SNPs Tell Tales About What Myelodysplasia Is Made Of

Detection of chromosomal rearrangements in patients with myelodysplastic syndromes (MDS) is useful in several respects. To the clinical pathologist, finding a somatic chromosomal abnormality confirms the clonal nature of the patient’s bone marrow failure syndrome, supporting a diagnosis of MDS or another neoplastic myeloid disorder rather than a reactive, non-neoplastic cause for the cytopenias. To clinicians, the specifics of patients’ abnormal karyotypes are prognostically important, as per the familiar 1997 International Prognostic Scoring System, as well as the more recent and comprehensive cytogenetic clinical outcomes dataset from a German-Austrian MDS consortium organized by Detlef Haase and Christian Steidl.¹  To the scientist interested in MDS pathobiology, recurrent chromosomal abnormalities indicate genetic loci worthy of further laboratory investigation. For instance, frequent loss of heterozygosity (LOH) at chromosomes 4q24 and 7q35 contributed to discovery of recurrent TET2 and EZH2 mutations, respectively, in MDS and related myeloid neoplasms.

Yet nearly one-half of patients with MDS have a normal G-banded metaphase karyotype. The mechanisms of disease in such patients remain largely obscure; some cannot even obtain a clear diagnosis of MDS, and instead may need to be unhelpfully labeled “Idiopathic Cytopenias of Undetermined Significance (ICUS),” and followed expectantly. A normal metaphase karyotype does not mean, of course, that the patients’ chromosomes are normal — counting a few hundred stainable bands on 20 or 30 metaphase preparations is an insensitive technique for chromosomal assessment, offering detection only of large translocations, or deletions and additions involving many megabasepairs of DNA.

The first attempts to improve on metaphase karyotyping in MDS included panels of fluorescent in situ hybridization (FISH) probes targeted to common chromosomal abnormalities, such as deletions of chromosomes 5 or 7. While MDS FISH panels assess as many as 500 cells and can be useful if karyotyping fails or the patient refuses a bone marrow exam, the yield of such FISH panels in patients with a good metaphase karyotype prepared in a competent clinical laboratory is quite low, and FISH probes can only assay already-recognized abnormalities. In recent years, several groups of investigators have begun to explore newer whole-genome scanning techniques in MDS, including comparative genomic hybridization (CGH) and single nucleotide polymorphism (SNP) arrays. The latest human SNP arrays include millions of genetic markers, offering unprecedented resolution for detecting copy-number variation and LOH across the genome.

In this study, an international consortium of investigators brought together by Dr. Jaroslaw Maciejewski of Cleveland Clinic assessed samples from 430 patients with MDS, acute myeloid leukemia arising from MDS, or MDS/myeloproliferative overlap syndromes. The array-based technology detected chromosomal defects in 74 percent of patients, compared to only 44 percent by metaphase cytogenetics. It also found abnormal results in patients with normal metaphase cytogenetics, as well as additional abnormalities in patients already known to have abnormal cytogenetics. Dr. Maciejewski and colleagues compared paired marrow and CD3+ selected non-clonal cells whenever possible, since it can be difficult to distinguish germline and somatic copy number variations on size criteria alone.²  Abnormal SNP array results had a negative prognostic value independent of existing riskstratification criteria. It seems, then, that SNP arrays and related techniques may offer new insights into not just what MDS might be “made of,” but also which cases are less likely to behave indolently (i.e., move like a snail) or evolve more rapidly (i.e., like a frisky puppy dog tail), and perhaps even which patients need to be treated only with “sugar and spice” versus something not quite so nice.