Chromosomal Aberrations Identified in CD34+ Peripheral Blood Cells of MDS Patients by FISH- and SNP Array Analysis

Chromosomal banding analysis (CBA) of bone marrow metaphases is the gold standard to identify chromosomal abnormalities in myelodysplastic syndromes (MDS). To detect and follow chromosomal abnormalities during the course of the disease without the need of repeated bone marrow biopsies, we are currently performing serial fluorescence in situ hybridization (FISH) analyses of CD34+ peripheral blood cells (PBC) in ongoing studies. To complement genetic analysis on peripheral blood we started a pilot study to establish SNP array analysis (SNP-A) on CD34+ PBC to identify chromosomal abnormalities not detectable by FISH.

We analyzed eleven MDS and two AML-patients with known karyotypes and compared CBA with FISH and SNP-A of CD34+ peripheral blood and/or bone marrow cells. The FISH panel comprised up to 13 probes. The Affymetrix Genome-Wide Human SNP Array 6.0 and/or the Affymetrix Cytogenetics Whole-Genome 2.7M Array were used. We also included serial samples from a RAEB-II patient where bone marrow and/or peripheral blood were available from six time points collected over a period of 6 months.

In 13 patients analyzed using CBA, FISH, and SNP-A in parallel, 10/60 (17%) chromosomal abnormalities were exclusively detected by SNP-A. Using CBA and FISH we detected 28 chromosomal abnormalities in 12 patients. Additional SNP-A revealed 6 further aberrations (upd(7)(q11qter), upd(10)(q23.33q25.1), upd(17)(pterp11.2), del(9)(q22.33q31.1), del(13)(q12.3q22.2), del(15)(q15.1)). In one patient SNP-A increased the number of detectable chromosomal abnormalities from 22 to 26 (amplifications on 6p, del(15)(q11.2q21.1), del(18)(pterp11), upd(20)(q11.22q12)). Additional abnormalities were also detected in the serial sample: The major clone detectable by CBA at three different time points was 44,XX,del(5)(q13q33),-7,del(12)(p13p11.2),-17,-20,+der(20)t(17;20)(q10;p10). We could confirm all these abnormalities in CD34+ peripheral blood and bone marrow cells using a FISH panel that includes del(5q31)/EGR1, −7/CEP7, del(12p13)/TEL, del(17p13)/TP53, and del(20q12)/D20S108. FISH on CD34+ PBC confirmed a stable number of aberrant cells as 5q- was detectable in 94–98% of CD34+ PBC at all six available time points. We could also confirm all abnormalities of the major clone by SNP-A in CD34+ PBC in month 2 and in CD34+ bone marrow cells in month 6. Additional abnormalities occurring in sub-clones changed over time. A sub-clone exclusively detectable by CBA was identified in the first available sample in 2/25 (8%) metaphases: 44,idem,+der(3)t(3;6)(p10;q10),-6. Supplementary FISH and SNP-A revealed a 9.6 Mb del(13q14) in 44% of CD34+ PBC that was not detectable by CBA and had subsequently disappeared in the last available sample. SNP-A on CD34+ bone marrow cells of the last sample revealed two additional abnormalities in the absence of clinical signs of progression (del(2)(q31q32), del(4)(q24q26)). The del(4q)/TET2 could be confirmed by FISH.

Detection and follow-up of chromosomal abnormalities during the course of the disease is possible without the need of bone marrow biopsies by parallel FISH and SNP-A of CD34+ peripheral blood cells. Detailed knowledge about the acquirement of chromosomal aberrations could be used to improve prognostication, to support therapy decisions and to unravel genetic evolutionary steps towards acute leukemia.

No relevant conflicts of interest to declare.