Displaying publications 101 - 120 of 1014 in total

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  1. Selvavinayagam ST, Sankar S, Yong YK, Murugesan A, Suvaithenamudhan S, Hemashree K, et al.
    Sci Rep, 2024 Jul 30;14(1):17476.
    PMID: 39080396 DOI: 10.1038/s41598-024-68678-z
    In December 2023, we observed a notable shift in the COVID-19 landscape, when JN.1 omicron emerged as the predominant SARS-CoV-2 variant with a 95% incidence. We characterized the clinical profile, and genetic changes in JN.1, an emerging SARS-CoV-2 variant of interest. Whole genome sequencing was performed on SARS-CoV-2 positive clinical specimens, followed by sequence analysis. Mutations within the spike protein sequences were analysed and compared with the previously reported lineages and sub-lineages, to identify the potential impact of the unique mutations on protein structure and possible alterations in the functionality. Several unique and dynamic mutations were identified herein. Molecular docking analysis showed changes in the binding affinity, and key interacting residues of wild-type and mutated structures with key host cell receptors of SARS-CoV-2 entry viz., ACE2, CD147, CD209L and AXL. Our data provides key insights on the emergence of newer variants and highlights the necessity for robust and sustained global genomic surveillance of SARS-CoV-2.
    Matched MeSH terms: Mutation*
  2. Shepherdson JL, Hutchison K, Don DW, McGillivray G, Choi TI, Allan CA, et al.
    Am J Hum Genet, 2024 Mar 07;111(3):487-508.
    PMID: 38325380 DOI: 10.1016/j.ajhg.2024.01.007
    Pathogenic variants in multiple genes on the X chromosome have been implicated in syndromic and non-syndromic intellectual disability disorders. ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not been characterized in association with disease. Here, we present clinical and molecular characterization of 18 individuals with germline ZFX variants. Exome or genome sequencing revealed 11 variants in 18 subjects (14 males and 4 females) from 16 unrelated families. Four missense variants were identified in 11 subjects, with seven truncation variants in the remaining individuals. Clinical findings included developmental delay/intellectual disability, behavioral abnormalities, hypotonia, and congenital anomalies. Overlapping and recurrent facial features were identified in all subjects, including thickening and medial broadening of eyebrows, variations in the shape of the face, external eye abnormalities, smooth and/or long philtrum, and ear abnormalities. Hyperparathyroidism was found in four families with missense variants, and enrichment of different tumor types was observed. In molecular studies, DNA-binding domain variants elicited differential expression of a small set of target genes relative to wild-type ZFX in cultured cells, suggesting a gain or loss of transcriptional activity. Additionally, a zebrafish model of ZFX loss displayed an altered behavioral phenotype, providing additional evidence for the functional significance of ZFX. Our clinical and experimental data support that variants in ZFX are associated with an X-linked intellectual disability syndrome characterized by a recurrent facial gestalt, neurocognitive and behavioral abnormalities, and an increased risk for congenital anomalies and hyperparathyroidism.
    Matched MeSH terms: Mutation, Missense/genetics
  3. Ariffin H, Geikowski A, Chin TF, Chau D, Arshad A, Abu Bakar K, et al.
