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Lee CK, Huan PT, Chai CN, Ng LJ, Koay ESC, Lee OF, Tan M, Loh TP. Novel thiopurine S-methyltransferase ( TPMT) variant identified in Malay individuals. Clin Chem Lab Med 2024; 0:cclm-2024-0494. [PMID: 38661453 DOI: 10.1515/cclm-2024-0494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Chun Kiat Lee
- Department of Laboratory Medicine, 150744 National University Health System , Singapore, Singapore
| | - Pei Tee Huan
- Department of Paediatrics, Yong Loo Lin School of Medicine, 37580 National University of Singapore , Singapore, Singapore
| | - Chean Nee Chai
- Department of Laboratory Medicine, 150744 National University Health System , Singapore, Singapore
| | - Li Jie Ng
- Department of Laboratory Medicine, 150744 National University Health System , Singapore, Singapore
| | - Evelyn Siew-Chuan Koay
- Department of Pathology, Yong Loo Lin School of Medicine, 37580 National University of Singapore , Singapore, Singapore
| | - Ogestelli Fabia Lee
- School of Life and Physical Sciences, 464889 PSB Academy , Singapore, Singapore
| | - Malcolm Tan
- Department of Gastroenterology and Hepatology, 37581 Singapore General Hospital , Singapore, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, 150744 National University Health System , Singapore, Singapore
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Lee CK, Ng SY, Chai CN, Lim YF, Hu TJ, Lee OF, Yan G. Successful Confirmation of Dual Genital Herpes Co-Infection with Herpes Simplex Virus 1 and Herpes Simplex Virus 2 Using Unbiased Metagenomic Next-Generation Sequencing. Viruses 2023; 15:1957. [PMID: 37766363 PMCID: PMC10534666 DOI: 10.3390/v15091957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Dual co-infection with both HSV-1 and HSV-2 is rare, with few cases reported in the literature. In this case report, we describe the successful use of unbiased metagenomic next-generation sequencing (mNGS) as a rapid and alternative method for confirming dual genital herpes co-infection. Our case involves a 74-year-old woman who presented with genital lesions and initially tested positive for both HSV-1 and HSV-2 via the Luminex ARIES HSV 1&2 assay. The entire mNGS process, from nucleic acid extraction to result analysis, was completed in less than 48 h. Using mNGS, we identified mapped reads specific to either HSV-1 or HSV-2 and screened the sequences to rule out mis-genotyping by the Luminex ARIES assay. Notably, the generated sequences can reveal sequence variations within multiple gene regions, demonstrating the potential of mNGS for identifying novel HSV-1 and HSV-2 variants. Our findings suggest that mNGS can serve as a rapid and reliable alternative confirmatory method for dual genital herpes infections, providing valuable information to guide appropriate treatment options for patients. By eliminating the need for prior knowledge of causative agents, mNGS offers an unbiased approach for detecting and characterizing viral co-infections.
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Affiliation(s)
- Chun Kiat Lee
- Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
| | - Sau Yoke Ng
- Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
| | - Chean Nee Chai
- Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
| | - Yu Feng Lim
- Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
| | - Tiffany Jingyan Hu
- Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
| | - Ogestelli Fabia Lee
- School of Life and Physical Sciences, PSB Academy, Singapore 039594, Singapore
| | - Gabriel Yan
- Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
- Department of Medicine, National University Health System, Singapore 119228, Singapore
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Lee CK, Tham JWM, Png S, Chai CN, Ng SC, Tan EJM, Ng LJ, Chua RP, Sani M, Seow Y, Yan G, Tang J. Clinical performance of Roche cobas 6800, Luminex ARIES, MiRXES Fortitude Kit 2.1, Altona RealStar, and Applied Biosystems TaqPath for SARS-CoV-2 detection in nasopharyngeal swabs. J Med Virol 2021; 93:4603-4607. [PMID: 33719033 PMCID: PMC8250924 DOI: 10.1002/jmv.26940] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 01/21/2023]
Abstract
We compared the performance of five assays for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) detection on nasopharyngeal swab samples: Roche “cobas,” Luminex “ARIES,” MiRXES “Fortitude,” Altona “RealStar,” and Thermo Fisher Scientific “TaqPath.” A total of 94 nasopharyngeal swab samples were obtained from 80 confirmed coronavirus disease 2019 cases in the first 2 weeks of illness (median, 7 days; range, 2–14 days) and 14 healthy controls. After collection, all samples were transported to the hospital clinical laboratory within 24 h. These samples were tested on all five assays within 3 days of sample receipt. Of the 94 samples, 69 yielded the same result on all platforms, resulting in an agreement of 73.4% (69 of 94). Of these, 14 were the healthy control swabs which all tested negative, demonstrating good specificity across all platforms. The ARIES assay had the lowest detection rate (68.8%), followed by Fortitude (85.0%), RealStar (86.3%), cobas (95.0%), and TaqPath (100%). Statistically significant differences were observed for ARIES, Fortitude, and RealStar when compared against the best performing TaqPath using McNemar's χ2 test. A consensus result was established based on the results obtained by the cobas, Fortitude, RealStar, and TaqPath. Six discrepancies had failed to reach a consensus and were adjudicated using the Cepheid Xpert Xpress SARS‐CoV‐2. Overall, the TaqPath and cobas assays were the most sensitive at detecting their designated SARS‐CoV‐2 gene targets. On the other hand, the ARIES assay was the least sensitive, thus warranting the need for assay re‐optimization before go‐live at the testing laboratory.
