De Novo and Therapy-Related Acute Myeloid Leukemia and Myelodysplastic Syndrome: Similarities and Differences in SNP-Array Detected Chromosomal Aberrations in Pre-Transplant Blood Samples

• Published in: Blood Vol. 134; no. Supplement_1; p. 1430
• Main Authors: Wang, Youjin, Zhou, Weiyin, McReynolds, Lisa J., Griffiths, Elizabeth A., Thota, Swapna, Machiela, Mitchell, Chanock, Stephen J, Yeager, Meredith, McCarthy, Philip L., Pasquini, Marcelo C., Wang, Junke, Karaesmen, Ezgi, Rizvi, Abbas A., Preus, Leah, Tang, Hancong, Wang, Yiwen, Stram, Daniel, Pooler, Loreall, Sheng, Xin, Haiman, Christopher, Van Den Berg, David, Spellman, Stephen R., Wang, Tao, Kuxhausen, Michelle, Lee, Stephanie J., Hahn, Theresa E., Sucheston-Campbell, Lara E., Gadalla, Shahinaz M
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 13.11.2019
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2019-129110

Introduction: Clinical cytogenetics is the most important prognostic test for patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS); however, current tools do not provide a complete genome-wide picture of somatic chromosomal aberrations in those patients. We used a high-resolution genome-wide single-nucleotide polymorphism (SNP) array to identify large clonal chromosomal aberrations in pre-hematopoietic cell transplant (HCT) peripheral blood samples of patients with de novo or therapy-related AML and MDS. Methods: We used the HumanOmniExpress-24 BeadChip SNP array genotyping data generated in the DISCOVeRY-BMT study (includes patients with acute leukemia or MDS who received unrelated donor HCT between 2000-2011). Clinical data and biospecimens were obtained from the Center for International Blood and Marrow Transplant Research. Blood samples were collected at median of 7 days before HCT. We limited our analysis to patients with AML (N=1,982) and MDS (N=608). We calculated the log2 R ratio and B allele frequency (BAF) and used the Circular Binary Segmentation (SBC) algorithm to identify chromosomal aberrations spanning ≥2Mb. Results: Median age at sample collection was 48.2 (range=0.6-78.0) and 53.0 (range=0.0-74.0) years for AML and MDS, respectively. About 53% of AML and 59% of MDS patients were males, and 7.4% of AML and 15.8% of MDS patients had therapy-related disease. Among AML patients, 47.9% were in 1st complete remission and 22.8% in 2nd complete remission. For MDS, 56.1% of patients were in early stage (refractory anemia with or without ringed sideroblasts) at the time of HCT. Chromosomal aberrations were detected in 14.6% of the AML patients (n=289) and 34.7% of the MDS patients (n=211). In AML, 6.6% of those with hematological or molecular remission vs. 35.9% of those with advanced disease (not in remission) had SNP-array detected aberrations, with 0.7% of the patients vs. 8.9%, respectively carrying aberrations in ≥3 chromosomes. For MDS, chromosomal aberrations were detected in 31.4 vs. 39.0% of patients with early and advanced MDS, respectively. No differences by patient sex or race were detected in both AML and MDS (p>0.05). Figure 1 shows disease-specific type and frequency of detected chromosomal aberrations. Copy-losses in chr7 (chr7-), chr5 (chr5-), and copy-neutral loss of heterozygosity (CNLOH) in chromosome 17 (chr17-CNLOH) were the most common aberrations in both diseases, with higher frequencies in MDS (chr7-, 13.8 vs. 2.4%, respectively; chr5-, 7.2 vs. 1.8%; chr17-CNLOH, 4.4 vs. 1.5%, respectively, all p<0.0001). In comparison, CNLOH in chr13 was more frequent in AML than MDS (1.5 vs. 0.2%, respectively, p<0.01). Figure 2A shows detected chromosomal aberrations in de novo and therapy-related AML (tAML). The following were more frequently detected in tAML than de novo disease: copy-losses of chr5 (4.8 vs. 1.6%, p=0.02) and chr13 (2.7 vs. 0.6%, p=0.02). Aberrations in chromosomes 3, 10, 14, 15, 16 and 22 were found in de novo but not in tAML. The frequencies of chr7- (4.1 vs. 2.0%, in tAML and de novo, respectively, p=0.12) and copy-gain in chr8 (0.7 vs. 1.3%, p>0.99) were similar in the two disease subtypes. Figure 2B shows detected chromosomal aberrations in de novo and treatment-related MDS (tMDS). The following were more common in tMDS than de Novo MDS: copy losses in chr5 (16.7 vs. 5.5%, p<0.001), chr7 (26.0 vs. 11.5%, p<0.001), and chr18 (7.3 vs. 1.6%, p<0.01); also copy-gain in chr11 (4.2 vs. 0.4%, p<0.01), and chr17-CNLOH (9.4 vs. 3.5%, p=0.03). Unique aberrations in de novo MDS included CNLOHs in chr7 (2.5%), chr14 (1.2%), chr1 (1.0%), chr4 (1.0%) and copy-gain in chr17 (1.0%). Conclusion: High-resolution SNP array analysis provided a genome-wide landscape of large chromosomal aberrations in patients with AML and MDS. Detected aberrations were more frequent in MDS than AML patients; this is possibly affected by differences in pre-HCT initial therapy. This study showed the expected genomic landscape similarities between AML and MDS, but differences were also present (most noted was chr13-CNLOH predominance in AML). The observed differences between de novo and t-AML or t-MDS likely reflect distinct pathogenic processes. Differences between t-AML and t-MDS could be related to antecedent malignancy and/or therapeutic regimen. The impact of these detected aberrations on HCT outcomes is under investigation. [Display omitted] Griffiths:Novartis Inc.: Consultancy; Celgene, Inc: Consultancy, Research Funding; Celgene, Inc: Consultancy, Research Funding; New Link Genetics: Consultancy; New Link Genetics: Consultancy; Persimmune: Consultancy; Boston Scientific: Consultancy; Boston Scientific: Consultancy; Persimmune: Consultancy; Genentech, Inc.: Research Funding; Abbvie, Inc.: Consultancy, PI on a clinical trial; Astex Phramaceuticals/Otsuka Pharmaceuticals: Consultancy, Research Funding; Abbvie, Inc.: Consultancy; Astex Phramaceuticals/Otsuka Pharmaceuticals: Consultancy, Research Funding; Genentech, Inc.: Research Funding; Novartis Inc.: Consultancy; Appelis Pharmaceuticals: Other: PI on a clinical trial; Onconova Therapeutics: Other: PI on a clinical trial; Appelis Pharmaceuticals: Other: PI on a clinical trial; Onconova Therapeutics: Other: PI on a clinical trial; Partner Therapeutics: Consultancy; Partner Therapeutics: Consultancy. Thota:Incyte, Inc.: Speakers Bureau. Pasquini:Novartis: Research Funding; Kit Pharma: Research Funding; BMS: Research Funding; Medigene: Consultancy; Amgen: Consultancy; Pfizer: Other: Advisory Board. Lee:Takeda: Research Funding; Novartis: Research Funding; Amgen: Research Funding; Syndax: Research Funding; Incyte: Research Funding; Kadmon: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; AstraZeneca: Research Funding.