Archiving of Somatic Novel Mutations Using Whole-Exome Sequencing in Pakistani Myeloid Leukemic Patients

Introduction

Acute myeloid leukemia (AML) is a highly malignant cancer of the bone marrow, clinically and genetically

heterogenous clonal disease illustrated by the accumulation of acquired somatic genetic alterations in hematopoietic progenitor cells that modify normal mechanisms of self-renewal, proliferation and differentiation. AML cytogenetic studies provide important diagnostic and prognostic information for AML patients. However, approximately 50% of AML patients have a normal karyotype (NK- AML). Large number of causal mutations of AML has not yet been uncovered. Although disease etiology is still unknown after multiple OMIC's study were published. In this review an attempt is made to approach the subject in the light of currently available literature.

Material and Methods

Material and information of diagnosed cases of de novo AML (n=14) used after approval of Institutional Ethics Review Committee. Morphological subtypes of AML were classified according to WHO classification. A researcher used retrospective medical record review to obtain clinical, diagnostic data including disease status and blood chemistry and as well as archived genomic DNA of untreated cases. Mutational analysis was done to identify AML somatic mutations using the whole-exome sequencing. The library preparation along with the capture used the illumina TruSeq DNA Exome kit. NGS HS Kit -Proposed sequencing platform - illumina® NovaSeq 6000, 300 cycles -100X coverage - approx. 6Gb per sample. We explored the functional impact of the genes identified in the mutational analyses through an integrated Gene Ontology (GO) and pathway analysis.

Results

Majority of patients were 10 male with median age 40 range (23-60 years). AML with normal karyo type AML (NK-AML) were five included with maturation, without maturation and monocytic lineage. Significant somatic single nucleotide variants (SNVs) were identified and pathway analysis performed to determine frequently affected signaling pathways. We identified significant, novel recurrent mutations in MAML3 gene (8 patients). No significant novel gene identified in three abnormal karyo type AML (AK-AML). Five out of the 30 novel genes have previously been reported to be associated with other diseases. MAML3 showed statistical significance exclusively in NK-AML patients(n=5). A total of 700 genes identified 500 missense, 25 nonsense, 90 frameshift indels, and/or three stop codon deletions. Using the IntOGen platform, we identified MAP kinase, cell cycle, actin cytoskeleton regulation, PI3K-Akt signaling and other pathways in cancer as affected in the samples.

Conclusion

This data is the first of its kind from the Pakistani population.Specific patterns of genomic alterations may play an important role in sub types of morphological AML. Future studies to evaluate the usefulness of these genes in genetic testing for the early diagnosis and prognostic prediction of AML patients would be worthwhile.

Keywords:

Acute myeloid leukemia, Gene ontology, Pathway analysis, Somatic mutation, Subtype-specific mutation, Whole-exome sequencing