title: Use of whole-genome sequencing to diagnose a cryptic fusion oncogene.
abstract: BACKGROUND
  Whole-genome sequencing is becoming increasingly available for research purposes, but it has not yet been routinely used for clinical diagnosis.
  
  
  OBJECTIVE
  To determine whether whole-genome sequencing can identify cryptic, actionable mutations in a clinically relevant time frame.
  
  
  METHODS
  We were referred a difficult diagnostic case of acute promyelocytic leukemia with no pathogenic X-RARA fusion identified by routine metaphase cytogenetics or interphase fluorescence in situ hybridization (FISH). The case patient was enrolled in an institutional review board-approved protocol, with consent specifically tailored to the implications of whole-genome sequencing. The protocol uses a "movable firewall" that maintains patient anonymity within the entire research team but allows the research team to communicate medically relevant information to the treating physician.
  
  
  METHODS
  Clinical relevance of whole-genome sequencing and time to communicate validated results to the treating physician.
  
  
  RESULTS
  Massively parallel paired-end sequencing allowed identification of a cytogenetically cryptic event: a 77-kilobase segment from chromosome 15 was inserted en bloc into the second intron of the RARA gene on chromosome 17, resulting in a classic bcr3 PML-RARA fusion gene. Reverse transcription polymerase chain reaction sequencing subsequently validated the expression of the fusion transcript. Novel FISH probes identified 2 additional cases of t(15;17)-negative acute promyelocytic leukemia that had cytogenetically invisible insertions. Whole-genome sequencing and validation were completed in 7 weeks and changed the treatment plan for the patient.
  
  
  CONCLUSIONS
  Whole-genome sequencing can identify cytogenetically invisible oncogenes in a clinically relevant time frame.
authors.affiliation: Department of Medicine, Washington University, St Louis, Missouri, USA.
authors.forename: John S
authors.initials: JS
authors.lastname: Welch
authors.forename: Peter
authors.initials: P
authors.lastname: Westervelt
authors.forename: Li
authors.initials: L
authors.lastname: Ding
authors.forename: David E
authors.initials: DE
authors.lastname: Larson
authors.forename: Jeffery M
authors.initials: JM
authors.lastname: Klco
authors.forename: Shashikant
authors.initials: S
authors.lastname: Kulkarni
authors.forename: John
authors.initials: J
authors.lastname: Wallis
authors.forename: Ken
authors.initials: K
authors.lastname: Chen
authors.forename: Jacqueline E
authors.initials: JE
authors.lastname: Payton
authors.forename: Robert S
authors.initials: RS
authors.lastname: Fulton
authors.forename: Joelle
authors.initials: J
authors.lastname: Veizer
authors.forename: Heather
authors.initials: H
authors.lastname: Schmidt
authors.forename: Tammi L
authors.initials: TL
authors.lastname: Vickery
authors.forename: Sharon
authors.initials: S
authors.lastname: Heath
authors.forename: Mark A
authors.initials: MA
authors.lastname: Watson
authors.forename: Michael H
authors.initials: MH
authors.lastname: Tomasson
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Link
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Graubert
authors.forename: John F
authors.initials: JF
authors.lastname: DiPersio
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Ley
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
mesh_terms: D000328:Adult; D056905:Chromosome Breakpoints; D002884:Chromosomes, Human, Pair 15 / Q000235:genetics; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics; D050939:Gene Fusion; D015894:Genome, Human; D006801:Humans; D007438:Introns; D015473:Leukemia, Promyelocytic, Acute / Q000235:genetics* / Q000628:therapy; D008297:Male; D009687:Nuclear Proteins / Q000235:genetics*; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D000071156:Promyelocytic Leukemia Protein; D018168:Receptors, Retinoic Acid / Q000235:genetics*; D000072482:Retinoic Acid Receptor alpha; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics*; D025521:Tumor Suppressor Proteins / Q000235:genetics*
chemical_list: D009687:Nuclear Proteins; D015514:Oncogene Proteins, Fusion; D000071156:Promyelocytic Leukemia Protein; C000607071:RARA protein, human; D018168:Receptors, Retinoic Acid; D000072482:Retinoic Acid Receptor alpha; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; C070576:PML protein, human