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11. Systematic characterization and comparison of the CYP2C9 variability of the Orang Asli in Malaysia with 12 populations

Author

Teh, Lay Kek, Subramaniam, Vinothini, Tuan Abdu Aziz, Tuan Azlin, Lee, Lian Shien, Ismail, Mohamed Izwan, Yu, Choo Yee, Ang, Geik Yong, James Johari, Richard, Ismet, Rose Iszati, Sahak, Noor Saadah, Ahmad, Aminuddin, Rahman, Thuhairah Abdul, Nor @ Ghazali, Fadzilah Mohd, Shaari, SyahrulAzlin, Omar, Mustaffa, Ismail, Adzrool Idzwan, Md. Isa, Kamarudzaman, Salleh, Hood, and Salleh, Mohd Zaki

Published
2016
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20. Lateral flow immunoassays for SARS-CoV-2

Author

Ang, Geik Yong, Chan, Kok Gan, Yean, Chan Yean, Yu, Choo Yee, Ang, Geik Yong, Chan, Kok Gan, Yean, Chan Yean, and Yu, Choo Yee

Abstract

The continued circulation of SARS-CoV-2 virus in different parts of the world opens up the possibility for more virulent variants to evolve even as the coronavirus disease 2019 transitions from pandemic to endemic. Highly transmissible and virulent variants may seed new disruptive epidemic waves that can easily put the healthcare system under tremendous pressure. Despite various nucleic acid-based diagnostic tests that are now commercially available, the wide applications of these tests are largely hampered by specialized equipment requirements that may not be readily available, accessible and affordable in less developed countries or in low resource settings. Hence, the availability of lateral flow immunoassays (LFIs), which can serve as a diagnostic tool by detecting SARS-CoV-2 antigen or as a serological tool by measuring host immune response, is highly appealing. LFI is rapid, low cost, equipment-free, scalable for mass production and ideal for point-of-care settings. In this review, we first summarize the principle and assay format of these LFIs with emphasis on those that were granted emergency use authorization by the US Food and Drug Administration followed by discussion on the specimen type, marker selection and assay performance. We conclude with an overview of challenges and future perspective of LFI applications.

Published
2022

23. Selangor Darul Ehsan

Author

Lim Siu Cin and Yu Choo Yee

Subjects
Business, Socioeconomics
Abstract

While consumers are becoming more health conscious due to the wide dissemination of health-related information, statistics involving chronic illnesses continued to increase against the backdrop of increasing expenditure on supplements, gym membership, organic food, etc.

Published
2020
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24. Harnessing CRISPR-Cas to combat COVID-19: from diagnostics to therapeutics

Author

Kok, Gan Chan, Geik, Yong Ang, Yu, Choo Yee, Chan, Yean Yean, Kok, Gan Chan, Geik, Yong Ang, Yu, Choo Yee, and Chan, Yean Yean

Abstract

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global threat with an ever-increasing death toll even after a year on. Hence, the rapid identification of infected individuals with diagnostic tests continues to be crucial in the on-going effort to combat the spread of COVID-19. Viral nucleic acid detection via real-time reverse transcription polymerase chain reaction (rRT-PCR) or sequencing is regarded as the gold standard for COVID-19 diagnosis, but these technically intricate molecular tests are limited to centralized laboratories due to the highly specialized instrument and skilled personnel requirements. Based on the current development in the field of diagnostics, the programmable clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system appears to be a promising technology that can be further explored to create rapid, cost-effective, sensitive, and specific diagnostic tools for both laboratory and point-of-care (POC) testing. Other than diagnostics, the potential application of the CRISPR–Cas system as an antiviral agent has also been gaining attention. In this review, we highlight the recent advances in CRISPR–Cas-based nucleic acid detection strategies and the application of CRISPR–Cas as a potential antiviral agent in the context of COVID-19.

Published
2021

27. Mitochondrial DNA mutations in Malaysian female breast cancer patients

Author

Omasanggar, Raevathi, Yu, Choo Yee, Ang, Geik Yong, Emran, Nor Aina, Kitan, Normayah, Baghawi, Anita, Ahmad, Atiki Falparado, Abdullah, Maizaton Atmadini, Teh, Lay Kek, Maniam, Sandra, Omasanggar, Raevathi, Yu, Choo Yee, Ang, Geik Yong, Emran, Nor Aina, Kitan, Normayah, Baghawi, Anita, Ahmad, Atiki Falparado, Abdullah, Maizaton Atmadini, Teh, Lay Kek, and Maniam, Sandra

