title: Molecular profiling of appendiceal epithelial tumors using massively parallel sequencing to identify somatic mutations.
abstract: BACKGROUND
  Some epithelial neoplasms of the appendix, including low-grade appendiceal mucinous neoplasm and adenocarcinoma, can result in pseudomyxoma peritonei (PMP). Little is known about the mutational spectra of these tumor types and whether mutations may be of clinical significance with respect to therapeutic selection. In this study, we identified somatic mutations using the Ion Torrent AmpliSeq Cancer Hotspot Panel v2.
  
  
  METHODS
  Specimens consisted of 3 nonneoplastic retention cysts/mucocele, 15 low-grade mucinous neoplasms (LAMNs), 8 low-grade/well-differentiated mucinous adenocarcinomas with pseudomyxoma peritonei, and 12 adenocarcinomas with/without goblet cell/signet ring cell features. Barcoded libraries were prepared from up to 10 ng of extracted DNA and multiplexed on single 318 chips for sequencing. Data analysis was performed using Golden Helix SVS. Variants that remained after the analysis pipeline were individually interrogated using the Integrative Genomics Viewer.
  
  
  RESULTS
  A single Janus kinase 3 (JAK3) mutation was detected in the mucocele group. Eight mutations were identified in the V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) and GNAS complex locus (GNAS) genes among LAMN samples. Additional gene mutations were identified in the AKT1 (v-akt murine thymoma viral oncogene homolog 1), APC (adenomatous polyposis coli), JAK3, MET (met proto-oncogene), phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA), RB1 (retinoblastoma 1), STK11 (serine/threonine kinase 11), and tumor protein p53 (TP53) genes. Among the PMPs, 6 mutations were detected in the KRAS gene and also in the GNAS, TP53, and RB1 genes. Appendiceal cancers showed mutations in the APC, ATM (ataxia telangiectasia mutated), KRAS, IDH1 [isocitrate dehydrogenase 1 (NADP+)], NRAS [neuroblastoma RAS viral (v-ras) oncogene homolog], PIK3CA, SMAD4 (SMAD family member 4), and TP53 genes.
  
  
  CONCLUSIONS
  Our results suggest molecular heterogeneity among epithelial tumors of the appendix. Next generation sequencing efforts have identified mutational spectra in several subtypes of these tumors that may suggest a phenotypic heterogeneity showing mutations that are relevant for targeted therapies.
authors.affiliation: Departments of Pathology.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Liu
authors.affiliation: Medicine-Section of Hematology/Oncology.
authors.forename: Kabir
authors.initials: K
authors.lastname: Mody
authors.affiliation: Departments of Pathology.
authors.forename: Francine B
authors.initials: FB
authors.lastname: de Abreu
authors.affiliation: Medicine-Section of Hematology/Oncology.
authors.forename: J Marc
authors.initials: JM
authors.lastname: Pipas
authors.affiliation: Departments of Pathology.
authors.forename: Jason D
authors.initials: JD
authors.lastname: Peterson
authors.affiliation: Departments of Pathology.
authors.forename: Torrey L
authors.initials: TL
authors.lastname: Gallagher
authors.affiliation: Departments of Pathology.
authors.forename: Arief A
authors.initials: AA
authors.lastname: Suriawinata
authors.affiliation: Medicine-Section of Hematology/Oncology.
authors.forename: Gregory H
authors.initials: GH
authors.lastname: Ripple
authors.affiliation: Medicine-Section of Hematology/Oncology.
authors.forename: Kathryn C
authors.initials: KC
authors.lastname: Hourdequin
authors.affiliation: Surgery.
authors.forename: Kerrington D
authors.initials: KD
authors.lastname: Smith
authors.affiliation: Surgery.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Barth
authors.affiliation: Surgery.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Colacchio
authors.affiliation: Radiology.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Tsapakos
authors.affiliation: Radiation Oncology.
authors.forename: Bassem I
authors.initials: BI
authors.lastname: Zaki
authors.affiliation: Medicine-Section of Gastroenterology and Hepatology.
authors.forename: Timothy B
authors.initials: TB
authors.lastname: Gardner
authors.affiliation: Medicine-Section of Gastroenterology and Hepatology.
authors.forename: Stuart R
authors.initials: SR
authors.lastname: Gordon
authors.affiliation: Center for Genomic Medicine and Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH and Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH.
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Amos
authors.affiliation: Departments of Pathology.
authors.forename: Wendy A
authors.initials: WA
authors.lastname: Wells
authors.affiliation: Departments of Pathology, gregory.j.tsongalis@hitchcock.org.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Tsongalis
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D002288:Adenocarcinoma, Mucinous / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D001063:Appendiceal Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D002276:Carcinoid Tumor / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D018279:Carcinoma, Signet Ring Cell / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D020869:Gene Expression Profiling; D006801:Humans; D009078:Mucocele / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D009154:Mutation; D010534:Peritoneal Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D000090063:Proto-Oncogene Mas; D011553:Pseudomyxoma Peritonei / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D017422:Sequence Analysis, DNA