Displaying publications 1 - 20 of 33 in total

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  1. Multiplexed genotyping of beta globin mutations with MALDI-TOF mass spectrometry
    Looi ML, Sivalingam M, Husin ND, Radin FZ, Isa RM, Zakaria SZ, et al.
    Clin Chim Acta, 2011 May 12;412(11-12):999-1002.
    PMID: 21315703 DOI: 10.1016/j.cca.2011.02.006
    BACKGROUND: Beta thalassemia represents a great heterogeneity as over 300 mutations have been identified and each population at-risk has its own spectrum of mutations. Molecular characterization with high accuracy, sensitivity and economics is required for population screening and genetic counseling.
    METHODS: We used the MALDI-TOF mass spectrometry (MS) platform to develop novel multiplex assays for comprehensive detection of 27 mutations in beta-thalassemia patients. Six multiplex assays were designed to detect 13 common known ß-mutations, namely CD41/42, CD71/72, IVS1-5, IVS1-1, CD26, IVS2-654, CAP+1, CD19, -28, -29, IVS1-2, InCD (T-G) and CD17; and 14 rare ß-mutations, i.e. InCD (A-C), CD8/9, CD43, -86, CD15, Poly A, Poly T/C, IVS2-1, CD1, CD35/36, CD27/28, CD16, CD37, and 619bpDEL in 165 samples. We compared the efficiencies of genotyping by MS and Amplification Refractory Mutation System (ARMS). Discrepant results were confirmed by sequencing analysis.
    RESULTS: A total of 88.7% (260/293 allele) of MS and ARMS results was in agreement. More than fifty percent of the discrepant result was due to the false interpretation of ARMS results. Failed CD19 assay by MS method might be due to the assay design. The MS method detected 5 rare ß-mutations (CD15, CD35/36, CD8/9, Poly A and Poly T/C) presented in 13 alleles, which were not included in the ARMS screening panel.
    CONCLUSION: We revealed that the MS method is a sensitive, high-throughput, highly automated, flexible, and cost-effective alternative to conventional ß-thalassemia genotyping methods.
  2. Beta-2 microglobulin as an immunological marker to assess the progression of human immunodeficiency virus infected patients on highly active antiretroviral therapy
    Chitra P, Bakthavatsalam B, Palvannan T
    Clin Chim Acta, 2011 May 12;412(11-12):1151-4.
    PMID: 21300045 DOI: 10.1016/j.cca.2011.01.037
    Acquired immune deficiency syndrome (AIDS) defines the end stage of Human immunodeficiency viral (HIV) infection before the introduction of highly active antiretroviral therapy (HAART). This study was carried out to assess the serum β-2 microglobulin (B2M) as a marker for progression of HIV infected patients undergoing HAART.
  3. Differences in serum creatinine concentration between Caucasians, Chinese, Indians and Malays
    Hawkins RC
    Clin Chim Acta, 2010 Sep 6;411(17-18):1393.
    PMID: 20580697 DOI: 10.1016/j.cca.2010.05.027
  4. Prevalence of beta-2 adrenergic receptor (beta 2 AR) polymorphisms and its influence on a model used to assess endothelial function using pulse wave analysis (PWA)
    Ibrahim NN, Rasool AH, Wong AR, Rahman AR
    Clin Chim Acta, 2009 Nov;409(1-2):62-6.
    PMID: 19723516 DOI: 10.1016/j.cca.2009.08.018
    Pulse wave analysis (PWA) combined with beta(2)-agonist challenge has recently been used to assess endothelial function. beta-2 adrenergic receptor (beta(2)AR) polymorphisms may affect response to beta(2)-agonist. We determined whether beta(2)AR polymorphisms influence endothelial response in our model using PWA and salbutamol.
  5. High prevalence of CYP2A6*4 and CYP2A6*9 alleles detected among a Malaysian population
    Yusof W, Gan SH
    Clin Chim Acta, 2009 May;403(1-2):105-9.
