Cytogenetic and SNP Array Study of CML Patients In Complete Cytogenetic Remission.

Abstract 3433

The development of Ph⁻ clones with new cytogenetic abnormalities has been reported among CML patients with complete cytogenetic remission (CCR) following diverse therapies such as Interferon and Imatinib (Gleevec). The etiologies for these abnormalities have not been characterized and have been attributed to drug effect, or underlying genetic instability in the bone marrow cells preceding or concomitant to the development of CML.

Here we report on 31 patients in CCR who, in addition to standard karyotyping, were also analyzed by high-resolution SNP 6.0 array-based genomic copy number analysis.

Of the 31 patients studied, 18 were male and 13 female. Their median age was 51 (range 19–71 years). Patients were in CCR for durations ranging from 6+ months to 156+ months (median duration of 24+ months). The duration of major molecular response (MMR) was similar to the duration of the CCR, apart from one patient where it was shorter (36 months versus 84 months).

Past medical therapies included Imatinib only in 17 patients, Interferon-α followed by Imatinib in 11 patients, and Interferon only in 3 patients. Two of the patients also received low-dose Cytarabine in addition to Interferon and Imatinib, four received Dasatinib in addition to Interferon and Imatinib, and one received Nilotinib in addition to Imatinib.

At the time of the sample collection four of the patients received Dasatinib, one received Nilotinib, three patients received no treatment, and 23 received continuous treatment with Imatinib.

Cytogenetic testing disclosed normal karyotype in 24 of the patients. In two of the patients cytogenetic abnormalities were seen in only 1/20 analyzed cells – a finding not considered significant. Of the remaining patients, one had del20q in 11/20 analyzed cells. One had inversion of chromosome 12q (q15, q24.1 in 30/30 cells). One patient had an additional Y chromosome in 2/20 cells, one had deletion of the Y chromosome on 6/20 cells, and one had an extra chromosome 9 in 2/20 analyzed cells.

SNP 6.0 array profiling was done on paired DNA samples from purified CML patient-derived CD34+/CD38- cells as well as buccal DNA. Data were analyzed using the previously validated software tool dChipSNP. Acquired genomic copy number aberrations (aCNA) were identified through visual inspection of paired heatmap displays and polymorphic copy number variants (CNVs) excluded. In total, one aCNA was identified in this cohort that was located on chromosome 20 (case #1 with corresponding cytogenetic finding of deletion of 20q) at physical position 30.856–48.002 Mb). Therefore, small or micro-aCNA do not exist in CML patient CCR marrows at appreciable frequencies or at sufficient (>25%) clonal representation.

Based on this limited study sample, SNP arrays did not identify any additional genomic changes to the standard karyotype analysis. However, the recurrent presence of low frequency genomically abnormal clones in the bone marrow of these remission patients cannot be ruled out.