Displaying publications 1 - 20 of 98 in total

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  1. Balraj P, Khoo AS, Volpi L, Tan JA, Nair S, Abdullah H
    Singapore Med J, 2002 Apr;43(4):194-7.
    PMID: 12188064
    Thirty patients with early onset breast cancer or familial breast cancer from Malaysia were analysed for germline mutation in the early onset breast cancer I gene (BRCA1). Direct sequencing of the entire coding region of BRCA1 identified a frameshift mutation, c.5447-5448insC (insC5447) (codon 1776 of exon 21) in a patient aged 32 of the Malay ethnic origin, who had no family history of breast and/or ovarian cancer. Eight polymorphisms (2201C > T, 2430T > C, P871L, E1038G, K1183R, 4427T > C, S1613G and IVS8-57delT) were identified in the samples tested.
  2. Tan KK, Tiong V, Tan JY, Wong JE, Teoh BT, Abd-Jamil J, et al.
    Trop Biomed, 2021 Sep 01;38(3):283-288.
    PMID: 34362871 DOI: 10.47665/tb.38.3.069
    Various methods have been developed for rapid and high throughput full genome sequencing of SARS-CoV-2. Here, we described a protocol for targeted multiplex full genome sequencing of SARS-CoV-2 genomic RNA directly extracted from human nasopharyngeal swabs using the Ion Personal Genome Machine (PGM). This protocol involves concomitant amplification of 237 gene fragments encompassing the SARS-CoV-2 genome to increase the abundance and yield of viral specific sequencing reads. Five complete and one near-complete genome sequences of SARS-CoV-2 were generated with a single Ion PGM sequencing run. The sequence coverage analysis revealed two amplicons (positions 13 751-13 965 and 23 941-24 106), which consistently gave low sequencing read coverage in all isolates except 4Apr20-64- Hu. We analyzed the potential primer binding sites within these low covered regions and noted that the 4Apr20-64-Hu possess C at positions 13 730 and 23 929, whereas the other isolates possess T at these positions. The genome nucleotide variations observed suggest that the naturally occurring variations present in the actively circulating SARS-CoV-2 strains affected the performance of the target enrichment panel of the Ion AmpliSeq™ SARS CoV 2 Research Panel. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq™ SARS CoV 2 Research Panel, hence, should be considered.
  3. Poh R, Tan JA, Deva JP, Poo D, Yong Y, Arjunan S
    West Indian Med J, 2012 Sep;61(6):569-73.
    PMID: 23441349
    To determine the activity of paraoxonase 1 (PON1) in keratoconus in a Malaysian population in comparison with non-keratoconic subjects.
  4. Velentzis LS, Hawkes D, Caruana M, Brotherton JM, Smith MA, Roeske L, et al.
    Tumour Virus Res, 2023 Jun;15:200255.
    PMID: 36736490 DOI: 10.1016/j.tvr.2023.200255
    Australia's cervical screening program transitioned from cytology to HPV-testing with genotyping for HPV16/18 in Dec'2017. We investigated whether program data could be used to monitor HPV vaccination program impact (commenced in 2007) on HPV16/18 prevalence and compared estimates with pre-vaccination benchmark prevalence. Pre-vaccination samples (2005-2008) (n = 1933; WHINURS), from 25 to 64-year-old women had been previously analysed with Linear Array (LA). Post-vaccination samples (2013-2014) (n = 2989; Compass pilot), from 25 to 64-year-old women, were analysed by cobas 4800 (cobas), and by LA for historical comparability. Age standardised pre-vaccination HPV16/18 prevalence was 4.85% (95%CI:3.81-5.89) by LA; post-vaccination estimates were 1.67% (95%CI:1.21-2.13%) by LA, 1.49% (95%CI:1.05-1.93%) by cobas, and 1.63% (95%CI:1.17-2.08%) for cobas and LA testing of non-16/18 cobas positives (cobas/LA). Age-standardised pre-vaccination oncogenic HPV prevalence was 15.70% (95%CI:13.79-17.60%) by LA; post-vaccination estimates were 9.06% (95%CI:8.02-10.09%) by LA, 8.47% (95%CI:7.47-9.47%) by cobas and cobas/LA. Standardised rate ratios between post-vs. pre-vaccination rates were significantly different for HPV16/18, non-16/18 HPV and oncogenic HPV: 0.34 (95%CI:0.23-0.50), 0.68 (95%CI:0.55-0.84) and 0.58 (95%CI:0.48-0.69), respectively. Additional strategies (LA for all cobas positives; combined cobas and LA results on all samples) had similar results. If a single method is applied consistently, it will provide important data on relative changes in HPV prevalence following vaccination.