Abstract

Cancer development has been ascribed with diverse genetic variations which are identified in both mitochondrial and nuclear genomes. Mitochondrial DNA (mtDNA) alterations have been detected in several tumours which include lung, colorectal, renal, pancreatic and breast cancer. Several studies have explored the breast tumour-specific mtDNA alteration mainly in Western population. This study aims to identify mtDNA alterations of 20 breast cancer patients in Malaysia by next generation sequencing analysis. Twenty matched tumours with corresponding normal breast tissues were obtained from female breast cancer patients who underwent mastectomy. Total DNA was extracted from all samples and the entire mtDNA (16.6kb) was amplified using long range PCR amplification. The amplified PCR products were sequenced using mtDNA next-generation sequencing (NGS) on an Illumina Miseq platform. Sequencing involves the entire mtDNA (16.6kb) from all pairs of samples with high-coverage (~ 9,544 reads per base). MtDNA variants were called and annotated using mtDNA-Server, a web server. A total of 18 of 20 patients had at least one somatic mtDNA mutation in their tumour samples. Overall, 65 somatic mutations were identified, with 30 novel mutations. The majority (59%) of the somatic mutations were in the coding region, whereas only 11% of the mutations occurred in the D-loop. Notably, somatic mutations in protein-coding regions were non-synonymous (49%) in which 15.4% of them are potentially deleterious. A total of 753 germline mutations were identified and four of which were novel mutations. Compared to somatic alterations, less than 1% of germline missense mutations are harmful. The findings of this study may enhance the current knowledge of mtDNA alterations in breast cancer. To date, the catalogue of mutations identified in this study is the first evidence of mtDNA alterations in Malaysian female breast cancer patients.

Published
2020

35. Detection of CYP2C19 Genetic Variants in Malaysian Orang Asli from Massively Parallel Sequencing Data

Author

Ang, Geik Yong, primary, Yu, Choo Yee, additional, Subramaniam, Vinothini, additional, Abdul Khalid, Mohd Ikhmal Hanif, additional, Tuan Abdu Aziz, Tuan Azlin, additional, Johari James, Richard, additional, Ahmad, Aminuddin, additional, Abdul Rahman, Thuhairah, additional, Mohd Nor, Fadzilah, additional, Ismail, Adzrool Idzwan, additional, Md. Isa, Kamarudzaman, additional, Salleh, Hood, additional, Teh, Lay Kek, additional, and Salleh, Mohd Zaki, additional

Published
2016
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38. A study on the genetic polymorphisms of <italic>CYP3A5</italic> among the Orang Asli in Malaysia using a next generation sequencing platform.

Author

Ang, Geik Yong, Yu, Choo Yee, Johari James, Richard, Ahmad, Aminuddin, Abdul Rahman, Thuhairah, Mohd Nor, Fadzilah, Shaari, Syahrul Azlin, Ismail, Adzrool Idzwan, Teh, Lay Kek, and Salleh, Mohd Zaki

Subjects
*ORANG Asal (Malaysian people), *GENETIC polymorphisms, *CYTOCHROME P-450, *SINGLE nucleotide polymorphisms, *INTRONS, *GENOTYPES, *PHARMACOGENOMICS
Abstract

Background: CYP3A5 is the predominant sub-family of biotransformation enzymes in the liver and the genetic variations in CYP3A5 are an important determinant of inter-individual and inter-ethnic differences in CYP3A-mediated drug disposition and response. Aim: This study aims to investigate the genetic polymorphisms of CYP3A5 among the Orang Asli in Peninsular Malaysia using a next generation sequencing platform. Methods: Genomic DNAs were extracted from blood samples of the three main Orang Asli tribes and whole-genome sequencing was performed. Results: 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 CYP3A5*3 (66.4%). The percentages of Orang Asli with CYP3A5*3/*3 (47.2%) and CYP3A5*1/*3 (38.1%) genotypes are more than twice the percentage of Orang Asli with CYP3A5*1/*1 (14.8%) genotype. Almost half of the Orang Asli harboured CYP3A5 non-expressor genotype (CYP3A5*3/*3). Conclusions: 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. [ABSTRACT FROM AUTHOR]

Published
2018
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45. Prevalence, Antimicrobial Resistance, and Genetic Diversity of Listeriaspp. Isolated from Raw Chicken Meat and Chicken-Related Products in Malaysia

Author

Chin, Pui San, Ang, Geik Yong, Yu, Choo Yee, Tan, Eng Lee, Tee, Kok Keng, Yin, Wai Fong, Chan, Kok Gan, and Tan, Geok Yuan Annie

Abstract

Listeriaspp. are ubiquitous in nature and can be found in various environmental niches such as soil, sewage, river water, plants, and foods, but the most frequently isolated species are Listeria monocytogenesand Listeria innocua. In this study, the presence of Listeriaspp. in raw chicken meat and chicken-related products sold in local markets in Klang Valley, Malaysia was investigated. A total of 44 Listeriastrains (42 L. innocuaand 2 L. welshimeri) were isolated from 106 samples. Antibiotic susceptibility tests of the L. innocuastrains revealed a high prevalence of resistance to clindamycin (92.9%), ceftriaxone (76.2%), ampicillin (73.8%), tetracycline (69%), and penicillin G (66.7%). Overall, 31 L. innocuaand 1 L. welshimeristrain were multidrug resistant, i.e., nonsusceptible to at least one antimicrobial agent in three or more antibiotic classes. The majority of the L. innocuastrains were placed into five AscI pulsogroups, and overall 26 distinct AscI pulsotypes were identified. The detection of multidrug-resistant Listeriastrains from different food sources and locations warrants attention because these strains could serve as reservoirs for antimicrobial resistance genes and may facilitate the spread and emergence of other drug-resistant strains.

