Genes Profiling of a Patient with Chronic Myeloid Leukemia on Illumina MiSeq Platform: A Cases Report

Ibraheem Ashankyty^1,2* & Edem Nuglozeh³

¹Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Ha’il, Ha’il, Saudi Arabia
²Department of Medical Laboratory Technology, College of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
³Department of Biochemistry, College of Medicine, University of Ha’il, Ha’il, Saudi Arabia

Dr. Ibraheem Ashankyty, Department of Medical Laboratory Technology, College of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.

Keywords: Leukemia; CML; Philadelphia Chromosome; Exome Sequencing

Abstract

CML is a malignant disease of the pluripotent hematopoietic stem cell characterized by the Philadelphia chromosome (Ph) and a rearrangement between the BCR gene (break-point cluster region) and the ABL gene. Albeit multiple advances of research in this field, the molecular mechanisms leading to establishment and development of this disease are not completely understood. The incidence of CML is influenced by different parameters like: demography, gender, ethnicity and socio-economic difference.
We undertook this study to establish a repertoire of genes involved in the symptomatology of CML in Hail region (Saudi Arabia). We ran exome sequencing on blood genomic DNA (gDNA) from a 55-year-old Saudi patient on the Illumina Platform (San Diego, CA USA) as part of a pilot study preluding the establishment of genomic database in relation with this disease. The sequencing results were analysed using the GATK Bioinformatics suit system.
Indel realignment followed by base recalibration and HaplotypeCaller program generated a VCF file which outputs all the variants including SNPs and INDELS. After filtration and application of diseases association program and removal of genes of low quality and synonymous mutations, we obtained 244 unique genes that have been found to be associated with Leukemia. After intronic filtration variants, we obtained exonic variants: BCL6, CASP7, ILIA, RAGI, MMP8 and 14 are genes with possible association with CML. These genes are of great of interest in that, they are linked in the development and progression of CML. Lastly, using R-language data manipulation software and successive filtration of our raw data before exonic filtration, we obtained reduction variants. JAK1 and MLP resulted to be the variants of interest resulting from this merge and these two variants are associated with Myeloproliferative Disorders Philadelphia Chromosome.

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