Publication Date:
2016-12-02
Description:
Objective: We applied next generation sequencing (NGS) with a panel of 206-MPN-relevant genes, in order to identify non-driver mutation profile and prognostic value of non-driver mutations in PMF and Post-PV/ET myelofibrosis. Methods: Targeted capture sequencing assays were carried out on bone marrow DNA specimens obtained at time of referral. Gene list was shown in Figure 1. DNA libraries were prepared using Illumina standard protocol. The amplified DNA was captured by using biotinylated oligo-probes (MyGenosticsGenCap Enrichment technologies). Illumina utilizes a unique "bridged" amplification reaction that occurs on the surface of the flow cell. A flow cell containing millions of unique clusters is loaded into theHiSeq 2000 for automated cycles of extension and imaging. TheSolexa QA package, thecutadapt program, theSOAPaligner program, the Picard software, the GATK program, the Exome-assistant program, theMagicViewer, thePolyphen, the SIFT, the PANTHER and thePmut were used to bioinformatics analysis. Results: 54 PMF patients (median age 55 [21-77]yrs; 69% males) and 17 post-PV/ET patients (median age 59[46-83]yrs; 59% males) were tested. In PMF patients, 6 (13%) subjects were categorized as DIPPS low-risk group, 25 (56%) intermediate-1-riskgroup and 14 (31%) intermediate-2-risk group. JAK2 mutations were detected in 21 subjects (47%), CALR mutations in 4 (9%) , MPL mutation in 1(2%) and Tri-negative (no detectable mutation in JAK2, CALR or MPL) in 19 (42%). In post-PV/ET MF patients, JAK2 mutations were detected in 16 (94%) and CALR mutations in 1 (6%). In PMF patients, mutations other than JAK2, CALR or MPL, referred as non-driver mutation, were detected in 43 (96%) patients including 89% of "Tri-negative" subjects. 12 (27%) subjects harbored one, 9 (20%) two, 12 (26.7%) three and 10 (22%) four or more. Mutational frequencies were: ASXL1 33%, U2AF1 22%, TET2 16%, FAT1 16%, SETBP1 13%, CUX1 9%, EP300 9%, SRSF2 9%, FAT 2 6.7%, NOTCH3 6.7%, EZH2 6.7%, GATA3 6.7% and
Print ISSN:
0006-4971
Electronic ISSN:
1528-0020
Topics:
Biology
,
Medicine
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