    Med J Malaysia, 2014 Aug;69(4):193-4.
    PMID: 25500851 MyJurnal
    We report a case of Griscelli Syndrome (GS). Our patient initially presented with a diagnosis of haemophagocytic lymphistiocytosis (HLH). Subsequent microscopic analysis of the patient's hair follicle revealed abnormal distribution of melanosomes in the shaft, which is a hallmark for GS. Analysis of RAB27A gene in this patient revealed a homozygous mutation in exon 6, c.550C>T, p.R184X . This nonsense mutation causes premature truncation of the protein resulting in a dysfunctional RAB27A. Recognition of GS allows appropriate institution of therapy namely chemotherapy for HLH and curative haemotopoeitic stem cell transplantation.
    Matched MeSH terms: Mutation
  4. Ganikhodjaev N, Saburov M, Nawi AM
    ScientificWorldJournal, 2014;2014:835069.
    PMID: 25136693 DOI: 10.1155/2014/835069
    We shall explore a nonlinear discrete dynamical system that naturally occurs in population systems to describe a transmission of a trait from parents to their offspring. We consider a Mendelian inheritance for a single gene with three alleles and assume that to form a new generation, each gene has a possibility to mutate, that is, to change into a gene of the other kind. We investigate the derived models and observe chaotic behaviors of such models.
    Matched MeSH terms: Mutation
  5. Sng JH, Ali AB, Lee SC, Zahar D, Wong JE, Blake V, et al.
    J Med Genet, 2003 Oct;40(10):e117.
    PMID: 14569140
    Matched MeSH terms: Mutation*; Germ-Line Mutation; Mutation, Missense
  6. Shakinah Salleh, Zaiton Ahmad, Affrida Abu Hassan, Yahya Awang, Yutaka Oono
    MyJurnal
    Chrysanthemum morifolium is an important temperate cut flower for Malaysian floriculture
    industry and the lack of new local owned varieties led to this mutation breeding research. The
    objective of this study was to compare the effectiveness of ion beam irradiation in generating
    mutations on ray florets and nodal explants of Chrysanthemum morifolium cv. ‘Reagan Red’. Ion
    beams has become an efficient physical mutagen for mutation breeding. The ray florets and nodal
    explants were irradiated with ion beams at doses 0, 0.5, 1.0, 2.0, 3.0, 5.0, 8.0, 10, 15, 20 and 30 Gy.
    The 50% of in vitro shoot regeneration (RD50) for ray florets explants was 2.0 Gy and for nodal
    explants was 4.0 Gy. Thus, relative biological effectiveness (RBE) for ray florets was found 2.0
    times higher than the nodal explants. The regenerated plantlets were planted in the greenhouse at
    MARDI, Cameron Highlands for morphological screening. Overall performance of survival
    plantlets derived from in vitro nodal and ray floret explants was recorded. The characters studied
    include plant morphology and flowering characteristic. The ray florets explants were found to be
    more sensitive to ion beam irradiation and generated more mutations as compared to nodal
    explants.
    Matched MeSH terms: Mutation
  7. Zaw MT, Emran NA, Lin Z
    J Infect Public Health, 2018 04 26;11(5):605-610.
    PMID: 29706316 DOI: 10.1016/j.jiph.2018.04.005
    BACKGROUND: Rifampicin (RIF) plays a pivotal role in the treatment of tuberculosis due to its bactericidal effects. Because the action of RIF is on rpoB gene encoding RNA polymerase β subunit, 95% of RIF resistant mutations are present in rpoB gene. The majority of the mutations in rpoB gene are found within an 81bp RIF-resistance determining region (RRDR).

