Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes
Jason D. Merker,
Krishna M. Roskin,
Dana Ng,
Cuiping Pan,
Dianna G. Fisk,
Jasmine J. King,
Ramona Hoh,
Michael Stadler,
Lawrence M. Okumoto,
Parveen Abidi,
Rhonda Hewitt,
Carol D. Jones,
Linda Gojenola,
Michael J. Clark,
Bing Zhang,
Athena M. Cherry,
Tracy I. George,
Michael Snyder,
Scott D. Boyd,
James L. Zehnder,
Andrew Z. Fire,
Jason Gotlib
Affiliations
Jason D. Merker
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Krishna M. Roskin
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Dana Ng
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Cuiping Pan
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Dianna G. Fisk
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Jasmine J. King
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Ramona Hoh
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Michael Stadler
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Lawrence M. Okumoto
Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
Parveen Abidi
Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
Rhonda Hewitt
Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
Carol D. Jones
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Linda Gojenola
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Michael J. Clark
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Bing Zhang
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Athena M. Cherry
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Tracy I. George
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
Michael Snyder
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Scott D. Boyd
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
James L. Zehnder
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA;Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
Andrew Z. Fire
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA;Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Jason Gotlib
Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
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).
