Genomic Microarray Alterations Add Prognostic Power to the IPSS-R in MDS with Normal Karyotype

Background

Disease karyotype is the parameter with the strongest prognostic impact in the IPSS-R. Around 50% of MDS patients have a normal karyotype. Conventional G-banding cytogenetics has a resolution of 5-10 Mb. SNP microarrays is a genomic array with a higher resolution than cytogenetics and allows the detection of small copy number alterations (CNA) and absence of heterozygosity (AOH).

Our hypothesis is that in MDS patients with normal karyotype small cryptic alterations might exist, undetectable by conventional karyotyping, but with an impact on patient's outcome. Our aim is to study a series of MDS patients with normal karyotype belonging to the IWG-PM consortium (MDS Foundation) by SNP microarrays. Herein, we describe the preliminary findings as recruitment is ongoing and complete results will be presented at the meeting.

Patients and methods

We have recruited microarray data of 125 MDS patients with normal karyotype from centers belonging to the IWG-PM of the MDS Foundation. All cases included were studied with SNP array from Affymetrix®.

We collected clinical, biological and microarray data and we studied their impact on overall survival (OS) and acute myeloid leukemia (AML) evolution in 73 patients. The median age was 67.8 years (21.8-92.1), 51.2% were male and the most frequent subtype according 2008 WHO classification was refractory cytopenia with multilineage dysplasia (41.6%), followed by refractory anemia with excess of blasts-1 (RAEB-1) and -2, 18.4% and 16.8%, respectively. Median values at diagnosis were, for hemoglobin: 9.3g/dL, leukocytes count: 3.6x109/L, platelet count: 139x109/L, percentage of polymorphonuclear cells: 47%, and bone marrow blasts: 3.6%. Nineteen patients were analyzed with their matched germ-line control sample.

The statistical analysis was performed with SPSS and R software. As level of significance, 5% (two-sided) was chosen. No adjustment for multiple testing was applied.

Results

Fifty nine cases were found to be altered by microarrays (47.2%), with a median number of alterations of 1 (range: 1-8). CNA were detected in 36.8% of cases, in 8 cases CNA were larger than 5 Mb. AOH were detected in 18.4% of cases. The median size of the affected genome by CNA was 116 Kb, adding up CNA plus AOH was 24745.05Kb. There were significant differences, in distribution of FAB diagnosis and median percentage of bone marrow blasts, in patients altered by SNP arrays in comparison to patients with normal findings by this technique.

The impact on the outcome has been studied in 73 patients. The median OS was 35.6 months. The results of SNP array analysis showed that alterations detected by microarrays had no significant impact on outcome (P=0.237 for OS and P=0.807 for AML evolution), but the median OS is higher in cases with a "real" (neither visible by cytogenetics nor submicroscopic alterations) normal karyotype (53.48 vs. 25.90 months). Of note, the presence of AOH has a strong impact on OS (53.48 vs. 16.13 months, P=0.004), less on AML (P=0.086); also its size, greater than 25Mb, has an impact on OS (P=0.012) and AML evolution (P=0.050).

To compensate for differing risk distributions, we performed analyses adjusting for IPSS-R. Adjusted for risk, the microarray result adds prognostic power on OS (P=0.010) and AML evolution (P=0.059). As it was observed, the presence of AOH had prognostic impact on OS (P=0.008) and AML evolution (P=0.017). The affected genome size showed a significant impact on OS (P=0.006) and AML (P=0.024), four categories were defined: 0 Kb, >0-500 Kb, >500-20000 Kb and >20000 Kb.

Conclusions

MDS patients with normal karyotypes and alterations detected by genomic microarrays have lower OS and shorter time to AML compared to those without CNA. While not significant in marginal analysis, it can be demonstrated if adjustment for IPSS-R is performed. Alterations and, particularly, AOH have an independent prognostic impact and add prognostic power to IPSS-R.

Acknowledgments

Financial support: This work was supported, in part, by a grant from the Instituto de Salud Carlos III, Ministerio de Sanidad y Consumo, Spain (PI 11/02010); Red Temática de Investigación Cooperativa en Cáncer (RTICC, FEDER) (RD12/0036/0044); 2014 SGR225 (GRE) Generalitat de Catalunya; Fundació Internacional Josep Carreras, Obra Social “La Caixa”, Celgene Spain and NHRI-EX103-10003NI,Taiwan.

Special thanks to Dr. Al-Ali, Dr. Bäsecke, members of Grupo Español de SMD (GESMD) and MDS Foundation.