title: Discrepancies in cancer genomic sequencing highlight opportunities for driver mutation discovery.
abstract: Cancer genome sequencing is being used at an increasing rate to identify actionable driver mutations that can inform therapeutic intervention strategies. A comparison of two of the most prominent cancer genome sequencing databases from different institutes (Cancer Cell Line Encyclopedia and Catalogue of Somatic Mutations in Cancer) revealed marked discrepancies in the detection of missense mutations in identical cell lines (57.38% conformity). The main reason for this discrepancy is inadequate sequencing of GC-rich areas of the exome. We have therefore mapped over 400 regions of consistent inadequate sequencing (cold-spots) in known cancer-causing genes and kinases, in 368 of which neither institute finds mutations. We demonstrate, using a newly identified PAK4 mutation as proof of principle, that specific targeting and sequencing of these GC-rich cold-spot regions can lead to the identification of novel driver mutations in known tumor suppressors and oncogenes. We highlight that cross-referencing between genomic databases is required to comprehensively assess genomic alterations in commonly used cell lines and that there are still significant opportunities to identify novel drivers of tumorigenesis in poorly sequenced areas of the exome. Finally, we assess other reasons for the observed discrepancy, such as variations in dbSNP filtering and the acquisition/loss of mutations, to give explanations as to why there is a discrepancy in pharmacogenomic studies, given recent concerns with poor reproducibility of data.
authors.affiliation: Signalling Networks in Cancer Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Hudson
authors.affiliation: RNA Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.
authors.forename: Tim
authors.initials: T
authors.lastname: Yates
authors.affiliation: Computational Biology Support Team, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.
authors.forename: Yaoyong
authors.initials: Y
authors.lastname: Li
authors.affiliation: Signalling Networks in Cancer Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.
authors.forename: Eleanor W
authors.initials: EW
authors.lastname: Trotter
authors.affiliation: Signalling Networks in Cancer Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.
authors.forename: Shameem
authors.initials: S
authors.lastname: Fawdar
authors.affiliation: Computational Biology Support Team, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.
authors.forename: Phil
authors.initials: P
authors.lastname: Chapman
authors.affiliation: University of Manchester and The Christie NHS Foundation Trust, Manchester, M20 4BX, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Lorigan
authors.affiliation: Wolfson Wohl Translational Cancer Research Centre, University of Glasgow, G61 1QH, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Biankin
authors.affiliation: RNA Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.|Computational Biology Support Team, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.
authors.forename: Crispin J
authors.initials: CJ
authors.lastname: Miller
authors.affiliation: Signalling Networks in Cancer Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, UK.
authors.forename: John
authors.initials: J
authors.lastname: Brognard
mesh_terms: D045744:Cell Line, Tumor; D059472:Exome; D016147:Genes, Tumor Suppressor; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D009857:Oncogenes; D010597:Pharmacogenetics; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D054462:p21-Activated Kinases / Q000235:genetics
chemical_list: C116367:PAK4 protein, human; D054462:p21-Activated Kinases