Saudi Acute Myeloid Leukaemia (AML) Genome Reveals Significant Differences from That in the Western Population

Introduction

AML genome in the western populations has provided pathogenetic insights, prognosticators and selection of appropriate therapies. AML genome in the Middle East may differ from that in the west, because of younger population, racial, environmental and cultural factors including high consanguinity. We report for the first time, Whole Genome Sequencing (WGS) results in AML patients treated at the King Faisal Specialist Hospital and Research Centre in Riyadh, Saudi Arabia. The study was approved by KFSHRC ethics committee.

Method

The clinical data of 786 adult AML patients (18-89 years; median age 38) seen at KFSHRC from 2005 to 2023 was reviewed. In 217 (median age 42 years), bone marrow (BM) samples were available for WGS. The median follow up was 16 months (range 2-202 months). 198 cases were analysed at diagnosis, 19 at first relapse and 10 at both. DNA was extracted from BM; libraries were prepared using TruSeq DNA PCR-Free and Illumina DNA Prep, followed by paired-end sequencing with NovaSeq 6000 at 30-50× depth at KFSHRC. Germline and somatic SNVs/Indels were identified, using Mutect2, VarDict, and Strelka2 pipelines. Pathogenic and likely pathogenic variants were identified from ClinVar, COSMIC, and ACMG databases. Variants with minor allele frequency>1% specific to the Saudi population were filtered out. VAF thresholds were ≥35% for germline and ≥5% for somatic variants. The ichorCNA algorithm detected CNVs >5 Mbp, and structural variants were identified using Manta4. Extrachromosomal circular DNA (eccDNA) was detected with Amplicon Architect, and Kaplan–Meier and log-rank tests were used to assess survival.

Results

170 patients had denovo AML, 37 secondary AML, and 10 therapy-related AML. 112 patients had allogeneic and 16 autologous hematopoietic stem cell transplantation as consolidation. Of 198 patients at diagnosis, ELN risk of 46 were favourable (median survival, not reached), 80 intermediate (median survival 27 months), 63 adverse risk (median survival 15 months), and 5 APL, and not known in 4 patients.

WGS revealed additional alterations in 44 patients, leading to the reclassification within ELN risk categories of 27 individuals. WGS detected genetic alterations led to the reassignment of 23 patients to the adverse risk group and 3 cases with normal karyotype (NK) to favourable risk. The adverse risk AML was frequent in the Saudi cohort (43.4%). A novel MECOM::BCL11A rearrangement was found in a patient with sickle cell disease. Parental consanguinity was observed in 77(48.4%);46 were first cousin marriages. Germline variants were identified in 17/217(median age 30). Pathogenetic variants were detected in RUNX1 (4), FANCA (3), XPC (3), ANKRD26 (1), DDX41 (1), GATA2 (1), TP53 (1) and PTPN11(1). One patient each had Downs syndrome and clinical features of Fanconi Anemia without pathogenetic mutations in the known FANC genes.

Notably, 67 patients (30.8%) reported a past history of cancer; 14.9% had history of cancer, 44.7% in first-degree relatives, 31.3% in second-degree relatives and 7.5% in both. One patient had coexistent AML and colorectal cancer. Total of 360 somatic SNV/indels were detected in 152/182 (83.5%) patients at diagnosis. Mutations were seen in signalling pathway (26.4%), DNA methylation (26.4%), tumor suppressor (24.2%), FLT3 (21.4%), myeloid transcription factors(18.7%), chromatin modifiers(7.1%), NPM1(13.2%), (99% with insertion in exon12 ,75% with NK), spliceosome (6.6%), and cohesin-complex (2.7%) genes. Distinct differences emerged when comparing our cohort with the University of Washington and the BEAT datasets. NPM1 mutations were significantly less prevalent 13.2% vs 33.7% and 21.8% (p<0.05) and DTA, spliceosome, and cohesin-complex genes were also significantly less frequent (p<0.01). eccDNA was detected in 27 patients. Amplicons with AML-related genes (BCL2, FLT3, CALR, MYC, ASXL1) were present in four patients who failed to achieve CR, had a complex karyotype, and TP53 mutations.

Conclusion

Saudi AML patients are younger, with high consanguinity, family history of cancers and adverse risk features detected by WGS. Spectrum of germline mutations is different than in Western populations. NPM1, DTA, spliceosome and cohesin mutations are significantly less common than reported in Western literature, including those with NK. The study has important implications for pathogenesis and treatment of AML in Middle Eastern populations.