    PMID: 19361454 DOI: 10.1016/j.cca.2009.01.032
    CYP2A6 gene encodes the principal enzyme involved in the metabolism of many drugs including artesunate. We developed a simplified duplex nested PCR method for the detection of the CYP2A61B, CYP2A62, CYP2A64, CYP2A67, CYP2A68 and CYP2A69 variant alleles highly prevalent among Malaysian population.
  6. Candidate gene polymorphisms and their association with hypertension in Malays
    Ghazali DM, Rehman A, Abdul Rahman AR
    Clin Chim Acta, 2008 Feb;388(1-2):46-50.
    PMID: 17977523 DOI: 10.1016/j.cca.2007.10.002
    BACKGROUND: Knowledge of candidate gene polymorphisms in a population is useful for a variety of gene-disease association studies, particularly for some complex traits. A single nucleotide variant of the angiotensinogene gene (AGT M235T) and endothelial nitric oxide synthase gene (eNOS G894T) have been associated with hypertension.
    METHOD: A cross-sectional study consisting of 200 hypertensives and 198 age- and sex-matched controls was conducted. Subjects involved in this study were pure Malay for 3 generations. The AGT M235T and eNOS G894T polymorphisms were determined by PCR-RFLP method.
    RESULTS: The distribution of M235T genotype in the population was 3.5% for MM, 30.4% for MT and 66.1% for TT. No significant difference was observed in genotype (chi(2)=1.30, p=0.52) and allele (chi(2)=0.87, p=0.35) frequencies among the 2 study group. In contrast, the distribution of genotypes for G894T was 74.1% for GG, 24.6% for GT and 1.3% for TT, respectively. Similarly, no significant difference was observed in genotype (chi(2)=0.94, p=0.33) and allele (chi(2)=0.60, p=0.44) frequencies between both study groups.
    CONCLUSION: The AGT M235T and eNOS G894T polymorphisms are unlikely to play an important role in the pathogenesis of hypertension in Malays.
    Study site: Outpatient clinic, Hospital Universiti Sains Malaysia (HUSM); government clinics, Kelantan, Malaysia.
  7. Genetic polymorphisms of CYP3A4: CYP3A4*18 allele is found in five healthy Malaysian subjects
    Ruzilawati AB, Suhaimi AW, Gan SH
    Clin Chim Acta, 2007 Aug;383(1-2):158-62.
    PMID: 17601520 DOI: 10.1016/j.cca.2007.05.004
    BACKGROUND: Cytochrome P450 3A4 (CYP3A4) is the major cytochrome involved in metabolizing of >60% of all drugs used in humans. A number of allelic variations in CYP3A4 gene are known to affect catalytic activity including CYP3A4*4, CYP3A4*5 and CYP3A4*18. We investigated the frequencies of CYP3A4*4, CYP3A4*5 and CYP3A4*18 alleles in a Malaysian population. This will impact treatment of patients receiving drugs metabolized by these alleles.

    METHODS: The study was conducted in 121 healthy Malaysian volunteers. DNA was extracted from leucocytes and the 3 alleles were determined by PCR-RFLP. The PCR product was later digested with restriction enzymes BstMA I, BshV I and Hpa II.

    RESULTS: No mutations were detected for CYP3A4*4 and CYP3A4*5 alleles. The frequency of the CYP3A4*18 allele in the Malaysian population is 2.1%. All 5 subjects with CYP3A4*18 mutations were found to be heterozygous.

    CONCLUSION: The present study describes polymorphisms of CYP3A4 among Malaysian subjects. Clinical relevance of these genetic variants in these healthy volunteers is under investigation.
  8. Comparison of oxidative damage in Malaysian end-stage renal disease patients with or without non-insulin-dependent diabetes mellitus
    Kuppusamy UR, Indran M, Ahmad T, Wong SW, Tan SY, Mahmood AA
    Clin Chim Acta, 2005 Jan;351(1-2):197-201.