    METHODOLOGY: Literatures on RIF resistant mutations published between 2010 and 2016 were thoroughly reviewed.

    RESULTS: The most commonly mutated codons in RRDR of rpoB gene are 531, 526 and 516. The possibilities of absence of mutation in RRDR of rpoB gene in MDR-TB isolates in few studies was due to existence of other rare rpoB mutations outside RRDR or different mechanism of rifampicin resistance.

    CONCLUSION: Molecular methods which can identify extensive mutations associated with multiple anti-tuberculous drugs are in urgent need so that the research on drug resistant mutations should be extended.

    Matched MeSH terms: Mutation
  8. Alifah Nadia Abu Hassan, Ezalia Esa, Nur Aisyah Aziz, Faidatul Syazlin Abd Hamid, Zubaidah Zakaria, Siti Aisyah Lazim
    MyJurnal
    Thalassaemia screening programme was conducted to reduce the burden of the disease [1]. Here, we describe one unexpected discovery in a 33-year-old gentleman and also the importance of DNA analysis in detecting the globin gene mutation.
    Matched MeSH terms: Mutation
  9. Mustafa HMJ, Ayob M, Albashish D, Abu-Taleb S
    PLoS One, 2020;15(6):e0232816.
    PMID: 32525869 DOI: 10.1371/journal.pone.0232816
    The text clustering is considered as one of the most effective text document analysis methods, which is applied to cluster documents as a consequence of the expanded big data and online information. Based on the review of the related work of the text clustering algorithms, these algorithms achieved reasonable clustering results for some datasets, while they failed on a wide variety of benchmark datasets. Furthermore, the performance of these algorithms was not robust due to the inefficient balance between the exploitation and exploration capabilities of the clustering algorithm. Accordingly, this research proposes a Memetic Differential Evolution algorithm (MDETC) to solve the text clustering problem, which aims to address the effect of the hybridization between the differential evolution (DE) mutation strategy with the memetic algorithm (MA). This hybridization intends to enhance the quality of text clustering and improve the exploitation and exploration capabilities of the algorithm. Our experimental results based on six standard text clustering benchmark datasets (i.e. the Laboratory of Computational Intelligence (LABIC)) have shown that the MDETC algorithm outperformed other compared clustering algorithms based on AUC metric, F-measure, and the statistical analysis. Furthermore, the MDETC is compared with the state of art text clustering algorithms and obtained almost the best results for the standard benchmark datasets.
    Matched MeSH terms: Mutation
  10. Koya Kutty S, Mulroy E, Magrinelli F, Di Lazzaro G, Latorre A, Bhatia KP
    Parkinsonism Relat Disord, 2021 09;90:120-122.
    PMID: 33640251 DOI: 10.1016/j.parkreldis.2021.02.022
    Matched MeSH terms: Mutation
  11. Koay BT, Chiow MY, Ismail J, Fahmy NK, Yee SY, Mustafa N, et al.
    Mol Med Rep, 2022 Dec;26(6).
    PMID: 36281931 DOI: 10.3892/mmr.2022.12882
    Autosomal dominant polycystic kidney disease (ADPKD) is the most common type of inherited cystic kidney disease. The feasibility of whole‑exome sequencing (WES) to obtain molecular diagnosis of ADPKD is still in question as previous studies showed conflicting results. Utilizing WES on a patient with ADPKD, standard bioinformatics pipeline demonstrated no pathogenic variant in the genes of interest. By visualizing read alignments using the Integrative Genomics Viewer, a region with atypical alignment of numerous soft‑clipped reads at exon 45 of polycystin 1, transient receptor potential channel interacting (PKD1) gene was demonstrated. A total of four visual inspection steps were outlined to assess the origin of these soft‑clipped reads as strand bias during capture, poor mapping, sequencing error or DNA template contamination. Following assessment, the atypical alignment at PKD1 was hypothesized to be caused by an insertion/deletion mutation. Sanger sequencing confirmed the presence of a novel 20‑bp insertion in PKD1 (NM_001009944.3; c.12143_12144insTCC​CCG​CAG​TCT​TCC​CCG​CA; p.Val4048LeufsTer157), which introduced a premature stop codon and was predicted to be pathogenic. The present study demonstrated that WES could be utilized as a molecular diagnostic tool for ADPKD. Furthermore, visual inspection of read alignments was key in identifying the pathogenic variant. The proposed visual inspection steps may be incorporated into a typical WES data analysis workflow to improve the diagnostic yield.
    Matched MeSH terms: Mutation
  12. Tan SL, Ahmad Narihan MGB, Koa AJ
    BMC Pediatr, 2023 Oct 28;23(1):541.
    PMID: 37898736 DOI: 10.1186/s12887-023-04376-5
    BACKGROUND: Coffin-Lowry syndrome (CLS) is a rare X-linked condition with intellectual disability, growth retardation, characteristic facies and skeletal anomalies. To date, hypertriglyceridemia has not been reported in literature to be associated with CLS.

    CASE PRESENTATION: Herein, we report a case of very severe hypertriglyceridemia 32 mmol/L (2834 mg/dL) detected incidentally at three months old in an otherwise well boy born late preterm with intrauterine growth restriction, when he presented with lipaemic plasma. He was later diagnosed with CLS. No pathogenic mutations were found for hypertriglyceridemia, and no secondary causes could explain his very severe hypertriglyceridemia.

    CONCLUSIONS: The very severe hypertriglyceridemia in this case may appear to be a serious presentation of an unrecognised clinical feature of CLS, further expanding its phenotype.