  5. Yong HS, Song SL, Chua KO, Wayan Suana I, Eamsobhana P, Tan J, et al.
    Sci Rep, 2021 May 21;11(1):10680.
    PMID: 34021208 DOI: 10.1038/s41598-021-90162-1
    Spiders of the genera Nephila and Trichonephila are large orb-weaving spiders. In view of the lack of study on the mitogenome of these genera, and the conflicting systematic status, we sequenced (by next generation sequencing) and annotated the complete mitogenomes of N. pilipes, T. antipodiana and T. vitiana (previously N. vitiana) to determine their features and phylogenetic relationship. Most of the tRNAs have aberrant clover-leaf secondary structure. Based on 13 protein-coding genes (PCGs) and 15 mitochondrial genes (13 PCGs and two rRNA genes), Nephila and Trichonephila form a clade distinctly separated from the other araneid subfamilies/genera. T. antipodiana forms a lineage with T. vitiana in the subclade containing also T. clavata, while N. pilipes forms a sister clade to Trichonephila. The taxon vitiana is therefore a member of the genus Trichonephila and not Nephila as currently recognized. Studies on the mitogenomes of other Nephila and Trichonephila species and related taxa are needed to provide a potentially more robust phylogeny and systematics.
  6. Lee BKB, Gan CP, Chang JK, Tan JL, Fadlullah MZ, Abdul Rahman ZA, et al.
    J Dent Res, 2018 07;97(8):909-916.
    PMID: 29512401 DOI: 10.1177/0022034518759038
    Head and neck cancer (HNC)-derived cell lines represent fundamental models for studying the biological mechanisms underlying cancer development and precision therapies. However, mining the genomic information of HNC cells from available databases requires knowledge on bioinformatics and computational skill sets. Here, we developed a user-friendly web resource for exploring, visualizing, and analyzing genomics information of commonly used HNC cell lines. We populated the current version of GENIPAC with 44 HNC cell lines from 3 studies: ORL Series, OPC-22, and H Series. Specifically, the mRNA expressions for all the 3 studies were derived with RNA-seq. The copy number alterations analysis of ORL Series was performed on the Genome Wide Human Cytoscan HD array, while copy number alterations for OPC-22 were derived from whole exome sequencing. Mutations from ORL Series and H Series were derived from RNA-seq information, while OPC-22 was based on whole exome sequencing. All genomic information was preprocessed with customized scripts and underwent data validation and correction through data set validator tools provided by cBioPortal. The clinical and genomic information of 44 HNC cell lines are easily assessable in GENIPAC. The functional utility of GENIPAC was demonstrated with some of the genomic alterations that are commonly reported in HNC, such as TP53, EGFR, CCND1, and PIK3CA. We showed that these genomic alterations as reported in The Cancer Genome Atlas database were recapitulated in the HNC cell lines in GENIPAC. Importantly, genomic alterations within pathways could be simultaneously visualized. We developed GENIPAC to create access to genomic information on HNC cell lines. This cancer omics initiative will help the research community to accelerate better understanding of HNC and the development of new precision therapeutic options for HNC treatment. GENIPAC is freely available at http://genipac.cancerresearch.my/ .
  7. Chong VH, Telisinghe PU, Lim E, Tan J, Chong CF
    Asian Pac J Cancer Prev, 2016;17(2):845-9.
    PMID: 26925690
    BACKGROUND: Worldwide, the incidence of cancers is increasing and is becoming a major public health issue, including those in the Asia Pacific region. South-East Asia is a region with diverse populations with different disease spectra. This study looked at the spectrum of cancers among South-East Asians working in Brunei Darussalam.

