title: Focused molecular analysis of small cell lung cancer: feasibility in routine clinical practice.
abstract: BACKGROUND
  There is an urgent need to identify molecular signatures in small cell lung cancer (SCLC) that may select patients who are likely to respond to molecularly targeted therapies. In this study, we investigate the feasibility of undertaking focused molecular analyses on routine diagnostic biopsies in patients with SCLC.
  
  
  METHODS
  A series of histopathologically confirmed formalin-fixed, paraffin-embedded SCLC specimens were analysed for epidermal growth factor receptors (EGFR), KRAS, NRAS and BRAF mutations, ALK gene rearrangements and MET amplification. EGFR and KRAS mutation testing was evaluated using real time polymerase chain reaction (RT-PCR cobas(®)), BRAF and NRAS mutations using multiplex PCR and capillary electrophoresis-single strand conformation analysis, and ALK and MET aberrations with fluorescent in situ hybridization. All genetic aberrations detected were validated independently.
  
  
  RESULTS
  A total of 105 patients diagnosed with SCLC between July 1990 and September 2006 were included. 60 (57 %) patients had suitable tumour tissue for molecular testing. 25 patients were successfully evaluated for all six pre-defined molecular aberrations. Eleven patients failed all molecular analysis. No mutations in EGFR, KRAS and NRAS were detected, and no ALK gene rearrangements or MET gene amplifications were identified. A V600E substitution in BRAF was detected in a Caucasian male smoker diagnosed with SCLC with squamoid and glandular features.
  
  
  CONCLUSIONS
  The paucity of patients with sufficient tumour tissue, quality of DNA extracted and low frequency of aberrations detected indicate that alternative molecular characterisation approaches are necessary, such as the use of circulating plasma DNA in patients with SCLC.
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. fatma.abdelraouf@nhs.net.|Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt. fatma.abdelraouf@nhs.net.
authors.forename: Fatma
authors.initials: F
authors.lastname: Abdelraouf
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. adam.sharp@rmh.nhs.uk.|The Institute of Cancer Research, London, UK. adam.sharp@rmh.nhs.uk.
authors.forename: Adam
authors.initials: A
authors.lastname: Sharp
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. manisha.maurya@icr.ac.uk.
authors.forename: Manisha
authors.initials: M
authors.lastname: Maurya
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. debbie.mair@icr.ac.uk.
authors.forename: Debbie
authors.initials: D
authors.lastname: Mair
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. andrew.wotherspoon@rmh.nhs.uk.
authors.forename: Andrew
authors.initials: A
authors.lastname: Wotherspoon
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. leary.alex@gmail.com.
authors.forename: Alex
authors.initials: A
authors.lastname: Leary
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. david.gonzalez-de-castro@icr.ac.uk.
authors.forename: David
authors.initials: D
authors.lastname: Gonzalez de Castro
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. jaishree.bhosle@rmh.nhs.uk.
authors.forename: Jaishree
authors.initials: J
authors.lastname: Bhosle
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. aya_nasef4g@hotmail.com.|Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt. aya_nasef4g@hotmail.com.
authors.forename: Ayatallah
authors.initials: A
authors.lastname: Nassef
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. tagrid8@yahoo.com.|Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt. tagrid8@yahoo.com.
authors.forename: Taghrid
authors.initials: T
authors.lastname: Gaafar
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. sanjay.popat@rmh.nhs.uk.|National Heart and Lung institute, London, UK. sanjay.popat@rmh.nhs.uk.
authors.forename: Sanjay
authors.initials: S
authors.lastname: Popat
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. timothy.yap@icr.ac.uk.|The Institute of Cancer Research, London, UK. timothy.yap@icr.ac.uk.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Yap
authors.affiliation: Lung Cancer Unit, Department of Medicine, Royal Marsden NHS Foundation Trust, Downs Road, Sutton, London, SM2 5PT, UK. mary.obrien@rmh.nhs.uk.
authors.forename: Mary
authors.initials: M
authors.lastname: O'Brien
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000077548:Anaplastic Lymphoma Kinase; D004252:DNA Mutational Analysis / Q000379:methods; D066246:ErbB Receptors / Q000235:genetics / Q000378:metabolism; D005240:Feasibility Studies; D005260:Female; D020558:GTP Phosphohydrolases / Q000235:genetics / Q000378:metabolism; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D008175:Lung Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism; D008297:Male; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods; D009154:Mutation; D016612:Paraffin Embedding / Q000379:methods; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics / Q000378:metabolism; D019859:Proto-Oncogene Proteins c-met / Q000235:genetics / Q000378:metabolism; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics / Q000378:metabolism; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D055752:Small Cell Lung Carcinoma / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism; D016707:Tissue Fixation / Q000379:methods
chemical_list: C117307:KRAS protein, human; D008565:Membrane Proteins; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; C512478:EGFR protein, human; D066246:ErbB Receptors; C491743:MET protein, human; D019859:Proto-Oncogene Proteins c-met; D020794:Receptor Protein-Tyrosine Kinases; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D020558:GTP Phosphohydrolases; C579846:NRAS protein, human; D016283:Proto-Oncogene Proteins p21(ras)