    Matched MeSH terms: Mutation
  13. Saeidi H, Ismail P, Samudi Raju C, Khairul-Asri MG, Bakrin IH
    Malays J Pathol, 2023 Aug;45(2):149-155.
    PMID: 37658525
    Prostate cancer is the second-most frequently diagnosed cancer in men worldwide. Serum prostatespecific antigen is currently used for the early detection of prostate cancer. However, new biomarkers are needed to decrease over diagnosis and over treatment of prostate cancer due to limitations of prostate-specific antigen. Recently, molecular biomarkers have shown promising results for diagnosis and prognosis of prostate cancer. Molecular biomarkers have improved the sensitivity and specificity of prostate-specific antigen and studies are ongoing to identify molecular biomarkers as a replacement for prostate-specific antigen. This review aims to give an overview of emerging molecular biomarkers for diagnosis and prognosis of prostate cancer.
    Matched MeSH terms: Mutation
  14. Reungwetwattana T, Cho BC, Lee KH, Pang YK, Fong CH, Kang JH, et al.
    J Thorac Oncol, 2023 Oct;18(10):1351-1361.
    PMID: 37702629 DOI: 10.1016/j.jtho.2023.06.016
    INTRODUCTION: Lazertinib is a third-generation central nervous system-penetrant tyrosine kinase inhibitor targeting mutant EGFR in NSCLC. Lazertinib exhibited improved efficacy versus gefitinib in the LASER301 study; this subset analysis compared lazertinib with gefitinib among Asian patients.

    METHODS: The phase 3 LASER301 study evaluated lazertinib efficacy and safety in treatment-naive patients with EGFR-mutated (exon 19 deletion or L858R) locally advanced or metastatic NSCLC. Patients were randomized one-to-one and received either lazertinib or gefitinib. The primary end point was investigator-assessed progression-free survival using Response Evaluation Criteria in Solid Tumors version 1.1. Secondary end points included overall survival, objective response rate, duration of response, and safety.

    RESULTS: Between February 13, 2020, and July 29, 2022, among 258 patients of Asian descent, the median progression-free survival was significantly longer with lazertinib than gefitinib (20.6 versus 9.7 mo; hazard ratio: 0.46; 95% confidence interval [CI]: 0.34-0.63, p < 0.001), and the benefit was consistent across predefined subgroups (exon 19 deletion, L858R, baseline central nervous system metastases). Objective response rate and disease control rates were similar between treatment groups. The median duration of response was 19.4 months (95% CI: 16.6-24.9) versus 9.6 months (95% CI: 6.9-12.4) in the lazertinib versus gefitinib group. Adverse event rates in Asian patients were comparable with the overall LASER301 population. Adverse events leading to discontinuation in the lazertinib and gefitinib groups were 13% and 12%, respectively.

    CONCLUSIONS: In LASER301, efficacy and safety results in Asian patients were consistent with the overall population. Lazertinib exhibited better efficacy than gefitinib in Asian patients with a tolerable safety profile.

    Matched MeSH terms: Mutation
  15. Zhong Y, Tan GW, Bult J, Veltmaat N, Plattel W, Kluiver J, et al.
    BMC Cancer, 2024 Apr 02;24(1):407.
    PMID: 38566053 DOI: 10.1186/s12885-024-12191-z
    BACKGROUND: Primary central nervous system lymphoma (PCNSL) are rare mature B-cell lymphoproliferative diseases characterized by a high incidence of MYD88 L265P and CD79B Y196 hotspot mutations. Diagnosis of PCNSL can be challenging. The aim of the study was to analyze the detection rate of the MYD88 L265P and CD79B Y196 mutation in cell free DNA (cfDNA) in plasma of patients with PCNSL.

    METHODS: We analyzed by digital droplet PCR (ddPCR) to determine presence of the MYD88 L265P and CD79B Y196 hotspot mutations in cfDNA isolated from plasma of 24 PCNSL patients with active disease. Corresponding tumor samples were available for 14 cases. Based on the false positive rate observed in 8 healthy control samples, a stringent cut-off for the MYD88 L265P and CD79B Y196 mutation were set at 0.3% and 0.5%, respectively.

    RESULTS: MYD88 L265P and CD79B Y196 mutations were detected in 9/14 (64%) and 2/13 (15%) tumor biopsies, respectively. In cfDNA samples, the MYD88 L265P mutation was detected in 3/24 (12.5%), while the CD79B Y196 mutation was not detected in any of the 23 tested cfDNA samples. Overall, MYD88 L265P and/or CD79B Y196 were detected in cfDNA in 3/24 cases (12.5%). The detection rate of the combined analysis did not improve the single detection rate for either MYD88 L265P or CD79B Y196.