    MATERIALS AND METHODS: The cancer registry from 1994 to 2012 maintained by the State Laboratory was retrospectively reviewed. Crude incidence rates were calculated based on the population census of 2010.

    RESULTS: Altogether, there was a total of 418 cancer cases diagnosed among South-East Asians, giving an incidence of 5.1% (n=418/8,253). The affected nationals in decreasing frequency were Malaysians (53.1%), followed by Filipinos (25.8%), Indonesians (15.3%), Thais (3.8%), Myanmese (1.7%) and Vietnamese (0.2%) with no recorded cases for Singapore and the People's Republic of Laos. The overall mean age of diagnosis was 46.1±4.2 years old, with an increasing trend over the years (p<0.05 ANOVA). The overall gender ratio was 42.3:57.7 (male:female), more females among the Filipinos and Indonesians, more males among the Thais, and equal representation among the Malaysians and the Myanmese. The most common were cancers of the digestive system (19.9%), followed by female reproductive/gynecologic system (16.0%), breast (15.6%), hematological/lymphatic (12.0%) and head/neck (8.1%). There were differences in the prevalence of cancers among the various nationalities with highest crude incidence rate among the Myanmese (141.2/100,000), followed by the Malaysian (88.5/100,000), and the Filipinos (40.6/100,000) and the lowest among the Thais (18.4/100,000), Indonesians (10.5/100,000) and the Vietnamese (6.3/100,000).

    CONCLUSIONS: Cancers among South-East Asian residing in Brunei Darussalam accounted for 5.1% of all cancers. The most common cancers were cancers of the digestive, gynecologic/female reproductive system and breast with certain types slowly increasing in proportions. There mean age of diagnoses was increasing.

