title: Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes.
abstract: In order to identify novel somatic mutations associated with classic BCR/ABL1-negative myeloproliferative neoplasms, we performed high-coverage genome sequencing of DNA from peripheral blood granulocytes and cultured skin fibroblasts from a patient with MPL W515K-positive primary myelofibrosis. The primary myelofibrosis genome had a low somatic mutation rate, consistent with that observed in similar hematopoietic tumor genomes. Interfacing of whole-genome DNA sequence data with RNA expression data identified three somatic mutations of potential functional significance: i) a nonsense mutation in CARD6, implicated in modulation of NF-kappaB activation; ii) a 19-base pair deletion involving a potential regulatory region in the 5'-untranslated region of BRD2, implicated in transcriptional regulation and cell cycle control; and iii) a non-synonymous point mutation in KIAA0355, an uncharacterized protein. Additional mutations in three genes (CAP2, SOX30, and MFRP) were also evident, albeit with no support for expression at the RNA level. Re-sequencing of these six genes in 178 patients with polycythemia vera, essential thrombocythemia, and myelofibrosis did not identify recurrent somatic mutations in these genes. Finally, we describe methods for reducing false-positive variant calls in the analysis of hematologic malignancies with a low somatic mutation rate. This trial is registered with ClinicalTrials.gov (NCT01108159).
authors.affiliation: jdmerker@stanford.edu.
authors.forename: Jason D
authors.initials: JD
authors.lastname: Merker
authors.forename: Krishna M
authors.initials: KM
authors.lastname: Roskin
authors.forename: Dana
authors.initials: D
authors.lastname: Ng
authors.forename: Cuiping
authors.initials: C
authors.lastname: Pan
authors.forename: Dianna G
authors.initials: DG
authors.lastname: Fisk
authors.forename: Jasmine J
authors.initials: JJ
authors.lastname: King
authors.forename: Ramona
authors.initials: R
authors.lastname: Hoh
authors.forename: Michael
authors.initials: M
authors.lastname: Stadler
authors.forename: Lawrence M
authors.initials: LM
authors.lastname: Okumoto
authors.forename: Parveen
authors.initials: P
authors.lastname: Abidi
authors.forename: Rhonda
authors.initials: R
authors.lastname: Hewitt
authors.forename: Carol D
authors.initials: CD
authors.lastname: Jones
authors.forename: Linda
authors.initials: L
authors.lastname: Gojenola
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Clark
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.forename: Athena M
authors.initials: AM
authors.lastname: Cherry
authors.forename: Tracy I
authors.initials: TI
authors.lastname: George
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Scott D
authors.initials: SD
authors.lastname: Boyd
authors.forename: James L
authors.initials: JL
authors.lastname: Zehnder
authors.forename: Andrew Z
authors.initials: AZ
authors.lastname: Fire
authors.forename: Jason
authors.initials: J
authors.lastname: Gotlib
mesh_terms: D002478:Cells, Cultured; D056726:Genetic Association Studies / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation / Q000235:genetics*; D055728:Primary Myelofibrosis / Q000175:diagnosis* / Q000235:genetics*