title: Inter-Laboratory Evaluation of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia.
abstract: Acute myeloid leukemia (AML) is a heterogeneous clonal disorder often associated with dismal overall survival. The clinical diversity of AML is reflected in the range of recurrent somatic mutations in several genes, many of which have a prognostic and therapeutic value. Targeted next-generation sequencing (NGS) of these genes has the potential for translation into clinical practice. In order to assess this potential, an inter-laboratory evaluation of a commercially available AML gene panel across three diagnostic centres in the UK and Ireland was performed.
  
  
  
  DNA from six AML patient samples was distributed to each centre and processed using a standardised workflow, including a common sequencing platform, sequencing chips and bioinformatics pipeline. A duplicate sample in each centre was run to assess inter- and intra-laboratory performance.
  
  
  
  An average sample read depth of 2725X (range 629-5600) was achieved using six samples per chip, with some variability observed in the depth of coverage generated for individual samples and between centres. A total of 16 somatic mutations were detected in the six AML samples, with a mean of 2.7 mutations per sample (range 1-4) representing nine genes on the panel. 15/16 mutations were identified by all three centres. Allelic frequencies of the mutations ranged from 5.6 to 53.3 % (median 44.4 %), with a high level of concordance of these frequencies between centres, for mutations detected.
  
  
  
  In this inter-laboratory comparison, a high concordance, reproducibility and robustness was demonstrated using a commercially available NGS AML gene panel and platform.
authors.affiliation: Cancer Molecular Diagnostics, Central Pathology Laboratory, St. James's Hospital, Dublin 8, Ireland. khaslam@stjames.ie.
authors.forename: Karl
authors.identifier: 0000-0003-0042-7947
authors.initials: K
authors.lastname: Haslam
authors.affiliation: Centre for Cancer Research and Cell Biology, Queens University, Belfast, UK.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Catherwood
authors.affiliation: Department of Haematology, Western General Hospital, Edinburgh, UK.|Almac Diagnostics, Craigavon, UK.
authors.forename: Edwina
authors.initials: E
authors.lastname: Dobbin
authors.affiliation: Department of Haematology, Western General Hospital, Edinburgh, UK.
authors.forename: Anne
authors.initials: A
authors.lastname: Sproul
authors.affiliation: Cancer Molecular Diagnostics, Central Pathology Laboratory, St. James's Hospital, Dublin 8, Ireland.
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Langabeer
authors.affiliation: Centre for Cancer Research and Cell Biology, Queens University, Belfast, UK.
authors.forename: Ken I
authors.initials: KI
authors.lastname: Mills
mesh_terms: D000483:Alleles; D014408:Biomarkers, Tumor; D004252:DNA Mutational Analysis / Q000379:methods / Q000592:standards; D005787:Gene Frequency; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000592:standards; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000175:diagnosis* / Q000235:genetics*; D009154:Mutation; D011933:Reagent Kits, Diagnostic / Q000592:standards; D015203:Reproducibility of Results
chemical_list: D014408:Biomarkers, Tumor; D011933:Reagent Kits, Diagnostic