  8. Dwiyanto J, Huët MAL, Hussain MH, Su TT, Tan JBL, Toh KY, et al.
    NPJ Biofilms Microbiomes, 2023 Aug 12;9(1):55.
    PMID: 37573460 DOI: 10.1038/s41522-023-00425-0
    The prevalence of antibiotic-resistant bacteria in Southeast Asia is a significant concern, yet there is limited research on the gut resistome and its correlation with lifestyle and environmental factors in the region. This study aimed to profile the gut resistome of 200 individuals in Malaysia using shotgun metagenomic sequencing and investigate its association with questionnaire data comprising demographic and lifestyle variables. A total of 1038 antibiotic resistance genes from 26 classes were detected with a mean carriage rate of 1.74 ± 1.18 gene copies per cell per person. Correlation analysis identified 14 environmental factors, including hygiene habits, health parameters, and intestinal colonization, that were significantly associated with the resistome (adjusted multivariate PERMANOVA, p 
  9. Tan J, Khalil MA, Tan SY, Khalil M, Ahmed D, Zinna S, et al.
    J Transplant, 2014;2014:784805.
    PMID: 25478205 DOI: 10.1155/2014/784805
    Objectives. Brunei Darussalam has a high prevalence and incidence of end stage renal disease (ESRD). Up until 2012, all renal transplantations were performed in overseas centres, either as government-sponsored (living-related transplantation) or as self-sponsored (commercialized transplantation) ones. We hypothesize that graft and patient survival of Brunei renal transplant patients are on a par with international standards. Materials and Methods. Data of all renal transplant patients in Brunei were analysed over a twenty-year period from registry records and case notes. Comparative survival data from other countries were obtained from PubMed-listed literature. Results. A total of 49 transplantation procedures were performed in foreign centres between 1993 and 2012. 29 were government-sponsored and 20 were self-sponsored transplantations. The 5- and 10-year overall patient survival rates were 93.3% and 90.1%, respectively. The 5- and 10-year overall graft survival rates were 91.1% and 81.2%. There is no difference in the survival outcomes of government-sponsored and self-sponsored patients. Living-related (government-sponsored) and commercialised (self-sponsored) grafts had equivalent survival to those reported in the literature. Conclusion. Our survival data was on par with those achieved in many countries. We hope to use this information to convince local stakeholders and patients to favour transplantation as the preferred modality of RRT.
  10. Tan J. Y. S., R. Surendran, Mohd Noh Malehah, Shaila Kabir, Chong Y. Y. Eleen
    MyJurnal
    Introduction: Ascariasis is a parasitic infection, which commonly affects immunocompromised patients. Most pa-tients remained asymptomatic during the early larval migration stage and respond well with conventional anti-hel-minthic drugs. Previous literature had reported symptomatic Ascaris infection mimicking bacterial pneumonia and the typical eosinophilia found in Loeffler syndrome was absent in patients on corticosteroids. Thus, a high index of suspicion for ascariasis is needed for immunosuppressed patients presented with infection. We present here a case of severe ascariasis infection in a systemic lupus erythematosus patient. Case description: A 16-year-old boy presented with fever, generalized maculopapular rash associated with neutropenia and thrombocytopenia. He was treated initially as Dengue Fever initially. However his symptoms did not resolve at even day 14 of admission. On further assessment, we were convinced he has SLE based upon presence of malar rash, oral ulcers, urinary protein-uria, persistent leucopenia, thrombocytopenia with low complements and ANA positive. He was promptly started on IV hydrocortisone. He showed a good progress in the first few days. On day 5 of admission, he coughed out a round worm which later identified as Ascarisis lumbricoides. He was started on Albendazole. Unfortunately he developed hemoptysis and respiratory compromisation where he required intubation. Post intubation he went into cardiac arrest, which required CPR. Following that event, his condition further deteriorated with multi organ failure. He succumbed to his illness three days later. Conclusion: Immunocompromised patients are prone to opportunistic infections including parasitic infections. we present here a case of ascariasis in an SLE patient who unfortunately succumbed to the illness. Due to the variable clinical symptoms that mimic other infections, screening for parasitic infections needs to be considered especially if the patients do not respond to antibiotics and routine treatments.
  11. Putra MA, Teh KC, Tan J, Choong TSY
    Environ Sci Pollut Res Int, 2020 Aug;27(23):29352-29360.
    PMID: 32440875 DOI: 10.1007/s11356-020-09207-z
    Cement is a vital material used in the construction of concrete buildings. World annual cement demand is increasing rapidly along with the improvement in infrastructure development. However, cement manufacturing industries are facing challenges in reducing the environmental impacts of cement production. To resolve this issue, a suitable methodology is crucial to ensure the selected processes are effective and efficient and at the same time environmentally friendly. Different technologies and equipment have potential to produce variations in operational effectiveness, environmental impacts, and manufacturing costs in cement manufacturing industries. Therefore, this work aims to present the sustainability assessment of cement plants by taking into consideration of environmental, social, and economic impacts. Three cement production plants located in Western Indonesian are used as case studies where social impact and environmental impact are evaluated via life cycle assessment (LCA) model. This model is integrated with analytic hierarchy process (AHP), a multi-criteria decision analysis tool in selecting the most sustainable cement manufacturing plant.
  12. Achin NA, Kit TJ, Ngah WZW, Makpol S, Mazlan M, Hamezah HS, et al.
    Curr Aging Sci, 2018;11(3):182-194.
    PMID: 30338748 DOI: 10.2174/1874609811666181019141217
    BACKGROUND: Cognitive frailty emerges as one of the threats to healthy aging. It is in continuum with advancing of age with uncertain indicator between pathological and physiological changes. Alterations in pathways associated with the aging process have been observed including oxidative stress, lipid metabolism, and inflammation. However, the exact mechanisms leading to cognitive decline are still unclear.

