Oligonucleotide Array CGH Studies in Myeloproliferative Neoplasms and Comparison with Conventional Cytogenetic Analysis
Authors: Tefferi Ayalew , Sirhan Shireen , Sun Yi , Lasho Terra L. , LeDuc Charles A. , Finke Christy M. , Weisberger James , Bale Sherri , Compton John , Pardanani Animesh , Thorland Erik C. , Shevchenko Yuriy , Grodman Marc D. , Chung Wendy K. 
Published: April 2020

Abstract
Background: Conventional cytogenetic studies in myeloproliferative neoplasms (MPNs) have provided pathogenetic, diagnostic and prognostic information and in certain instances guide therapeutic decisions. It is therefore reasonable to hypothesize that a higher resolution examination of chromosomes might reveal additional changes that are scientifically as well as clinically relevant.
Methods: Granulocyte DNA from 70 patients (median age 56 years, range 18–84; 43 males) with classic BCR-ABL-negative MPNs were studied: 27 with primary myelofibrosis (PMF), 22 with polycythemia vera (PV), 12 with essential thrombocythemia (ET), 6 with post-ET MF and 3 with post-PV MF. Twelve healthy volunteers were used as controls. Cytogenetic information, collected at variable times before the current study, was available in 57 patients. Samples were analyzed by comparative genomic hybridization (CGH) with a gender matched normal control using oligoarrays with either 44,000 or 105,000 oligonucleotides. Data were analyzed with CGH Analytics (Agilent). Copy number changes were considered significant (CNCs) if they were defined by 4 or more adjacent oligonucleotides spanning at least 150,000 base pairs, contained at least one gene, and were not identified in the Database of Genomic Variants.
Results: Array CGH results were equivocal in 6 cases, which were therefore excluded from further analysis. Among the 12 normal controls, granulocyte DNA displayed no CNCs. The percentage of patients with CNCs was 52% for PMF, 32% for PV and 17% for ET. In addition, 2 of 6 patients with post-ET MF and 1 of 2 patients with post-PV MF displayed CNCs. There was no correlation between the occurrence of CNCs and JAK2V617F mutational status in PMF and ET. Array CGH revealed CNCs in 16 of 49 patients (33%) with normal and 7 of 8 patients (88%) with abnormal cytogenetic findings; one patient with t(2;12)(p13;q14) in 19 of 20 metaphases detected at 9 months prior to sample collection for the array CGH study displayed no CNCs. In patients with abnormal cytogenetic findings, array CGH also detected imbalances at chromosomal translocations, including t(1;6), t(9;11), and t(1;18), as well as additional abnormalities that were not detected by cytogenetic analysis. A total of 23 single occurrence CNCs were documented and included all the ET [del(2)(q31.3q32.1), del(10)(q11.21q11.22)] and post-ET MF [del(2p12), del(Xq12)] associated CNCs. In contrast, several specific abnormalities were shared between PV and PMF including del(6p22) and dup(15q11.2). As expected, del(13q) and del(20q) abnormalities were recurrent in PMF.
Conclusions: Conventional cytogenetic analysis underestimates the extent of genomic gains and losses in BCR-ABL-negative MPNs. The current study suggests that oligonucleotide array CGH is more sensitive to detect small genomic alterations and we are currently studying higher resolution arrays in a larger group of patients to detect additional genomic alterations as well as assess overall clinical utility. The current data also suggest that chromosomal translocations are commonly associated with imbalances.