    CONCLUSION: The low detection rate of MYD88 L265P and CD79B Y196 mutations in cfDNA in the plasma of PCNSL patients argues against its use in routine diagnostics. However, detection of MYD88 L265P by ddPCR in cfDNA in the plasma could be considered in challenging cases.

    Matched MeSH terms: Mutation
  16. Guo L, Malara D, Battaglia P, Waiho K, Davis DA, Deng Y, et al.
    Genome Biol Evol, 2024 Mar 02;16(3).
    PMID: 38408866 DOI: 10.1093/gbe/evae037
    The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.
    Matched MeSH terms: Mutation
  17. Fu JYL, Chong YM, Sam IC, Chan YF
    J Virol Methods, 2022 Mar;301:114462.
    PMID: 35026305 DOI: 10.1016/j.jviromet.2022.114462
    Emerging SARS-CoV-2 variants of concern (VOC) have been associated with enhanced transmissibility and immune escape. Next-generation sequencing (NGS) of the whole genome is the gold standard for variant identification for surveillance but is time-consuming and costly. Rapid and cost-effective assays that detect SARS-CoV-2 variants are needed. We evaluated Allplex SARS-CoV-2 Master Assay and Variants I Assay to detect HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H spike mutations in 248 positive samples collected in Kuala Lumpur, Malaysia, between January and May 2021. Spike variants were detected in 78/248 (31.5 %), comprising 60 VOC B.1.351 (beta) and 18 B.1.1.7 (alpha). With NGS as reference for 115 samples, the sensitivity for detecting the spike mutations was 98.7 % with the Master Assay and 100 % with the Variants I Assay. The emergence of beta variants correlated with increasing COVID-19 infections in Malaysia. The prevalence of alpha VOC and lineage B.1.466.2 was low. These assays detect mutations present in alpha, beta and gamma VOCs. Of the VOCs which have subsequently emerged, the assays should detect omicron (B.1.1.529) but not B.1.617.2 (delta). In conclusion, spike variant PCR assays can be used to rapidly monitor selected SARS-CoV-2 VOCs in resource-limited settings, but require updates as new variants emerge.
    Matched MeSH terms: Mutation
  18. Hassan S, Ahmad R, Zakaria Z, Zulkafli Z, Abdullah WZ
    Malays J Med Sci, 2013 Jan;20(1):13-20.
    PMID: 23613656
    β-thalassaemia is one of the most common single-gene disorders worldwide. Each ethnic population has its own common mutations, accounting for the majority of cases, with a small number of mutations for the rarer alleles. Due to the heterogeneity of β-thalassaemia and the multi-ethnicity of Malaysians, molecular diagnostics may be expensive and time consuming.
    Matched MeSH terms: Mutation
  19. Hasan MM, Das R, Rasheduzzaman M, Hussain MH, Muzahid NH, Salauddin A, et al.
    Virus Res, 2021 May;297:198390.
    PMID: 33737154 DOI: 10.1016/j.virusres.2021.198390
    Coronavirus Disease 2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations, and pathogenesis. Nearly 0.4 million mutations have been identified so far among the ∼60,000 SARS-CoV-2 genomic sequences. In this study, we compared a total of 371 SARS-CoV-2 published whole genomes reported from different parts of Bangladesh with 467 sequences reported globally to understand the origin of viruses, possible patterns of mutations, and availability of unique mutations. Phylogenetic analyses indicated that SARS-CoV-2 viruses might have transmitted through infected travelers from European countries, and the GR clade was found as predominant in Bangladesh. Our analyses revealed 4604 mutations at the RNA level including 2862 missense mutations, 1192 synonymous mutations, 25 insertions and deletions and 525 other types of mutation. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (98 %) in Bangladeshi isolates. Interestingly, we found the average number of mutations in ORF1ab, S, ORF3a, M, and N were significantly higher (p < 0.001) for sequences containing the G614 variant compared to those having D614. Previously reported frequent mutations, such as R203K, D614G, G204R, P4715L and I300F at protein levels were also prevalent in Bangladeshi isolates. Additionally, 34 unique amino acid changes were revealed and categorized as originating from different cities. These analyses may increase our understanding of variations in SARS-CoV-2 virus genomes, circulating in Bangladesh and elsewhere.
    Matched MeSH terms: Mutation
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