    PMID: 15563890 DOI: 10.1016/j.cccn.2004.09.014
    BACKGROUND: Comparisons of oxidative indices and total antioxidant status between end-stage renal disease (ESRD) patients with or without diabetes is scant, especially in the Asian population.
    METHOD: The assays were carried out according to known established protocols.
    RESULT: The present study showed that ESRD patients with or without non-insulin-dependent diabetes mellitus (NIDDM) did not have any significant differences in antioxidant enzyme activities, advanced glycated end products (AGE), advanced oxidized protein products (AOPP) and ferric reducing ability of plasma (FRAP), indicating that hyperglycemia does not exacerbate oxidative damage in ESRD. The regulation of catalase and glutathione peroxidase is also altered in ESRD. Elevated FRAP was observed in both ESRD groups (with and without NIDDM). The dialysis process did not alter the antioxidant enzyme activities but decreased AGEs and FRAP and increased AOPP levels.
    CONCLUSION: Oxidative stress is present in ESRD but this is not significantly exacerbated by hyperglycemia. The contribution of components in the pathology of renal failure towards oxidative stress exceeds that of hyperglycemia.
  9. A simple multiplex PCR method for the concurrent detection of three CYP2C8 variants
    Muthiah YD, Lee WL, Teh LK, Ong CE, Salleh MZ, Ismail R
    Clin Chim Acta, 2004 Nov;349(1-2):191-8.
    PMID: 15469873 DOI: 10.1016/j.cccn.2004.06.024
    BACKGROUND: Cytochrome P450 (CYP) 2C8 is a principle enzyme responsible for the metabolism of many clinically important drugs as well as endogenous compounds such as arachidonic acid. The enzyme is genetically polymorphic but a simple method is not available to study its genetic polymorphism. We developed and optimized a variant-specific PCR techniques to detect CYP2C8*2, CYP2C8*3 and CYP2C8*4.
    METHOD: Genomic DNA was extracted from blood using standard extraction methods. A two-step PCR method was developed to detect simultaneously three CYP2C8 variants. In the first PCR (PCR1), specific regions from exons 3, 5 and 8 of the CYP2C8 gene were amplified. The products were used as templates in parallel alleles-specific PCR (PCR2). This method was tested against DNA samples obtained from 57 healthy Malaysian volunteers.
    RESULT: The bands of interest were successfully amplified. This method showed specific and reproducible results when tested on healthy volunteers. DNA sequencing further confirmed genotype results obtained from current method.
    CONCLUSION: We have successfully developed and optimized a multiplex PCR method suitable for use in population studies of CYP2C8 polymorphism.
  10. Plasma homocysteine reference values of adult Malaysians from three ethnic groups
    Lopez JB, Peng CL
    Clin Chim Acta, 2004 Feb;340(1-2):235-8.
    PMID: 14734218 DOI: 10.1016/j.cccn.2003.11.007
  11. Association between plasma soluble RAGE and renal function is unaffected by medication usage and enzymatic antioxidants in chronic kidney disease with type 2 diabetes
    Wong FN, Tan JA, Keng TC, Ng KP, Chua KH, Kuppusamy UR
    Clin Chim Acta, 2016 Jan 30;453:56-61.
    PMID: 26657980 DOI: 10.1016/j.cca.2015.12.002
    BACKGROUND: This study aimed to investigate the relationship between soluble RAGE and estimated glomerular filtration rate (eGFR) in patients with chronic kidney disease (CKD) after controlling for the potential confounding factors such as medication usage and enzymatic antioxidants.
    METHODS: A total of 222 CKD patients whose eGFR is less than 60ml/min/1.73m(2) and 111 non-CKD individuals were recruited. The study subjects were classified based on their diabetes status. The plasma glutathione peroxidase (GPx) and superoxide dismutase (SOD) activities as well as plasma soluble RAGE level were measured.
