Metaphase spreads have an established value in the routine diagnostic workup of myeloid malignancies and bone marrow failure disorders. In myelodysplastic syndrome (MDS) abnormal karyotypes play a large role in scoring systems and may greatly impact prognosis, or even predict responsiveness to certain therapies. In aplastic anemia (AA) cytogenetic abnormalities detected by metaphase karyotyping may rule out hypoplastic MDS. In myeloproliferative neoplasia (MPN), an abnormal karyotype may distinguish between reactive or malignant proliferation.
Due to technical problems, including specimen quality, viability, hypocellularity or a failure of growth, this routine test may fail to yield conclusive results in some patients. With the advent of SNP-A karyotyping, which only requires extracted DNA, non-informative cases can be resolved. As a cytogenetic test, single nucleotide polymorphism array (SNP-A) analysis can provide an opportunity to improve risk assessment and selection of proper treatment modalities. The advantages of SNP-A include excellent resolution, detection of copy neutral loss of heterozygosity (also known as uniparental disomy or UPD), and perhaps most importantly, the ability to test archived DNA samples, rather than actively dividing cells. However, unlike metaphase cytogenetics, this technology cannot detect subsets of abnormal populations or certain classes of genomic rearrangements, such as balanced translocation, inversion or ring chromosomes.
In this study, we examined the prognosis and disease characterization for patients with non-informative cytogenetics (N=144) collected over the last 8 years. SNP-A-based karyotyping has been performed for a representative subset of these patients (N=60) to assess whether this technique could provide clinically relevant information. These patients included patients with MDS (N=20), AA (N=20), AML (N=12) and MDS/MPN (N=3). Bone marrow obtained following induction chemotherapy was excluded. We have detected 27 somatic microdeletions and 33 microduplications (<10Mb) after eliminating germ line copy number variants seen in an internal control cohort (N=1355), publicly available databases or those present in paired non-clonal samples. However, for the purpose of subsequent analysis, somatic microdeletions and duplications were not included, as their prognostic significance has not been validated in large cohorts. (These microalterations may indicate edges of balanced translocations or true clonal pathogenic lesions.) None of these microdeletions were recurrent.
Based on these criteria, SNP-A analysis revealed an abnormal karyotype in 14 (23%) patients; 3 with AA and 11 with myeloid disorders. The most common recurrent abnormalities included deletion 5q (N=5) and del7/7q (N=3) but other lesions including13q-, del20, +8p were also seen. Of note we have also detected somatic UPD (regions >25Mb) in 2 cases, including 22q11.23qter and 14q12-q22.1. In 4/60 (7%) a complex karyotype was detected, while 10 had sole lesions (>10Mb).
In presumed AA patients, we have identified 2 patients with monosomy 7, prompting a change of diagnosis to MDS and thereby altering their clinical management. In MDS, when cytogenetic prognostic groupings were applied in previously unscored patients, 10/20 had IPSS scores of 3 or greater. The presence of chromosomal abnormalities detected by SNP-At indictated the presence of advanced risk disease and thereby contributed into poorer survival as predicted by IPSS.
No relevant conflicts of interest to declare.
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