title: Diagnostic Mutation Profiling and Validation of Non-Small-Cell Lung Cancer Small Biopsy Samples using a High Throughput Platform.
abstract: BACKGROUND
  A single platform designed for the synchronous screening of multiple mutations can potentially enable molecular profiling in samples of limited tumor tissue. This approach is ideal for the assessment of advanced non-small-cell lung cancer (NSCLC) diagnostic specimens, which often comprise small biopsies. Therefore, we aimed in this study to validate the mass spectrometry-based Sequenom LungCarta panel and MassARRAY platform using DNA extracted from a single 5 μM formalin-fixed paraffin-embedded tissue section.
  
  
  METHODS
  Mutations, including those with an equivocal spectrum, detected in 90 cases of NSCLC (72 lung biopsies, 13 metastatic tissue biopsies, three resections, and two cytology samples) were validated by a combination of standard sequencing techniques, immunohistochemical staining for p53 protein, and next-generation sequencing with the TruSight Tumor panel.
  
  
  RESULTS
  Fifty-five mutations were diagnosed in 47 cases (52%) in the following genes: TP53 (22), KRAS (15), EGFR (5), MET (3), PIK3CA (3), STK11 (2), NRF-2 (2), EPHA5 (1), EPHA3 (1), and MAP2K1 (1). Of the 90 samples, one failed testing due to poor quality DNA. An additional 7 TP53 mutations were detected by next-generation sequencing, which facilitated the interpretation of p53 immunohistochemistry but required 5 × 10 μM tumor sections per sample tested.
  
  
  CONCLUSIONS
  The LungCarta panel is a sensitive method of screening for multiple alterations (214 mutations across 26 genes) and which optimizes the use of limited amounts of tumor DNA isolated from small specimens.
authors: Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester and St. Mary's Hospital, Manchester, UK. Electronic address: amquinn2003@yahoo.co.uk.
authors: Anne Marie
authors: AM
authors: Quinn
authors: Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester and St. Mary's Hospital, Manchester, UK.
authors: Nicholas
authors: N
authors: Hickson
authors: Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester and St. Mary's Hospital, Manchester, UK.
authors: Megan
authors: M
authors: Adaway
authors: Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
authors: Lynsey
authors: L
authors: Priest
authors: Illumina Inc., San Diego, CA.
authors: Erich
authors: E
authors: Jaeger
authors: Illumina Inc., San Diego, CA.
authors: Nitin
authors: N
authors: Udar
authors: Pathology, Manchester Royal Infirmary, Manchester, UK.
authors: Catherine
authors: C
authors: Keeling
authors: Pathology, Manchester Royal Infirmary, Manchester, UK.
authors: Martyna
authors: M
authors: Kamieniorz
authors: Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
authors: Caroline
authors: C
authors: Dive
authors: Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester and St. Mary's Hospital, Manchester, UK.
authors: Andrew
authors: A
authors: Wallace
authors: Pathology, Manchester Royal Infirmary, Manchester, UK.
authors: Richard J
authors: RJ
authors: Byers
authors: Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester and St. Mary's Hospital, Manchester, UK.
authors: William G
authors: WG
authors: Newman
authors: The Christie NHS Foundation Trust, Manchester, UK.
authors: Daisuke
authors: D
authors: Nonaka
authors: The Christie NHS Foundation Trust, Manchester, UK; Medical Oncology, Institute of Cancer Studies, University of Manchester, Manchester, UK.
authors: Fiona H
authors: FH
authors: Blackhall
mesh_terms: D000091162:AMP-Activated Protein Kinase Kinases; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001706:Biopsy; D002289:Carcinoma, Non-Small-Cell Lung / Q000737:chemistry / Q000235:genetics* / Q000556:secondary*; D058534:Class I Phosphatidylinositol 3-Kinases; D004252:DNA Mutational Analysis / Q000379:methods*; D005260:Female; D018773:Genes, erbB-1 / Q000235:genetics; D011905:Genes, ras / Q000235:genetics; D005820:Genetic Testing / Q000379:methods; D006801:Humans; D008168:Lung / Q000473:pathology*; D008175:Lung Neoplasms / Q000737:chemistry / Q000235:genetics* / Q000473:pathology*; D048369:MAP Kinase Kinase 1 / Q000235:genetics; D008297:Male; D013058:Mass Spectrometry; D008875:Middle Aged; D009154:Mutation; D051267:NF-E2-Related Factor 2 / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D019859:Proto-Oncogene Proteins c-met / Q000235:genetics; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics; D036121:Receptor, EphA3; D036123:Receptor, EphA5 / Q000235:genetics; D016159:Tumor Suppressor Protein p53 / Q000032:analysis / Q000235:genetics
chemical_list: D000091162:AMP-Activated Protein Kinase Kinases; D058534:Class I Phosphatidylinositol 3-Kinases; D048369:MAP Kinase Kinase 1; D051267:NF-E2-Related Factor 2; D019869:Phosphatidylinositol 3-Kinases; D017346:Protein Serine-Threonine Kinases; D019859:Proto-Oncogene Proteins c-met; D020794:Receptor Protein-Tyrosine Kinases; D036121:Receptor, EphA3; D036123:Receptor, EphA5; D016159:Tumor Suppressor Protein p53; C495635:NFE2L2 protein, human; C484760:PIK3CA protein, human; C491718:EPHA3 protein, human; C484173:EPHA5 protein, human; C491743:MET protein, human; C109790:STK11 protein, human; C482125:MAP2K1 protein, human