    OBJECTIVE: This study was sought to assess the level of cognitive functions and linked with blood oxidative status during normal aging in rats.

    METHODS: A longitudinal study using male Sprague Dawley rats was performed starting from the age of 14 months old to 27 months old. Cognitive functions tests such as open field, Morris water maze and object recognition were determined at the age of 14, 18, 23, and 27 months old and were compared with group 3 months old. Blood was collected from the orbital venous sinus and oxidative status was determined by measuring the level of DNA damage, lipid peroxidation, protein oxidation and antioxidant enzymes activity.

    RESULTS: Aged rats showed declining exploratory behavior and increased in the level of anxiety as compared to the young rats. The level of DNA damage increased with increasing age. Interestingly, our study found that both levels of malondialdehyde and plasma carbonyl content decreased with age. In addition, the level of superoxide dismutase activity was significantly decreased with age whereas catalase activity was significantly increased from 18 months of age. However, no significant difference was found in glutathione peroxidase activity among all age groups.

    CONCLUSION: The progressions of cognitive impairment in normal aging rats are linked to the increment in the level of DNA damage.

  13. Yong HS, Lim PE, Tan J, Song SL, Suana IW, Eamsobhana P
    PLoS One, 2015;10(6):e0129455.
    PMID: 26090853 DOI: 10.1371/journal.pone.0129455
    Bactrocera caudata is a pest of pumpkin flower. Specimens of B. caudata from the northern hemisphere (mainland Asia) and southern hemisphere (Indonesia) were analysed using the partial DNA sequences of the nuclear 28S rRNA and internal transcribed spacer region 2 (ITS-2) genes, and the mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and 16S rRNA genes. The COI, COII, 16S rDNA and concatenated COI+COII+16S and COI+COII+16S+28S+ITS-2 nucleotide sequences revealed that B. caudata from the northern hemisphere (Peninsular Malaysia, East Malaysia, Thailand) was distinctly different from the southern hemisphere (Indonesia: Java, Bali and Lombok), without common haplotype between them. Phylogenetic analysis revealed two distinct clades (northern and southern hemispheres), indicating distinct genetic lineage. The uncorrected 'p' distance for the concatenated COI+COII+16S nucleotide sequences between the taxa from the northern and southern hemispheres ('p' = 4.46-4.94%) was several folds higher than the 'p' distance for the taxa in the northern hemisphere ('p' = 0.00-0.77%) and the southern hemisphere ('p' = 0.00%). This distinct difference was also reflected by concatenated COI+COII+16S+28S+ITS-2 nucleotide sequences with an uncorrected 'p' distance of 2.34-2.69% between the taxa of northern and southern hemispheres. In accordance with the type locality the Indonesian taxa belong to the nominal species. Thus the taxa from the northern hemisphere, if they were to constitute a cryptic species of the B. caudata species complex based on molecular data, need to be formally described as a new species. The Thailand and Malaysian B. caudata populations in the northern hemisphere showed distinct genetic structure and phylogeographic pattern.
  14. Ng BH, Tan JK, Andrea Ban YL, Faisal AH
    Med J Malaysia, 2020 03;75(2):181-183.
    PMID: 32281606
    In the past, many case series have reported the effectiveness of autologous blood patch pleurodesis (ABPP) in recurrent secondary spontaneous pneumothorax (SSP), particularly in those who were unfit for surgery. We describe two cases of persistent air leak in pneumoconiosis and pulmonary fibrosis with bronchiectasis, whereby the techniques employed had improved the success rate of ABPP. The determining factors that lead to the success of ABPP were determined by the volume of autologous blood instilled, Trendelenburg position post instillation, and early chest physiotherapy with mobilisation by application of pneumostat.
