Development of Paralogue Ratio Test for KIR Copy Number Quantification among Malaysian HIV-1 patients

Yeoh, Soo Ghee (2020) Development of Paralogue Ratio Test for KIR Copy Number Quantification among Malaysian HIV-1 patients. [Project Paper] (Submitted)

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Abstract

Killer cell immunoglobulin-like receptors (KIR) located on chromosome 19q13.4 are inhibitory and activating immune receptors, on natural killer (NK) cells. KIR plays a significant role in facilitating cytotoxic activity of NK cells against pathogenic cells. KIR activity diversifies the NK cell function in the anti-HIV immune response, so the presence of KIR may influence HIV-1 infectious. KIR exhibits Copy Number Variation (CNV) and could affect HIV susceptibility attribute to gene dosage effect. Previous studies using real-time PCR, have shown an association between higher copy number of KIR gene and reduced risk of HIV-1 in European and Caucasian populations due to the increased activation of NK cell antiviral response. Nevertheless, limited study of Paralogue Ratio Test (PRT) application on KIR CNV had been conducted particularly among Malaysian population. PRT is known as a comparative PCR based method that uses single pair of primers to amplify both the test and reference loci. Objective: Thus, this study generally aimed to develop the PRT assay for KIR copy number quantification and association in Malaysian HIV-1 patients. Specifically to analyse the association of KIR CNV with CD4+ level. Methodology: A total of 130 extracted DNA samples from HIV-1 Malaysian patients (Malay: 52, Chinese: 49 & Indian: 29) and 163 of controls (Malay : 83, Chinese : 42 & Indian : 38) have been amplified by using PRT assay. PCR products were then electrophoresed and visualized under UV illumination, followed by capillary electrophoresis for peak scanner analysis through outsource of Apical Scientific Company. The genotypes were recorded and compared with the 163 of control samples. The results obtained were analyzed using Likelihood ratio test. Result and discussion: PRT assay has been unambiguously assigned 0.44 % of deletion and 0.3% of duplication KIR gene copies. However, distribution of KIR variable copy number was found not significantly associated with three major ethnics in Malaysia. Consequently, case-control analysis showed no association between the KIR copy number variables gene and Malaysia HIV-1 patients. Moreover, there is no significant correlation of CD4+ level with KIR CNV in Malaysia was found. Conclusion: Nevertheless, this study illustrates that PRT has been successfully detected CNV of KIR gene by showing there are variable KIR copies in HIV-1 and control, while KIR CNV is independent with ethnicity and CD4+ level after HAART.

Item Type:	Project Paper
Faculty:	Faculty of Medicine and Health Science
Depositing User:	Ms. Nor Safa'aton Saidin
Date Deposited:	22 Aug 2023 07:56
Last Modified:	22 Aug 2023 07:56
URI:	http://psaspb.upm.edu.my/id/eprint/1299

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