A study on the genetic polymorphisms of <i>CYP3A5</i> among the Orang Asli in Malaysia using a next generation sequencing platform

<p><b>Background:</b> CYP3A5 is the predominant sub-family of biotransformation enzymes in the liver and the genetic variations in <i>CYP3A5</i> are an important determinant of inter-individual and inter-ethnic differences in CYP3A-mediated drug disposition and response.</p> <p><b>Aim:</b> This study aims to investigate the genetic polymorphisms of <i>CYP3A5</i> among the Orang Asli in Peninsular Malaysia using a next generation sequencing platform.</p> <p><b>Methods:</b> Genomic DNAs were extracted from blood samples of the three main Orang Asli tribes and whole-genome sequencing was performed.</p> <p><b>Results:</b> A total of 61 single nucleotide polymorphisms were identified and all the SNPs were located in introns except rs15524, which is in the 3’UTR, and 11 of these polymorphisms were novel. Two allelic variants and three genotypes were identified in the Orang Asli. The major allelic variant was the non-functional <i>CYP3A5*3</i> (66.4%). The percentages of Orang Asli with <i>CYP3A5*3/*3</i> (47.2%) and <i>CYP3A5</i>*1/*3 (38.1%) genotypes are more than twice the percentage of Orang Asli with <i>CYP3A5*1/*1</i> (14.8%) genotype. Almost half of the Orang Asli harboured CYP3A5 non-expressor genotype (<i>CYP3A5*3/*3</i>).</p> <p><b>Conclusions:</b> The predominance of the CYP3A5 non-expressor genotype among the Orang Asli was unravelled and the findings in this study may serve as a guide for the optimisation of pharmacotherapy for the Orang Asli community.</p

<i>CYP2C19</i> genotype frequencies in the Orang Asli.

<p><i>CYP2C19</i> genotype frequencies in the Orang Asli.</p

Analysis of haplotype structures at CYP2C19 locus in the Orang Asli.

<p>(a) Linkage disequilibrium map showing 19 haplotype blocks along with the reference SNP cluster ID (rs). Bright red depicts very strong LD (LOD ≥2; D’ = 1), pink red (LOD ≥2; D’ < 1) and blue (LOD < 2; D’ = 1) for intermediate LD and white for no LD (LOD < 2, D’ < 1) between the pair of SNPs. Numbers in the square were the D’ value multiplied by 100. (b) Haplotype structures of CYP2C19 with tagged SNP indicated by an inverted triangle. Frequency of each haplotype is shown at the edge and the multi-allelic D’ value between each block is shown beneath. The most common crossings between haplotypes are indicated by thick lines whereas less common crossings are indicated by thinner lines.</p

Comparison of <i>CYP2C19</i> allele frequencies between the Orang Asli and various populations.

<p>Comparison of <i>CYP2C19</i> allele frequencies between the Orang Asli and various populations.</p

Allele frequencies of <i>CYP2C19</i> in the Orang Asli.

<p>Allele frequencies of <i>CYP2C19</i> in the Orang Asli.</p

Detection of <i>CYP2C19</i> Genetic Variants in Malaysian Orang Asli from Massively Parallel Sequencing Data

<div><p>The human cytochrome P450 (CYP) is a superfamily of enzymes that have been a focus in research for decades due to their prominent role in drug metabolism. CYP2C is one of the major subfamilies which metabolize more than 10% of all clinically used drugs. In the context of CYP2C19, several key genetic variations that alter the enzyme’s activity have been identified and catalogued in the CYP allele nomenclature database. In this study, we investigated the presence of well-established variants as well as novel polymorphisms in the <i>CYP2C19</i> gene of 62 Orang Asli from the Peninsular Malaysia. A total of 449 genetic variants were detected including 70 novel polymorphisms; 417 SNPs were located in introns, 23 in upstream, 7 in exons, and 2 in downstream regions. Five alleles and seven genotypes were inferred based on the polymorphisms that were found. Null alleles that were observed include <i>CYP2C19*3</i> (6.5%), <i>*2</i> (5.7%) and <i>*35</i> (2.4%) whereas allele with increased function <i>*17</i> was detected at a frequency of 4.8%. The normal metabolizer genotype was the most predominant (66.1%), followed by intermediate metabolizer (19.4%), rapid metabolizer (9.7%) and poor metabolizer (4.8%) genotypes. Findings from this study provide further insights into the <i>CYP2C19</i> genetic profile of the Orang Asli as previously unreported variant alleles were detected through the use of massively parallel sequencing technology platform. The systematic and comprehensive analysis of <i>CYP2C19</i> will allow uncharacterized variants that are present in the Orang Asli to be included in the genotyping panel in the future.</p></div