-fixed paraffin-embedded (FFPE) biopsy tissue to evaluate the spectrum of DNA alterations seen in advanced PCa.
  
  
  METHODS
  FFPE samples (including archival prostatectomies and prostate needle biopsies) were obtained from 45 patients representing the spectrum of disease: localized PCa, metastatic hormone-naive PCa, and metastatic castration-resistant PCa (CRPC). We also assessed paired primaries and metastases to understand disease heterogeneity and disease progression.
  
  
  METHODS
  At least 50 ng of tumor DNA was extracted from FFPE samples and used for hybridization capture and NGS using the Illumina HiSeq 2000 platform.
  
  
  METHODS
  A total of 3320 exons of 182 cancer-associated genes and 37 introns of 14 commonly rearranged genes were evaluated for genomic alterations.
  
  
  CONCLUSIONS
  We obtained an average sequencing depth of >900X. Overall, 44% of CRPCs harbored genomic alterations involving the androgen receptor gene (AR), including AR copy number gain (24% of CRPCs) or AR point mutation (20% of CRPCs). Other recurrent mutations included transmembrane protease, serine 2 gene (TMPRSS2):v-ets erythroblastosis virus E26 oncogene homolog (avian) gene (ERG) fusion (44%); phosphatase and tensin homolog gene (PTEN) loss (44%); tumor protein p53 gene (TP53) mutation (40%); retinoblastoma gene (RB) loss (28%); v-myc myelocytomatosis viral oncogene homolog (avian) gene (MYC) gain (12%); and phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit α gene (PIK3CA) mutation (4%). There was a high incidence of genomic alterations involving key genes important for DNA repair, including breast cancer 2, early onset gene (BRCA2) loss (12%) and ataxia telangiectasia mutated gene (ATM) mutations (8%); these alterations are potentially targetable with poly(adenosine diphosphate-ribose)polymerase inhibitors. A novel and actionable rearrangement involving the v-raf murine sarcoma viral oncogene homolog B1 gene (BRAF) was also detected.
  
  
  CONCLUSIONS
  This first-in-principle study demonstrates the feasibility of performing in-depth DNA analyses using FFPE tissue and brings new insight toward understanding the genomic landscape within advanced PCa.
authors.affiliation: Department of Medicine, Division of Hematology and Medical Oncology, Weill Medical College of Cornell University, New York, NY 10065, USA.
authors.forename: Himisha
authors.initials: H
authors.lastname: Beltran
authors.forename: Roman
authors.initials: R
authors.lastname: Yelensky
authors.forename: Garrett M
authors.initials: GM
authors.lastname: Frampton
authors.forename: Kyung
authors.initials: K
authors.lastname: Park
authors.forename: Sean R
authors.initials: SR
authors.lastname: Downing
authors.forename: Theresa Y
authors.initials: TY
authors.lastname: MacDonald
authors.forename: Mirna
authors.initials: M
authors.lastname: Jarosz
authors.forename: Doron
authors.initials: D
authors.lastname: Lipson
authors.forename: Scott T
authors.initials: ST
authors.lastname: Tagawa
authors.forename: David M
authors.initials: DM
authors.lastname: Nanus
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Stephens
authors.forename: Juan Miguel
authors.initials: JM
authors.lastname: Mosquera
authors.forename: Maureen T
authors.initials: MT
authors.lastname: Cronin
authors.forename: Mark A
authors.initials: MA
authors.lastname: Rubin
mesh_terms: D000726:Androgen Antagonists / Q000627:therapeutic use; D018931:Antineoplastic Agents, Hormonal; D001707:Biopsy, Needle; D019008:Drug Resistance, Neoplasm; D005091:Exons; D005240:Feasibility Studies; D005404:Fixatives; D005557:Formaldehyde; D015972:Gene Expression Regulation, Neoplastic; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns; D008297:Male; D060787:Neoplasm Grading; D009361:Neoplasm Invasiveness; D009919:Orchiectomy; D016612:Paraffin Embedding; D018579:Patient Selection; D010641:Phenotype; D057285:Precision Medicine; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000473:pathology / Q000628:therapy; D017422:Sequence Analysis, DNA / Q000379:methods*; D016707:Tissue Fixation
chemical_list: D000726:Androgen Antagonists; D018931:Antineoplastic Agents, Hormonal; D005404:Fixatives; D005557:Formaldehyde