    RESULTS: The plasma GPx and SOD activities were significantly lower and the plasma soluble RAGE level was significantly higher in the CKD patients than in the non-CKD individuals, regardless of the diabetes status. Soluble RAGE was significantly correlated with eGFR in both diabetic CKD (D-CKD) and non-diabetic CKD (ND-CKD) patients. The association between soluble RAGE and eGFR remained largely unaffected by the confounding factors in D-CKD patients. However, the confounding effect of enzymatic antioxidants in the relationship between eGFR and soluble RAGE was observed in ND-CKD patients.
    CONCLUSION: The increased plasma level of soluble RAGE is a better indicator of renal function decline in diabetic CKD patients instead of non-diabetic CKD patients.
    KEYWORDS: Chronic kidney disease; Diabetes; Enzymatic antioxidants; Glomerular filtration rate; Medications; Soluble RAGE
  12. Inclusion bodies of recombinant Epstein-Barr virus capsid antigen p18 as potential immobilized antigens in enzyme immunoassays for detection of nasopharyngeal carcinoma
    Lim CS, Goh SL, Kariapper L, Krishnan G, Lim YY, Ng CC
    Clin Chim Acta, 2015 Aug 25;448:206-10.
    PMID: 26164385 DOI: 10.1016/j.cca.2015.07.008
    Development of indirect enzyme-linked immunosorbent assays (ELISAs) often utilizes synthetic peptides or recombinant proteins from Escherichia coli as immobilized antigens. Because inclusion bodies (IBs) formed during recombinant protein expression in E. coli are commonly thought as misfolded aggregates, only refolded proteins from IBs are used to develop new or in-house diagnostic assays. However, the promising utilities of IBs as nanomaterials and immobilized enzymes as shown in recent studies have led us to explore the potential use of IBs of recombinant Epstein-Barr virus viral capsid antigen p18 (VCA p18) as immobilized antigens in ELISAs for serologic detection of nasopharyngeal carcinoma (NPC).
  13. Autoantibody profile of patients infected with knowlesi malaria
    Liew J, Amir A, Chen Y, Fong MY, Razali R, Lau YL
    Clin Chim Acta, 2015 Aug 25;448:33-8.
    PMID: 26086445 DOI: 10.1016/j.cca.2015.06.006
    Autoantibodies or antibodies against self-antigens are produced either during physiological processes to maintain homeostasis or pathological process such as trauma and infection. Infection with parasites including Plasmodium has been shown to generally induce elevated self-antibody (autoantibody) levels. Plasmodium knowlesi is increasingly recognized as one of the most important emerging human malaria in Southeast Asia that can cause severe infection leading to mortality. Autoimmune-like phenomena have been hypothesized to play a role in the protective immune responses in malaria infection.
  14. Current aspects in hemoglobin A1c detection: a review
    Ang SH, Thevarajah M, Alias Y, Khor SM
    Clin Chim Acta, 2015 Jan 15;439:202-11.
    PMID: 25451954 DOI: 10.1016/j.cca.2014.10.019
    Type 2 diabetes mellitus (T2DM) is a pressing health issue that threatens global health and the productivity of populations worldwide. Despite its long-recognized role in diabetes management, glycated hemoglobin (HbA1c) only received WHO endorsement as a T2DM diagnostic tool in 2011. Although conventional plasma-specific tests have long been utilized to diagnose T2DM, the public should be informed that plasma-specific tests are not markedly better than HbA1c tests, particularly in terms of variability and convenience for diagnosing diabetes. In the midst of the debates associated with establishing HbA1c as the preeminent diabetes diagnostic tool, unceasing efforts to standardize HbA1c tests have played an integral part in achieving more efficient communication from laboratory to clinical practice and thus better diabetes care. This review discusses the current status of HbA1c tests in the diagnosis, prevention, treatment and management of T2DM across the globe, focusing on increasing the recognition of glycated hemoglobin variants with effective utilization of different HbA1c methods, updating the current status of HbA1c standardization programs, tapping into the potential of POC analyzers to establish a cost-effective HbA1c test for diabetes care, and inspiring the advancement of HbA1c biosensors for future clinical usage.