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Affiliation(s)
- Chun Kiat Lee
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Jason Wei Ming Tham
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Siyu Png
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Chean Nee Chai
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Shu Chi Ng
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Eunice Jia Min Tan
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Li Jie Ng
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Rui Ping Chua
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Musa Sani
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Yiqi Seow
- Institute of Bioengineering and Nanotechnology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Gabriel Yan
- Department of Medicine, National University Health System, Singapore, Singapore
| | - Julian Tang
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
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Tham JWM, Ng SC, Chai CN, Png S, Tan EJM, Ng LJ, Chua RP, Sani M, Chiang D, Tan KX, Tee NWS, Jureen R, Tan SS, Yan G, Yan B, Lee CK. Parallel testing of 241 clinical nasopharyngeal swabs for the detection of SARS-CoV-2 virus on the Cepheid Xpert Xpress SARS-CoV-2 and the Roche cobas SARS-CoV-2 assays. Clin Chem Lab Med 2020; 59:e45-e48. [PMID: 33554503 DOI: 10.1515/cclm-2020-1338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/08/2020] [Indexed: 11/15/2022]
Affiliation(s)
- Jason Wei Ming Tham
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Shu Chi Ng
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Chean Nee Chai
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Siyu Png
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Eunice Jia Min Tan
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Li Jie Ng
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Rui Ping Chua
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Musa Sani
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Donald Chiang
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Ker Xin Tan
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Nancy Wen Sim Tee
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Roland Jureen
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Shaun S Tan
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - Gabriel Yan
- Department of Medicine, National University Health System, Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore.,Stronghold Diagnostic Lab, Agency for Science, Technology and Research, Singapore, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Health System, Singapore, Singapore
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Yow KS, Liu X, Chai CN, Tung ML, Yan B, Christopher D, Ong KH, Ooi MG. Relationship of JAK2 (V617F) Allelic Burden with Clinico- Haematological Manifestations of Philadelphia-Negative Myeloproliferative Neoplasms. Asian Pac J Cancer Prev 2020; 21:2805-2810. [PMID: 32986384 PMCID: PMC7779444 DOI: 10.31557/apjcp.2020.21.9.2805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 01/10/2023] Open
Abstract
JAK2 (V617F) allelic burden is the main genetic driver behind and a potential differentiator between individual myeloproliferative neoplasm (MPN) subtypes. This study aimed to explore the relationship between JAK2 (V617F) allelic burden, MPN subtypes and their clinico-haematological manifestations in a Singapore-based cohort. Analysis was performed on a retrospectively collected dataset of 128 patients diagnosed with JAK2 (V617F) positive Philadelphia-negative MPNs between 2016 to 2017 in Singapore. Genomic analysis was conducted on blood samples via DNA extraction and Droplet Digital Polymerase Chain Reaction (ddPCR). The mean age was 62.4 (SD=14.1). 85 out of the 128 (66.4%) patients were male. There was a statistically significant difference in allelic burdens between the different MPN disease subtypes χ2(3) = 9.064, p=0.028, with essential thrombocytosis (ET) patients having the lowest mean JAK2 percentage allelic burden (26.5%). Patients with an allelic burden >50% had higher leukocyte counts (MWU 1016.5, p=0.001), haemoglobin levels (MWU 1287.0, p=0.045), lactate dehydrogenase levels (MWU 611.5, p=0.001), and lower platelet levels (MWU 1164.0, p=0.008). Subgroup analysis revealed none of these correlations was significant in the ET subgroup. The results are largely in concordance with previous research in Asian cohorts demonstrating the association between allelic burden and clinico-haematological manifestations of MPN. However, in the ET subgroup, the JAK2 (V617F) allelic burden do not correlate positively for haematological parameters which is only seen in Asian patients.<br />.
