Genomic aberrations should not be overlooked in myelodysplastic syndromes

from Drs. Cecilia Yeung and Min Fang, Clinical Research Division
MDS patients tested with TGA (total genomic aberrations) exceeding 100Mb have a significantly shorter survival than patients tested with a TGA score below 100Mb.
MDS patients tested with TGA (total genomic aberrations) exceeding 100Mb have a significantly shorter survival than patients tested with a TGA score below 100Mb. Figure provided by Dr. Cecilia Yeung.

Myelodysplastic syndromes (MDS) are a group of genetic disorders affecting blood cell maturation. The only curative treatment available to date is hematopoietic (blood) stem cell transplantation using donor cells. The standard for establishing MDS diagnosis and identifying patients that could benefit from transplant is based on the World Health Organization (WHO) guidelines, and the International Program Scoring System, consisting in the identification and quantification of immature hematopoietic cells (blast), cell blood counts and karyotyping (identification of chromosomal anomalies based on appearance and number of chromosomes). However, half of MDS patients present a normal karyotype and are at risk for misdiagnosis. This is especially true for MDS patients with copy-neutral loss of heterozygosity or cnLOH. Each individual possesses two copies of each chromosome, one inherited from each parent. In tumor cells from patients with cnLOH patients both copies are from a single parent, decreasing gene variability and hence the so-called Loss-of-Heterozygosity. This acquired homozygosity increases the risk for disease development, as a dysfunctional gene from one copy will not be rescued by a functional gene from a different second copy.

A collaborative work between Drs. Cecilia Yeung and Min Fang (Clinical Research Division), recently published in the journal Modern Pathology, established chromosomal genetic array testing (CGAT) as a valuable tool for the identification of cnLOH in MDS patient diagnosis and risk stratification. The authors performed a retrospective study on 68 MDS patients diagnosed at the University of Washington Medical Center and Seattle Cancer Care Alliance between 2008 and 2014 who also underwent CGAT. CGAT was performed on genomic DNA isolated from thawed bone marrow aspirate samples. The results were correlated with other diagnosis criteria including cell phenotyping, gene expression characterization and karyotyping.

Among the 68 patients, 38 (56%) were initially identified with an abnormal karyotype while 26 (38%) had a normal karyotype. However, CGAT established that 50 patients (73%), instead of the 38 initially identified, presented some genetic anomalies, including 22 patients with cnLOH. 12 of these cnLOH patients belonged to the group with a normal karyotype.

The most frequent genomic aberrations (gain or loss) identified in the study have been commonly associated with MDS and included genes such as TET2 whose protein, Methylcytosine dioxygenase, is involved in DNA demethylation, JAK2 (Janus kinase 2) a tyrosine kinase involved in hematopoietic cell proliferation, or TP53, a tumor suppressor.

The identification of genomic aberrations were significantly associated with dysplastic cell morphology (abnormal cell development leading to abnormal morphology), (p=0.05 for cnLOH, p=0.003 for other genomic aberrations), and also associated with increased detection of immature cells, although the latter was not significant (p=0.07). Greater total genomic aberrations also led to increased number of affected dysplastic lineages. Dr. Yeung explained, “since MDS is a heterogeneous disease, we hypothesize that perhaps this relates to whether there is a driver mutational event such as 5q minus in those cases which show less dysplasia or if there are more complex chromosomal aberrations in those cases with multilineage dysplasia such as in cases of therapy related MDS”.

Follow-up data were available for 63 patients: 11 patients relapsed, 27 died and 32 are alive. Patients with cnLOH had the lowest overall survival (24.9 months) while patients with other genomic aberrations had a 35.8 months overall survival. Additionally, total genomic aberrations affecting more than 100Mb were associated with a lower overall survival compared to patients presenting total genomic aberrations below 100Mb (p=0.01). Among the 63 patients, 59% were transplanted after sample collection, and 11 patients relapsed without correlation with the total genomic aberrations, however small sample size warrant further analyses.

Collectively, these results clearly demonstrate that the inclusion of CGAT testing for MDS diagnosis would improve the diagnosis but also allow risk stratification for prognosis. Indeed, “we believe that CGAT will be helpful in the care of patients with MDS by being able to detect cases where there may be more chromosomal aberrations than detectable by karyotype analysis”, Dr. Yeung said before concluding, “we are most excited that our study showed CGAT may provide useful clinical data to aid our clinical colleagues in the management of their patients with MDS”.


Funding for this study was provided by a Pilot & Feasibility grant under the Core Center of Excellence in Hematology and the Cancer Center Support Grant, Adult Leukemia Research Center (National Cancer Institute / National Institutes of Health).


Yeung CCS,McElhone S,Chen XY,Ng D,Storer BE,Deeg HJ,Fang M. 2017. Impact of copy neutral loss of heterozygosity and total genome aberrations on survival in myelodysplastic syndrome. Modern Pathology. [Epub ahead of print]