  15. Evaluation of clinical and cytogenetic parameters in rheumatoid arthritis patients for effective diagnosis
    Chandirasekar R, Kumar BL, Jayakumar R, Uthayakumar V, Jacob R, Sasikala K
    Clin Chim Acta, 2015 Jan 15;439:77-83.
    PMID: 25307208 DOI: 10.1016/j.cca.2014.10.005
    BACKGROUND: Rheumatoid arthritis is the commonest inflammatory joint disease, affecting nearly 1% of the adult population worldwide. Early and accurate diagnosis and prognosis of rheumatoid arthritis (RA) have become increasingly important. In the present study, we aimed to elucidate the relationships between hematological, biochemical, immunological and cytogenetic parameters in rheumatoid arthritis patients and healthy normal controls.
    METHODS:The study group comprised of 126 RA patients and equal number of healthy normal control subjects. The blood wa s collected and analyzed for biochemical, immunological, enzymatic and cytogenetic parameters.
    RESULTS: Results of the present study indicated that 20% of RA patient's hematological, 31% of biochemical and 70% immunological parameters had a significant difference from the controls and reference range. The RF and anti-CCP antibody levels were also positive in 70% of RA patients. A significant increase in minor chromosomal abnormalities was also observed in patients as compared to controls.
    CONCLUSION: The knowledge about autoimmune diseases is very low among the South Indian population. The present study has thus helped in understanding the RA disease in a better way based on a pattern of various clinical markers of the disease condition which might help in planning therapeutic intervention strategies and create awareness about the disease management among RA patients of the population studied.
    KEYWORDS: Anti-cyclic citrullinated peptide (anti-CCP); Rheumatoid arthritis (RA); Rheumatoid factor (RF)
  16. On optimizing the blocking step of indirect enzyme-linked immunosorbent assay for Epstein-Barr virus serology
    Lim CS, Krishnan G, Sam CK, Ng CC
    Clin Chim Acta, 2013 Jan 16;415:158-61.
    PMID: 23043757 DOI: 10.1016/j.cca.2012.08.031
    Because blocking agent occupies most binding surface of a solid phase, its ability to prevent nonspecific binding determines the signal-to-noise ratio (SNR) and reliability of an enzyme-linked immunosorbent assay (ELISA).
  17. Differences in HbA1c between Caucasians, Chinese, Indians, Malays and Eurasians
    Hawkins R
    Clin Chim Acta, 2011 May 12;412(11-12):1167.
    PMID: 21396354 DOI: 10.1016/j.cca.2011.03.003
  18. Blood and urine biomarkers in chronic kidney disease: An update
    Bidin MZ, Shah AM, Stanslas J, Seong CLT
    Clin Chim Acta, 2019 Aug;495:239-250.
    PMID: 31009602 DOI: 10.1016/j.cca.2019.04.069
    INTRODUCTION: Chronic kidney disease (CKD) is a silent disease. Most CKD patients are unaware of their condition during the early stages of the disease which poses a challenge for healthcare professionals to institute treatment or start prevention. The trouble with the diagnosis of CKD is that in most parts of the world, it is still diagnosed based on measurements of serum creatinine and corresponding calculations of eGFR. There are controversies with the current staging system, especially in the methodology to diagnose and prognosticate CKD.

    OBJECTIVE: The aim of this review is to examine studies that focused on the different types of samples which may serve as a good and promising biomarker for early diagnosis of CKD or to detect rapidly declining renal function among CKD patient.

    METHOD: The review of international literature was made on paper and electronic databases Nature, PubMed, Springer Link and Science Direct. The Scopus index was used to verify the scientific relevance of the papers. Publications were selected based on the inclusion and exclusion criteria.