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Affiliation(s)
| | - Xin Liu
- Department of Haematology-Oncology, National University Hospital, Singapore
| | - Chean Nee Chai
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Hospital, Singapore
| | - Moon Ley Tung
- National University of Singapore, Singapore.,Department of Haematology-Oncology, National University Hospital, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Hospital, Singapore
| | | | - Kiat Hoe Ong
- Department of Haematology, Tan Tock Seng Hospital, Singapore
| | - Melissa G Ooi
- National University of Singapore, Singapore.,Department of Haematology-Oncology, National University Hospital, Singapore
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Villanueva A, Poon KS, Gallardo CA, Chai CN, Chiu L, Yan B, Ding CSL, Yong KJ, Zhou J, Lee J, Tan K, Ong KH. A novel JAK2 R564* variant in a patient with thrombocytosis. Int J Lab Hematol 2019; 42:e38-e41. [PMID: 31441587 DOI: 10.1111/ijlh.13090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Andre Villanueva
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kok Siong Poon
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Health System, Singapore
| | | | - Chean Nee Chai
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Health System, Singapore
| | - Lily Chiu
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Health System, Singapore
| | - Benedict Yan
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Health System, Singapore
| | - Cristine S L Ding
- Department of Pathology, Tan Tock Seng Hospital, National Healthcare Group, Singapore
| | - Kol Jia Yong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Joanne Lee
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Karen Tan
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Health System, Singapore
| | - Kiat Hoe Ong
- Department of Haematology, Tan Tock Seng Hospital, National Healthcare Group, Singapore
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Lee CK, Chai CN, Capinpin SM, Ang A, Ng SY, Lee PL, Ng CWS, Yan G, Lee HK, Chiu LL, Jureen R, Yan B, Loh TP. Evaluation of the Luminex ARIES HSV 1&2 Assay and Comparison with the FTD Neuro 9 and In-house Real-Time PCR Assays for Detecting Herpes Simplex Viruses. Ann Lab Med 2018; 38:440-445. [PMID: 29797814 PMCID: PMC5973918 DOI: 10.3343/alm.2018.38.5.440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/15/2017] [Accepted: 05/03/2018] [Indexed: 11/20/2022] Open
Abstract
Background Human herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) are responsible for a plethora of human diseases, of which cutaneous and mucocutaneous infections are the most prevalent. In its most severe form, HSV infection can cause meningitis/encephalitis. We compared the Luminex ARIES HSV 1&2 assay (Luminex Corp., Austin, TX, USA), an automated sample-to-result molecular solution, to two non-automated HSV DNA assays. Methods A total of 116 artificial controls were used to determine the analytical performance of the ARIES assay. Controls were prepared by spiking universal transport medium (UTM) and cerebrospinal fluid (CSF) samples from patients who tested negative for HSV by an in-house HSV-1 and -2 DNA assay with reference materials (SeraCare Life Sciences, MA, USA; ZeptoMetrix Corp., MA, USA). Another 117 clinical samples were then used to compare the clinical performance of the ARIES assay with those of an in-house assay and the FTD Neuro 9 assay (Fast Track Diagnostics, Junglinster, Luxembourg). Results The analytical sensitivity (95% limit of detection) of the ARIES assay was 318 copies/mL (UTM samples) and 935 copies/mL (CSF samples) for HSV-1 strain 96 and 253 copies/mL (UTM samples) and 821 copies/mL (CSF samples) for HSV-2 strain 09. No cross-reactivity was observed in samples spiked with 14 non-HSV microorganisms. Compared with the reference result (agreement between the in-house and FTD Neuro 9 results), the ARIES assay had overall concordance rates of 98.2% (111/113) and 100% (113/113) for HSV-1 and HSV-2, respectively. Conclusions The ARIES assay appears to be an excellent alternative for rapid detection and differentiation of HSV in skin and genital infections, meningitis, and encephalitis.
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Affiliation(s)
- Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, Singapore.
| | - Chean Nee Chai
- Department of Laboratory Medicine, National University Hospital, Singapore
| | | | - Alynn Ang
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Sau Yoke Ng
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Peak Ling Lee
- Department of Laboratory Medicine, National University Hospital, Singapore
| | | | - Gabriel Yan
- Department of Medicine, National University Health System, Singapore
| | - Hong Kai Lee
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Lily Lily Chiu
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Roland Jureen
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Singapore.,Biomedical Institute for Global Health Research and Technology, National University of Singapore, Singapore
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