1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Distribution of HLA alleles in malignant tissues of patients with hepatocellular carcinoma
Paper ID : 1285-ICB10
Authors:
Shahram Aliyari1, Zahra Salehi2, Mohammad Hossein Norouzi-Beirami3, Kaveh Kavousi *4
1Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran.
2Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
3Department of Computer Engineering, Osku Branch, Islamic Azad University, Osku, Iran
4University of Tehran
Abstract:
Hepatocellular carcinoma (HCC) is one of the most common malignancies and a leading cause of cancer-related deaths worldwide. Despite evident role of human leukocyte antigen (HLA) in immune detection and killing of cancer cells, patients. HLA genotypes has not been fully characterized in HCC. The present study aimed to investigate the distribution of HLA allele frequency in HCC patients by in Silico HLA typing using RNA-Sequencing (RNAseq) sequence reads. We inferred the HLA genotypes across 371 TCGA-LIHC primary tumor samples using arcasHLA tool from input RNA sequencing data. A total of 58 HLA-A, 87 HLA-B, 52 HLA-C, 41 HLA-DPB1, 27 HLA-DQA, 43 HLA-DQB1, and 43 HLA-DRB1 alleles were identified in the HCC population. The most frequent allele in the HLA-A, HLA-B, HLA-C, HLA-DPB1, HLA-DQA, HLA-DQB1, and HLA-DRB1 loci were (A*02:01:01, 14.5 %), (B*07:02:0, 8.7%), (C*07:02:01, 12.5%), (DPB1*04:01:01, 28.3%), (DQA1*01:02:01, 15%), (DQB1*03:01:01, 14.8%), and (DRB1*07:01:0, 10.2%), respectively. HLA-B (89%) and HLA-DQB1 (90%) showed the highest level of heterozygosity. Together, our findings showed high prevalence of some HLA alleles with probable clinical significance in HCC. To provide a better plan for disease prognosis and immunotherapy treatment further evaluations of the identified alleles, particularly in patients as well as healthy controls, is necessary.
Keywords:
Hepatocellular carcinoma; HLA; Allele; RNA-Sequencing
Status : Paper Accepted (Poster Presentation)