  15. Tan JH, Cheong FW, Lau YL, Fong MY
    Trop Biomed, 2023 Mar 01;40(1):37-44.
    PMID: 37356002 DOI: 10.47665/tb.40.1.004
    Circumsporozoite protein (CSP) central repeat region is one of the main target regions of the RTS,S/AS01 vaccine for falciparum infection as it consists of immunodominant B cell epitopes. However, there is a lack of study for P. knowlesi CSP central repeat region. This study aims to characterise the CSP repeat motifs of P. knowlesi isolates in Peninsular Malaysia. CSP repeat motifs of 64 P. knowlesi isolates were identified using Rapid Automatic Detection and Alignment of Repeats (RADAR). Antigenicity of the repeat motifs and linear B cell epitopes were predicted using VaxiJen 2.0, BepiPred-2.0 and BCPred, respectively. A total of 35 dominant repeat motifs were identified. The repeat motif "AGQPQAQGDGANAGQPQAQGDGAN" has the highest repeat frequency (n=15) and antigenicity index of 1.7986. All the repeat regions were predicted as B cell epitopes. In silico approaches revealed that all repeat motifs were antigenic and consisted of B cell epitopes which could be designed as knowlesi malaria vaccine.
  16. Peh SC, Shaminie J, Tai YC, Tan J, Gan SS
    Histopathology, 2004 Nov;45(5):501-10.
    PMID: 15500654
    Follicular lymphoma is frequently associated with t(14;18)(q32;q21) translocation. This study was undertaken to determine the pattern of Bcl-2, CD10 and Bcl-6 expression in relation to t(14;18) translocation in follicular lymphoma from a cohort of a multi-ethnic Asian population.
  17. Tan JK, Tan EL, Gan SY
    Exp Oncol, 2014 Sep;36(3):170-3.
    PMID: 25265349
    Deregulation of microRNA has been associated with cancer progression and the modification of cancer phenotypes could be achieved by targeting microRNA expression. This study aimed to determine the effects of miR-372 on cell progression and gene expression in nasopharyngeal carcinoma cell line, TW01.
  18. Jasuja S, Gallieni M, Jha V, Vachharajani T, Bhalla AK, Tan J, et al.
    Nephrology (Carlton), 2023 Dec;28(12):672-681.
    PMID: 37697492 DOI: 10.1111/nep.14236
    AIM: This cross-sectional survey aimed to determine the prevalence of Interventional Nephrology (IN) practice amongst nephrologists in the Asia-Pacific Region (APR), specifically related to dialysis access (DA).

    METHODS: The Association of VA and intervenTionAl Renal physicians (AVATAR) Foundation from India conducted a multinational online survey amongst nephrologists from the Asia-Pacific to determine the practice of IN in the planning, creation, and management of dialysis access. The treatment modalities, manpower and equipment availability, monthly cost of treatment, specifics of dialysis access interventions, and challenges in the training and practice of IN by nephrologists were included in the survey.

    RESULTS: Twenty-one countries from the APR participated in the survey. Nephrologists from 18 (85.7%) countries reported performing at least one of the basic dialysis access-related IN procedures, primarily the placement of non-tunnelled central catheters (n-TCC; 71.5%). Only 10 countries (47.6%) reported having an average of <4% of nephrologists performing any of the advanced IN access procedures, the most common being the placement of a peritoneal dialysis (PD) catheter (20%). Lack of formal training (57.14%), time (42.8%), incentive (38%), institutional support (38%), medico-legal protection (28.6%), and prohibitive cost (23.8%) were the main challenges to practice IN. The primary obstacles to implementing the IN training were a lack of funding and skilled personnel.

    CONCLUSION: The practice of dialysis access-related IN in APR is inadequate, mostly due to a lack of training, backup support, and economic constraints, whereas training in access-related IN is constrained by a lack of a skilled workforce and finances.

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