Published
2018
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47. Systematic characterization and comparison of the CYP2C9variability of the Orang Asli in Malaysia with 12 populations

Author

Teh, Lay Kek, Subramaniam, Vinothini, Tuan Abdu Aziz, Tuan Azlin, Lee, Lian Shien, Ismail, Mohamed Izwan, Yu, Choo Yee, Ang, Geik Yong, James Johari, Richard, Ismet, Rose Iszati, Sahak, Noor Saadah, Ahmad, Aminuddin, Rahman, Thuhairah Abdul, Nor @ Ghazali, Fadzilah Mohd, Shaari, SyahrulAzlin, Omar, Mustaffa, Ismail, Adzrool Idzwan, Md. Isa, Kamarudzaman, Salleh, Hood, and Salleh, Mohd Zaki

Abstract

We conducted a systematic characterization of CYP2C9variants in 61 Orang Asli and 96 Singaporean Malays using the whole genome sequences data and compared the variants with the other 11 HapMap populations. The frequency of rs1057910 (CYP2C9*3) is the highest in the Orang Asli compared to other populations. Three alleles with clinical implication were detected in the Orang Asli while 2 were found in the Singaporean Malays. Large numbers of the Orang Asli are predicted to have reduced metabolic capacity and therefore they would require a lower dose of drugs which are metabolized by CYP2C9. They are also at increased risks of adverse effects and therapeutic failures. A large number of CYP2C9 variants in the Orang Asli were not in the Hardy Weinberg Equilibrium which could be due to small sample size or mutations that disrupt the equilibrium of allele frequencies. In conclusion, different polymorphism patterns, allele frequencies, genotype frequencies and LD blocks are observed between the Orang Asli, the Singaporean Malays and the other populations. The study provided new information on the genetic polymorphism of CYP2C9which is important for the implementation of precision medicine for the Orang Asli.

Published
2016
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49. Molecular Evidence of Cholera Outbreak Caused by a Toxigenic Vibrio choleraeO1 El Tor Variant Strain in Kelantan, Malaysia

Author

Ang, Geik Yong, Yu, Choo Yee, Balqis, Kamarudin, Elina, Husni Tan, Azura, Hussin, Hani, Mat Hussin, and Yean, Chan Yean

Abstract

ABSTRACTA total of 20 Vibrio choleraeisolates were recovered for investigation from a cholera outbreak in Kelantan, Malaysia, that occurred between November and December 2009. All isolates were biochemically characterized as V. choleraeserogroup O1 Ogawa of the El Tor biotype. They were found to be resistant to multiple antibiotics, including tetracycline, erythromycin, sulfamethoxazole-trimethoprim, streptomycin, penicillin G, and polymyxin B, with 35% of the isolates being resistant to ampicillin. All isolates were sensitive to ciprofloxacin, norfloxacin, chloramphenicol, gentamicin, and kanamycin. Multiplex PCR analysis confirmed the biochemical identification and revealed the presence of virulence genes, viz., ace, zot, and ctxA, in all of the isolates. Interestingly, the sequencing of the ctxBgene showed that the outbreak strain harbored the classical cholera toxin gene and therefore belongs to the newly assigned El Tor variant biotype. Clonal analysis by pulsed-field gel electrophoresis demonstrated that a single clone of a V. choleraestrain was responsible for this outbreak. Thus, we present the first molecular evidence that the toxigenic V. choleraeO1 El Tor variant has invaded Malaysia, highlighting the need for continuous monitoring to facilitate early interventions against any potential epidemic by this biotype.

Published
2010
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50. Draft genome sequence of multidrug-resistant Salmonella entericaserovar Brancaster strain PS01 isolated from chicken meat, Malaysia

Author

Chin, Pui San, Yu, Choo Yee, Ang, Geik Yong, Yin, Wai-Fong, and Chan, Kok-Gan

Abstract

Salmonellaspp. represent one of the main diarrhoeal pathogens that are transmitted via the food supply chain. Here we report the draft genome sequence of a multidrug-resistant Salmonella entericaserovar Brancaster (PS01) that was isolated from poultry meat in Malaysia.

Published
2017
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