title: Identification of submicroscopic genetic changes and precise breakpoint mapping in myelofibrosis using high resolution mate-pair sequencing.
abstract: We used high resolution mate-pair sequencing (HRMPS) in 15 patients with primary myelofibrosis (PMF): eight with normal karyotype and seven with PMF-characteristic cytogenetic abnormalities, including der(6)t(1;6)(q21-23;p21.3) (n = 4), der(7)t(1;7)(q10;p10) (n = 2), del(20)(q11.2q13.3) (n = 3), and complex karyotype (n = 1). We describe seven novel deletions/translocations in five patients (including two with normal karyotype) whose breakpoints were PCR-validated and involved MACROD2, CACNA2D4, TET2, SGMS2, LRBA, SH3D19, INTS3, FOP (CHTOP), SCLT1, and PHF17. Deletions with breakpoints involving MACROD2 (lysine deacetylase; 20p12.1) were recurrent and found in two of the 15 study patients. A novel fusion transcript was found in one of the study patients (INTS3-CHTOP), and also in an additional non-study patient with PMF. In two patients with der(6)t(1;6)(q21-23;p21.3), we were able to map the precise translocation breakpoints, which involved KCNN3 and GUSBP2 in one case and HYDIN2 in another. This study demonstrates the utility of HRMPS in uncovering submicroscopic deletions/translocations/fusions, and precise mapping of breakpoints in those with overt cytogenetic abnormalities. The overall results confirm the genetic heterogeneity of PMF, given the low frequency of recurrent specific abnormalities, identified by this screening strategy. Currently, we are pursuing the pathogenetic relevance of some of the aforementioned findings.
authors.affiliation: Mayo College of Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
authors.forename: Terra
authors.initials: T
authors.lastname: Lasho
authors.forename: Sarah H
authors.initials: SH
authors.lastname: Johnson
authors.forename: David I
authors.initials: DI
authors.lastname: Smith
authors.forename: John D
authors.initials: JD
authors.lastname: Crispino
authors.forename: Animesh
authors.initials: A
authors.lastname: Pardanani
authors.forename: George
authors.initials: G
authors.lastname: Vasmatzis
authors.forename: Ayalew
authors.initials: A
authors.lastname: Tefferi
mesh_terms: D000368:Aged; D001483:Base Sequence; D056905:Chromosome Breakpoints; D002874:Chromosome Mapping; D002878:Chromosomes, Human, Pair 1; D002896:Chromosomes, Human, Pair 6; D002897:Chromosomes, Human, Pair 7; D005260:Female; D018740:Genetic Heterogeneity; D006801:Humans; D007621:Karyotyping; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D055728:Primary Myelofibrosis / Q000235:genetics* / Q000473:pathology; D017422:Sequence Analysis, DNA / Q000379:methods*; D017384:Sequence Deletion; D014178:Translocation, Genetic
chemical_list: D015514:Oncogene Proteins, Fusion