title: Potential pitfalls of mass spectrometry to uncover mutations in childhood soft tissue sarcoma: A report from the Children's Oncology Group.
abstract: Mass spectrometry-based methods have been widely applied - often as the sole method - to detect mutations in human cancer specimens. We applied this approach to 52 childhood soft tissue sarcoma specimens in an attempt to identify potentially actionable mutations. This analysis revealed that 25% of the specimens harbored high-confidence calls for mutated alleles, including a mutation encoding FLT3(I836M) that was called in four cases. Given the surprisingly high frequency and unusual nature of some of the mutant alleles, we carried out ultra-deep next generation sequencing to confirm them. We confirmed only three mutations, which encoded NRAS(A18T), JAK3(V722I) and MET(R970C) in three specimens. Beyond highlighting those mutations, our findings demonstrate potential pitfalls of primarily utilizing a mass spectrometry-based approach to broadly screen for DNA sequence variants in archived, clinical-grade tumor specimens. Duplicate mass spectrometric analyses and confirmatory next generation sequencing can help diminish false positive calls, but this does not ameliorate potential false negatives due in part to evaluating a limited panel of sequence variants.
authors.affiliation: Department of Pediatrics Division of Hematology/Oncology, and the Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, and the Pauline Allen Gill Center for Cancer and Blood Disorders, Children's Medical Center, Dallas, TX, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Xu
authors.affiliation: Department of Pediatrics Division of Hematology/Oncology, and the Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, and the Pauline Allen Gill Center for Cancer and Blood Disorders, Children's Medical Center, Dallas, TX, USA.
authors.forename: Raphael A
authors.initials: RA
authors.lastname: Wilson
authors.affiliation: Department of Pediatrics Division of Hematology/Oncology, and the Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, and the Pauline Allen Gill Center for Cancer and Blood Disorders, Children's Medical Center, Dallas, TX, USA.
authors.forename: Theodore W
authors.initials: TW
authors.lastname: Laetsch
authors.affiliation: Department of Pathology, and the Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: Dwight
authors.initials: D
authors.lastname: Oliver
authors.affiliation: Department of Pediatrics, Division of Hematology/Oncology, Stanford University School of Medicine, Palo Alto, CA, USA.
authors.forename: Sheri L
authors.initials: SL
authors.lastname: Spunt
authors.affiliation: Division of Hematology/Oncology, Seattle Children's Hospital, Fred Hutchison Cancer Research Center, University of Washington, Seattle, WA, USA.
authors.forename: Douglas S
authors.initials: DS
authors.lastname: Hawkins
authors.affiliation: Department of Pediatrics Division of Hematology/Oncology, and the Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, and the Pauline Allen Gill Center for Cancer and Blood Disorders, Children's Medical Center, Dallas, TX, USA.
authors.forename: Stephen X
authors.initials: SX
authors.lastname: Skapek
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D002648:Child; D004273:DNA, Neoplasm / Q000378:metabolism; D020558:GTP Phosphohydrolases / Q000235:genetics; D005787:Gene Frequency / Q000235:genetics; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008495:Medical Oncology; D008565:Membrane Proteins / Q000235:genetics; D009154:Mutation / Q000235:genetics*; D012509:Sarcoma / Q000235:genetics*
chemical_list: D004273:DNA, Neoplasm; D008565:Membrane Proteins; D020558:GTP Phosphohydrolases; C579846:NRAS protein, human