title: Clinical next-generation sequencing successfully applied to fine-needle aspirations of pulmonary and pancreatic neoplasms.
abstract: BACKGROUND
  Next-generation sequencing was performed on pulmonary and pancreatic fine-needle aspirations (FNAs) and on paired FNAs and resected primary tumors from the same patient.
  
  
  METHODS
  DNA was isolated in formalin-fixed, paraffin-embedded cell blocks from 16 pulmonary FNAs, 23 pancreatic FNAs, and 5 resected pancreatic primary tumors. Next-generation sequencing was performed for 4561 exons of 287 cancer-related genes and for 47 introns of 19 genes on indexed, adaptor-ligated, hybridization-captured libraries using a proprietary sequencing system (the Illumina HiSeq 2000).
  
  
  RESULTS
  Genomic profiles were generated successfully from 16 of 16 (100%) pulmonary FNAs, which included 14 nonsmall cell lung cancers (NSCLCs) and 2 small cell lung cancers (SCLCs). The NSCLC group included 6 adenocarcinomas, 5 squamous cell carcinomas, and 3 NSCLCs not otherwise specified. Genomic profiles were successfully obtained from 23 of 23 (100%) pancreatic FNAs and from 5 of 5 (100%) matched pancreatic primary tumors, which included 17 ductal adenocarcinomas, 3 mucinous adenocarcinomas, 2 adenocarcinomas NOS, and 1 neuroendocrine tumor. Eighty-one genomic alterations were identified in the 16 pulmonary FNAs (average, 5.1 genomic alterations per patient); and the most common genomic alterations were TP53, RB1, SOX2, PIK3CA, and KRAS. Eighty-seven genomic alterations were identified in the 23 pancreatic tumor FNAs (average, 3.8 genomic alterations per patient); and the most common genomic alterations were KRAS, TP53, CDKN2A/B, SMAD4, and PTEN. Among the pancreatic tumors, there was 100% concordance of 20 genomic alterations that were identified in 5 patient-matched FNA and surgical primary tumor pairs.
  
  
  CONCLUSIONS
  The authors were able to perform next-generation sequencing reliably on FNAs of pulmonary and pancreatic tumors, and the genomic alterations discovered correlated well with those identified in matched resected pancreatic tumors.
authors.affiliation: Foundation Medicine, Inc., Cambridge, Massachusetts.
authors.forename: Geneva
authors.initials: G
authors.lastname: Young
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Jie
authors.initials: J
authors.lastname: He
authors.forename: Geoff
authors.initials: G
authors.lastname: Otto
authors.forename: Matthew
authors.initials: M
authors.lastname: Hawryluk
authors.forename: Zac
authors.initials: Z
authors.lastname: Zwirco
authors.forename: Tina
authors.initials: T
authors.lastname: Brennan
authors.forename: Michelle
authors.initials: M
authors.lastname: Nahas
authors.forename: Amy
authors.initials: A
authors.lastname: Donahue
authors.forename: Roman
authors.initials: R
authors.lastname: Yelensky
authors.forename: Doron
authors.initials: D
authors.lastname: Lipson
authors.forename: Christine E
authors.initials: CE
authors.lastname: Sheehan
authors.forename: Ann B
authors.initials: AB
authors.lastname: Boguniewicz
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Stephens
authors.forename: Vincent A
authors.initials: VA
authors.lastname: Miller
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Ross
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics / Q000473:pathology; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D044963:Biopsy, Fine-Needle; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics / Q000473:pathology; D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000473:pathology; D015331:Cohort Studies; D005260:Female; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007150:Immunohistochemistry; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D010190:Pancreatic Neoplasms / Q000235:genetics* / Q000473:pathology; D012189:Retrospective Studies; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: copy number alterations; deletion; fine-needle aspiration biopsy; gene fusion; insertion; mutation; next-generation sequencing; nonsmall cell lung cancer; pancreatic cancer; targeted therapy