    RESULT: 63 publications were found to be compatible with the study objectives. Several biomarkers of interest with different sample types were taken for comparison.

    CONCLUSION: Biomarkers from urine samples yield more significant outcome as compare to biomarkers from blood samples. But, validation and confirmation with a different type of study designed on a larger population is needed. More comparison studies on different types of samples are needed to further illuminate which biomarker is the better tool for the diagnosis and prognosis of CKD.

  19. Proteogenomics: From next-generation sequencing (NGS) and mass spectrometry-based proteomics to precision medicine
    Ang MY, Low TY, Lee PY, Wan Mohamad Nazarie WF, Guryev V, Jamal R
    Clin Chim Acta, 2019 Nov;498:38-46.
    PMID: 31421119 DOI: 10.1016/j.cca.2019.08.010
    One of the best-established area within multi-omics is proteogenomics, whereby the underpinning technologies are next-generation sequencing (NGS) and mass spectrometry (MS). Proteogenomics has contributed significantly to genome (re)-annotation, whereby novel coding sequences (CDS) are identified and confirmed. By incorporating in-silico translated genome variants in protein database, single amino acid variants (SAAV) and splice proteoforms can be identified and quantified at peptide level. The application of proteogenomics in cancer research potentially enables the identification of patient-specific proteoforms, as well as the association of the efficacy or resistance of cancer therapy to different mutations. Here, we discuss how NGS/TGS data are analyzed and incorporated into the proteogenomic framework. These sequence data mainly originate from whole genome sequencing (WGS), whole exome sequencing (WES) and RNA-Seq. We explain two major strategies for sequence analysis i.e., de novo assembly and reads mapping, followed by construction of customized protein databases using such data. Besides, we also elaborate on the procedures of spectrum to peptide sequence matching in proteogenomics, and the relationship between database size on the false discovery rate (FDR). Finally, we discuss the latest development in proteogenomics-assisted precision oncology and also challenges and opportunities in proteogenomics research.
  20. Circulating miR-3197 and miR-2116-5p as novel biomarkers for diabetic retinopathy
    Ji H, Yi Q, Chen L, Wong L, Liu Y, Xu G, et al.
    Clin Chim Acta, 2020 Feb;501:147-153.
    PMID: 31678272 DOI: 10.1016/j.cca.2019.10.036
    Diabetic retinopathy (DR) is the leading cause of vision loss among older adults. The goal of this case-control study was to identify circulating miRNAs for the diagnosis of DR. The miRNeasy Serum/Plasma Kit was used to extract serum miRNAs. The μParaflo™ MicroRNA microarray was used to detect the expression levels of the miRNAs. The miRWalk algorithm was applied to predict the target genes of the miRNAs, which were further confirmed by the dual luciferase reporter gene system in HEK293T cells. A microarray was performed between 5 DR cases and 5 age-, sex-, body mass index-, and duration of diabetes-matched type 2 diabetic (T2DM) controls. The quantitative reverse transcription polymerase chain reaction technique was used to validate the differentially expressed circulating miRNAs in 45 DR cases and 45 well-matched controls. Receiver operating characteristic (ROC) curve analysis was used to evaluate the performance of the circulating miRNAs as diagnostic biomarkers for DR. Our microarray analysis screened out miR-2116-5p and miR-3197 as significantly up-regulated in DR cases compared with the controls. Furthermore, two miRNAs were validated in the 45 DR cases and 45 controls. The ROC analysis suggested that both miR-3197 and miR-2116-5p distinguished DR cases from controls. An additional dual-luciferase reporter gene assay confirmed that notch homolog 2 (NOTCH2) was the target gene of miR-2116-5p. Both miR-3197 and miR-2116-5p were identified as promising diagnostic biomarkers for DR. Future research is still needed to explore the molecular mechanisms of miR-3197 and miR-2116-5p in the pathogenesis of DR.
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