title: Using whole genome amplification (WGA) of low-volume biopsies to assess the prognostic role of EGFR, KRAS, p53, and CMET mutations in advanced-stage non-small cell lung cancer (NSCLC).
abstract: BACKGROUND
  Progression of non-small cell lung cancer (NSCLC) from early- to late-stage may signify the accumulation of gene mutations. An advanced-stage tumor's mutation profile may also have prognostic value, guiding treatment decisions. Mutation detection of multiple genes is limited by the low amount of deoxyribonucleic acid extracted from low-volume diagnostic lung biopsies. We explored whole genome amplification (WGA) to enable multiple molecular analyses.
  
  
  METHODS
  Eighty-eight advanced-stage NSCLC patients were enrolled. Their low-volume lung biopsies underwent WGA before direct sequencing for epidermal growth factor receptor (EGFR), KRAS (rat sarcoma virus), p53, and CMET (mesenchymal-epithelial transition factor) mutations. Overall survival impact was examined. Surgically-resected tumors from 133 early-stage NSCLC patients were sequenced for EGFR, KRAS and p53 mutations. We compared the mutation frequencies of both groups.
  
  
  RESULTS
  It is feasible for low-volume lung biopsies to undergo WGA for mutational analysis. KRAS and CMET mutations have a deleterious effect on overall survival, hazard ratios 5.05 (p = 0.009) and 23.65 (p = 0.005), respectively. EGFR and p53 mutations, however, do not have a survival impact. There also does not seem to be significant differences in the frequency of mutations in EGFR, KRAS, and p53 between early- and advanced-stage disease: 20% versus 24% (p = 0.48), 29% versus 27% (p = 0.75), 10% versus 6% (p = 0.27), respectively.
  
  
  CONCLUSIONS
  In advanced-stage NSCLC, KRAS, and CMET mutations suggest poor prognosis, whereas EGFR and p53 mutations do not seem to have survival impact. Mutations in EGFR, KRAS and p53 are unlikely to be responsible for the progression of NSCLC from early- to late-stage disease. WGA may be used to expand starting deoxyribonucleic acid from low-volume lung biopsies for further analysis of advanced-stage NSCLC.
authors.affiliation: Johns Hopkins Singapore International Medical Centre, Singapore. elaine_h_lim@yahoo.com
authors.forename: Elaine H
authors.initials: EH
authors.lastname: Lim
authors.forename: Shen-Li
authors.initials: SL
authors.lastname: Zhang
authors.forename: Jia-Liang
authors.initials: JL
authors.lastname: Li
authors.forename: Wee-See
authors.initials: WS
authors.lastname: Yap
authors.forename: Tse-Chiang
authors.initials: TC
authors.lastname: Howe
authors.forename: Bien-Peng
authors.initials: BP
authors.lastname: Tan
authors.forename: Yong-Shyan
authors.initials: YS
authors.lastname: Lee
authors.forename: Daniel
authors.initials: D
authors.lastname: Wong
authors.forename: Kay-Leong
authors.initials: KL
authors.lastname: Khoo
authors.forename: Kar-Yin
authors.initials: KY
authors.lastname: Seto
authors.forename: Lenny
authors.initials: L
authors.lastname: Tan
authors.forename: Thirugananam
authors.initials: T
authors.lastname: Agasthian
authors.forename: Heng-Nung
authors.initials: HN
authors.lastname: Koong
authors.forename: John
authors.initials: J
authors.lastname: Tam
authors.forename: Christie
authors.initials: C
authors.lastname: Tan
authors.forename: Michael
authors.initials: M
authors.lastname: Caleb
authors.forename: Alex
authors.initials: A
authors.lastname: Chang
authors.forename: Alan
authors.initials: A
authors.lastname: Ng
authors.forename: Patrick
authors.initials: P
authors.lastname: Tan
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics / Q000556:secondary / Q000601:surgery; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001483:Base Sequence; D001706:Biopsy; D018196:Carcinoma, Adenosquamous / Q000235:genetics / Q000556:secondary / Q000601:surgery; D018287:Carcinoma, Large Cell / Q000235:genetics / Q000556:secondary / Q000601:surgery; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000556:secondary / Q000601:surgery; D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000556:secondary / Q000601:surgery; D004273:DNA, Neoplasm / Q000235:genetics; D066246:ErbB Receptors / Q000235:genetics*; D005240:Feasibility Studies; D005260:Female; D005784:Gene Amplification; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology / Q000601:surgery; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D009367:Neoplasm Staging; D016133:Polymerase Chain Reaction; D011379:Prognosis; D011518:Proto-Oncogene Proteins / Q000235:genetics*; D019859:Proto-Oncogene Proteins c-met / Q000235:genetics*; D016283:Proto-Oncogene Proteins p21(ras); D012680:Sensitivity and Specificity; D015996:Survival Rate; D016159:Tumor Suppressor Protein p53 / Q000235:genetics* / Q000378:metabolism; D018631:ras Proteins / Q000235:genetics*
chemical_list: D004273:DNA, Neoplasm; C117307:KRAS protein, human; D011518:Proto-Oncogene Proteins; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; C512478:EGFR protein, human; D066246:ErbB Receptors; D019859:Proto-Oncogene Proteins c-met; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins