MyMedR

Displaying publications 1 - 20 of 949 in total

Abstract:

Sort:

Embracing Monogenic Parkinson's Disease: The MJFF Global Genetic PD Cohort

Vollstedt EJ, Schaake S, Lohmann K, Padmanabhan S, Brice A, Lesage S, et al.

Mov Disord, 2023 Feb;38(2):286-303.
PMID: 36692014 DOI: 10.1002/mds.29288

BACKGROUND: As gene-targeted therapies are increasingly being developed for Parkinson's disease (PD), identifying and characterizing carriers of specific genetic pathogenic variants is imperative. Only a small fraction of the estimated number of subjects with monogenic PD worldwide are currently represented in the literature and availability of clinical data and clinical trial-ready cohorts is limited.
OBJECTIVE: The objectives are to (1) establish an international cohort of affected and unaffected individuals with PD-linked variants; (2) provide harmonized and quality-controlled clinical characterization data for each included individual; and (3) further promote collaboration of researchers in the field of monogenic PD.
METHODS: We conducted a worldwide, systematic online survey to collect individual-level data on individuals with PD-linked variants in SNCA, LRRK2, VPS35, PRKN, PINK1, DJ-1, as well as selected pathogenic and risk variants in GBA and corresponding demographic, clinical, and genetic data. All registered cases underwent thorough quality checks, and pathogenicity scoring of the variants and genotype-phenotype relationships were analyzed.
RESULTS: We collected 3888 variant carriers for our analyses, reported by 92 centers (42 countries) worldwide. Of the included individuals, 3185 had a diagnosis of PD (ie, 1306 LRRK2, 115 SNCA, 23 VPS35, 429 PRKN, 75 PINK1, 13 DJ-1, and 1224 GBA) and 703 were unaffected (ie, 328 LRRK2, 32 SNCA, 3 VPS35, 1 PRKN, 1 PINK1, and 338 GBA). In total, we identified 269 different pathogenic variants; 1322 individuals in our cohort (34%) were indicated as not previously published.
CONCLUSIONS: Within the MJFF Global Genetic PD Study Group, we (1) established the largest international cohort of affected and unaffected individuals carrying PD-linked variants; (2) provide harmonized and quality-controlled clinical and genetic data for each included individual; (3) promote collaboration in the field of genetic PD with a view toward clinical and genetic stratification of patients for gene-targeted clinical trials. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Matched MeSH terms: Mutation
Application of a simple oligonucleotide-directed mutagenesis method for correction of a frameshift mutation

Chee HY, Sazaly AB

JUMMEC, 1997;2:27-30.

Matched MeSH terms: Mutation; Frameshift Mutation
Homologous recombination repair gene mutations in Malaysian prostate cancer patients

Saeidi H, Raju CS, Ismail P, Raub SHA, Omar N, Hisyam Bakrin I

Cell Mol Biol (Noisy-le-grand), 2022 Aug 31;68(8):22-26.
PMID: 36800845 DOI: 10.14715/cmb/2022.68.8.4

Genetic alterations in the homologous recombination repair (HRR) genes are associated with an increased risk of prostate cancer development, and patients harboring these mutations can benefit from targeted therapy. The main aim of this study is to identify genetic alterations in HRR genes as a potential target for targeted treatment. In this study, targeted next generation sequencing (NGS) is used to analyze mutations in the protein-coding regions of the 27 genes involved in HRR and mutations in hotspots of 5 cancer-associated genes in four FFPE samples and three blood samples from prostate cancer patients. We identified two mutations in TP53 and KRAS. We also identified four conflicting interpretations of pathogenicity variants in BRCA2, STK11 genes and one variant of uncertain significance in the RAD51B gene. In addition, we detected one drug response variant in TP53, and two novel variants in CDK12 and ATM. Our results revealed some actionable pathogenic and potential pathogenic variants that may be associated with response to the Poly (ADP-ribose) polymerase (PARP) inhibitor treatment. More studies in a larger cohort are needed to evaluate and determine the association of HRR mutations with prostate cancer.

Matched MeSH terms: Mutation
Fulltext An Overview of the Genetic Variations of the SARS-CoV-2 Genomes Isolated in Southeast Asian Countries

Yap PSX, Tan TS, Chan YF, Tee KK, Kamarulzaman A, Teh CSJ

J Microbiol Biotechnol, 2020 Jul 28;30(7):962-966.
PMID: 32627759 DOI: 10.4014/jmb.2006.06009

Monitoring the mutation dynamics of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in understanding its infectivity, virulence and pathogenicity for development of a vaccine. In an "age of mobility," the pandemic highlights the importance and vulnerability of regionalization and labor market interdependence in Southeast Asia. We intend to characterize the genetic variability of viral populations within the region to provide preliminary information for regional surveillance in the future. By analyzing 142 complete genomes from South East Asian (SEA) countries, we identified three central variants distinguished by nucleotide and amino acid changes.

Matched MeSH terms: Mutation*
Fulltext Increased yield performance of mutation induced Soybean genotypes at varied agro-ecological conditions

Bhuiyan MSH, Malek MA, Emon RM, Khatun MK, Khandaker MM, Alam MA

Braz J Biol, 2022;84:e255235.
PMID: 35019108 DOI: 10.1590/1519-6984.255235

In soybean breeding program, continuous selection pressure on traits response to yield created a genetic bottleneck for improvements of soybean through hybridization breeding technique. Therefore an initiative was taken to developed high yielding soybean variety applying mutation breeding techniques at Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Bangladesh. Locally available popular cultivar BARI Soybean-5 was used as a parent material and subjected to five different doses of Gamma ray using Co60. In respect to seed yield and yield attributing characters, twelve true breed mutants were selected from M4 generation. High values of heritability and genetic advance with high genotypic coefficient of variance (GCV) for plant height, branch number and pod number were considered as favorable attributes for soybean improvement that ensure expected yield. The mutant SBM-18 obtained from 250Gy provided stable yield performance at diversified environments. It provided maximum seed yield of 3056 kg ha-1 with highest number of pods plant-1 (56). The National Seed Board of Bangladesh (NSB) eventually approved SBM-18 and registered it as a new soybean variety named 'Binasoybean-5' for large-scale planting because of its superior stability in various agro-ecological zones and consistent yield performance.

Matched MeSH terms: Mutation/genetics
Fulltext Unraveling POLN germline mutations in familial nasopharyngeal carcinoma: Complementary evidence from gene association and molecular studies

Chong PP

EBioMedicine, 2022 Dec;86:104326.
PMID: 36335666 DOI: 10.1016/j.ebiom.2022.104326
Matched MeSH terms: Germ-Line Mutation*
Fulltext Infantile Progressive Hepatoencephalomyopathy with Combined OXPHOS Deficiency due to Mutations in the Mitochondrial Translation Elongation Factor Gene GFM1

Balasubramaniam S, Choy YS, Talib A, Norsiah MD, van den Heuvel LP, Rodenburg RJ

JIMD Rep, 2012;5:113-22.
PMID: 23430926 DOI: 10.1007/8904_2011_107

Mitochondrial disorders are a heterogeneous group of often multisystemic and early fatal diseases caused by defects in the oxidative phosphorylation (OXPHOS) system. Given the complexity and intricacy of the OXPHOS system, it is not surprising that the underlying molecular defect remains unidentified in many patients with a mitochondrial disorder. Here, we report the clinical features and diagnostic workup leading to the elucidation of the genetic basis for a combined complex I and IV OXPHOS deficiency secondary to a mitochondrial translational defect in an infant who presented with rapidly progressive liver failure, encephalomyopathy, and severe refractory lactic acidemia. Sequencing of the GFM1 gene revealed two inherited novel, heterozygous mutations: a.539delG (p.Gly180AlafsX11) in exon 4 which resulted in a frameshift mutation, and a second c.688G > A (p.Gly230Ser) mutation in exon 5. This missense mutation is likely to be pathogenic since it affects an amino acid residue that is highly conserved across species and is absent from the dbSNP and 1,000 genomes databases. Review of literature and comparison were made with previously reported cases of this recently identified mitochondrial disorder encoded by a nuclear gene. Although limited in number, nuclear gene defects causing mitochondrial translation abnormalities represent a new, rapidly expanding field of mitochondrial medicine and should potentially be considered in the diagnostic investigation of infants with progressive hepatoencephalomyopathy and combined OXPHOS disorders.

Matched MeSH terms: Mutation; Frameshift Mutation; Mutation, Missense
Fulltext Whole-exome sequencing and bioinformatic analyses revealed differences in gene mutation profiles in papillary thyroid cancer patients with and without benign thyroid goitre background

Eng ZH, Abdullah MI, Ng KL, Abdul Aziz A, Arba'ie NH, Mat Rashid N, et al.

Front Endocrinol (Lausanne), 2022;13:1039494.
PMID: 36686473 DOI: 10.3389/fendo.2022.1039494

BACKGROUND: Papillary thyroid cancer (PTC) is the most common thyroid malignancy. Concurrent presence of cytomorphological benign thyroid goitre (BTG) and PTC lesion is often detected. Aberrant protein profiles were previously reported in patients with and without BTG cytomorphological background. This study aimed to evaluate gene mutation profiles to further understand the molecular mechanism underlying BTG, PTC without BTG background and PTC with BTG background.
METHODS: Patients were grouped according to the histopathological examination results: (i) BTG patients (n = 9), (ii) PTC patients without BTG background (PTCa, n = 8), and (iii) PTC patients with BTG background (PTCb, n = 5). Whole-exome sequencing (WES) was performed on genomic DNA extracted from thyroid tissue specimens. Nonsynonymous and splice-site variants with MAF of ≤ 1% in the 1000 Genomes Project were subjected to principal component analysis (PCA). PTC-specific SNVs were filtered against OncoKB and COSMIC while novel SNVs were screened through dbSNP and COSMIC databases. Functional impacts of the SNVs were predicted using PolyPhen-2 and SIFT. Protein-protein interaction (PPI) enrichment of the tumour-related genes was analysed using Metascape and MCODE algorithm.
RESULTS: PCA plots showed distinctive SNV profiles among the three groups. OncoKB and COSMIC database screening identified 36 tumour-related genes including BRCA2 and FANCD2 in all groups. BRAF and 19 additional genes were found only in PTCa and PTCb. "Pathways in cancer", "DNA repair" and "Fanconi anaemia pathway" were among the top networks shared by all groups. However, signalling pathways related to tyrosine kinases were the most significantly enriched in PTCa while "Jak-STAT signalling pathway" and "Notch signalling pathway" were the only significantly enriched in PTCb. Ten SNVs were PTC-specific of which two were novel; DCTN1 c.2786C>G (p.Ala929Gly) and TRRAP c.8735G>C (p.Ser2912Thr). Four out of the ten SNVs were unique to PTCa.
CONCLUSION: Distinctive gene mutation patterns detected in this study corroborated the previous protein profile findings. We hypothesised that the PTCa and PTCb subtypes differed in the underlying molecular mechanisms involving tyrosine kinase, Jak-STAT and Notch signalling pathways. The potential applications of the SNVs in differentiating the benign from the PTC subtypes requires further validation in a larger sample size.

Matched MeSH terms: Mutation
Fulltext Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy

Kuan SW, Chua KH, Tan EW, Tan LK, Loch A, Kee BP

PeerJ, 2022;10:e13265.
PMID: 35441061 DOI: 10.7717/peerj.13265

Cardiomyopathy (CMP) constitutes a diverse group of myocardium diseases affecting the pumping ability of the heart. Genetic predisposition is among the major factors affecting the development of CMP. Globally, there are over 100 genes in autosomal and mitochondrial DNA (mtDNA) that have been reported to be associated with the pathogenesis of CMP. However, most of the genetic studies have been conducted in Western countries, with limited data being available for the Asian population. Therefore, this study aims to investigate the mutation spectrum in the mitochondrial genome of 145 CMP patients in Malaysia. Long-range PCR was employed to amplify the entire mtDNA, and whole mitochondrial genome sequencing was conducted on the MiSeq platform. Raw data was quality checked, mapped, and aligned to the revised Cambridge Reference Sequence (rCRS). Variants were named, annotated, and filtered. The sequencing revealed 1,077 variants, including 18 novel and 17 CMP and/or mitochondrial disease-associated variants after filtering. In-silico predictions suggested that three of the novel variants (m.8573G>C, m.11916T>A and m.11918T>G) in this study are potentially pathogenic. Two confirmed pathogenic variants (m.1555A>G and m.11778G>A) were also found in the CMP patients. The findings of this study shed light on the distribution of mitochondrial mutations in Malaysian CMP patients. Further functional studies are required to elucidate the role of these variants in the development of CMP.

Matched MeSH terms: Mutation/genetics
Fulltext Severe Developmental Delay, Epilepsy and Neonatal Diabetes (DEND) Syndrome: A Case Report

Helmi MAM, Hussain S

J ASEAN Fed Endocr Soc, 2020;35(1):125-128.
PMID: 33442181 DOI: 10.15605/jafes.035.01.22

Developmental delay, Epilepsy and Neonatal Diabetes (DEND) syndrome is the most severe form of Permanent Neonatal Diabetes with KCNJ11 gene mutation which accounts for most of the cases. We report the first DEND syndrome in Malaysia with heterozygous missense mutation Q52R at KCNJ11 (Kir6.2) gene with delayed presentation beyond 6 months of age and failure to transition to glibenclamide. This report signifies the phenotypical variability among patients with the same genetic mutation and the different response to treatment.

Matched MeSH terms: Mutation; Mutation, Missense
Fulltext Mutation Study of Malaysian Patients with Ornithine Transcarbamylase Deficiency: Clinical, Molecular, and Bioinformatics Analyses of Two Novel Missense Mutations of the OTC Gene

Ali EZ, Zakaria Y, Mohd Radzi MA, Ngu LH, Jusoh SA

Biomed Res Int, 2018;2018:4320831.
PMID: 30175132 DOI: 10.1155/2018/4320831

Ornithine transcarbamylase deficiency (OTCD), an X-linked disorder that results from mutations in the OTC gene, causes hyperammonemia and leads to various clinical manifestations. Mutations occurring close to the catalytic site of OTCase can cause severe OTCD phenotypes compared with those caused by mutations occurring on the surface of this protein. In this study, we report two novel OTC missense mutations, Q171H and N199H, found in Malaysian patients. Q171H and N199H caused neonatal onset OTCD in a male and late OTCD in a female, respectively. In silico predictions and molecular docking were performed to examine the effect of these novel mutations, and the results were compared with other 30 known OTC mutations. In silico servers predicted that Q171H and N199H, as well as 30 known missense mutations, led to the development of OTCD. Docking analysis indicated that N-(phosphonoacetyl)-L-ornithine (PALO) was bound to the catalytic site of OTCase mutant structure with minimal conformational changes. However, the mutations disrupted interatomic interactions in the catalytic site. Therefore, depending on the severity of disruption occurring at the catalytic site, the mutation may affect the efficiency of mechanism and functions of OTCase.

Matched MeSH terms: Mutation; Mutation, Missense*
Variable clinical phenotypes in a family with homozygous c.1159G>A mutation in the thyroid peroxidase gene

Lee CC, Harun F, Jalaludin MY, Heh CH, Othman R, Kang IN, et al.

Horm Res Paediatr, 2014;81(5):356-60.
PMID: 24717978 DOI: 10.1159/000359922

Defects in the thyroid peroxidase (TPO) gene have been associated with goitrous congenital hypothyroidism (CH).

Matched MeSH terms: Point Mutation*
ras gene mutations in Malaysian leukemia patients

Chin IY, Koh CL, Bosco JJ

Acta Haematol., 1992;87(1-2):107-8.
PMID: 1585764
Matched MeSH terms: Mutation*
Fulltext The occurrence of dihydrofolate reductase (DHFR) point mutation (SER-108-->ASN-108) in Malaysian isolates of Plasmodium falciparum

Lim PK, Tan SK, Khoo AS, Noor Rain A, Nagappan S, Mak JW

Southeast Asian J. Trop. Med. Public Health, 1998 Mar;29(1):27-30.
PMID: 9740263
Matched MeSH terms: Point Mutation*
Fulltext Optimal path test data generation based on hybrid negative selection algorithm and genetic algorithm

Mohi-Aldeen SM, Mohamad R, Deris S

PLoS One, 2020;15(11):e0242812.
PMID: 33253281 DOI: 10.1371/journal.pone.0242812

Path testing is the basic approach of white box testing and the main approach to solve it by discovering the particular input data of the searching space to encompass the paths in the software under test. Due to the increasing software complexity, exhaustive testing is impossible and computationally not feasible. The ultimate challenge is to generate suitable test data that maximize the coverage; many approaches have been developed by researchers to accomplish path coverage. The paper suggested a hybrid method (NSA-GA) based on Negative Selection Algorithm (NSA) and Genetic Algorithm (GA) to generate an optimal test data avoiding replication to cover all possible paths. The proposed method modifies the generation of detectors in the generation phase of NSA using GA, as well as, develops a fitness function based on the paths' prioritization. Different benchmark programs with different data types have been used. The results show that the hybrid method improved the coverage percentage of the programs' paths, even for complicated paths and its ability to minimize the generated number of test data and enhance the efficiency even with the increased input range of different data types used. This method improves the effectiveness and efficiency of test data generation and maximizes search space area, increasing percentage of path coverage while preventing redundant data.

Matched MeSH terms: Mutation/genetics
Fulltext Ion-Pair Interaction and Hydrogen Bonds as Main Features of Protein Thermostability in Mutated T1 Recombinant Lipase Originating from Geobacilluszalihae

Ishak SNH, Kamarudin NHA, Ali MSM, Leow ATC, Rahman RNZRA

Molecules, 2020 Jul 28;25(15).
PMID: 32731607 DOI: 10.3390/molecules25153430

A comparative structure analysis between space- and an Earth-grown T1 recombinant lipase from Geobacillus zalihae had shown changes in the formation of hydrogen bonds and ion-pair interactions. Using the space-grown T1 lipase validated structure having incorporated said interactions, the recombinant T1 lipase was re-engineered to determine the changes brought by these interactions to the structure and stability of lipase. To understand the effects of mutation on T1 recombinant lipase, five mutants were developed from the structure of space-grown T1 lipase and biochemically characterized. The results demonstrate an increase in melting temperature up to 77.4 °C and 76.0 °C in E226D and D43E, respectively. Moreover, the mutated lipases D43E and E226D had additional hydrogen bonds and ion-pair interactions in their structures due to the improvement of stability, as observed in a longer half-life and an increased melting temperature. The biophysical study revealed differences in β-Sheet percentage between less stable (T118N) and other mutants. As a conclusion, the comparative analysis of the tertiary structure and specific residues associated with ion-pair interactions and hydrogen bonds could be significant in revealing the thermostability of an enzyme with industrial importance.

Matched MeSH terms: Mutation, Missense*
Fulltext Single Residue Substitution at N-Terminal Affects Temperature Stability and Activity of L2 Lipase

Bukhari N, Leow ATC, Abd Rahman RNZR, Mohd Shariff F

Molecules, 2020 Jul 28;25(15).
PMID: 32731608 DOI: 10.3390/molecules25153433

Rational design is widely employed in protein engineering to tailor wild-type enzymes for industrial applications. The typical target region for mutation is a functional region like the catalytic site to improve stability and activity. However, few have explored the role of other regions which, in principle, have no evident functionality such as the N-terminal region. In this study, stability prediction software was used to identify the critical point in the non-functional N-terminal region of L2 lipase and the effects of the substitution towards temperature stability and activity were determined. The results showed 3 mutant lipases: A8V, A8P and A8E with 29% better thermostability, 4 h increase in half-life and 6.6 °C higher thermal denaturation point, respectively. A8V showed 1.6-fold enhancement in activity compared to wild-type. To conclude, the improvement in temperature stability upon substitution showed that the N-terminal region plays a role in temperature stability and activity of L2 lipase.

Matched MeSH terms: Mutation, Missense*
KID syndrome in a Malaysian child with identification of novel heterozygous missense mutation GJB2 c.581T>A(p. 194Phe>Tyr)

Tang MM, Surana U, Leong KF, Pramano ZAD

Int J Dermatol, 2021 Jul;60(7):e288-e290.
PMID: 33728648 DOI: 10.1111/ijd.15523
Matched MeSH terms: Mutation; Mutation, Missense
Fulltext Whole exome sequencing identifies compound heterozygous variants of CR2 gene in monozygotic twin patients with common variable immunodeficiency

Mat Ripen A, Ghani H, Chear CT, Chiow MY, Syed Yahya SNH, Kassim A, et al.

SAGE Open Med, 2020;8:2050312120922652.
PMID: 32547748 DOI: 10.1177/2050312120922652

Objectives: A pair of female Malay monozygotic twins who presented with recurrent upper respiratory tract infections, hepatosplenomegaly, bronchiectasis and bicytopenia were recruited in this study. Both patients were suspected with primary immunodeficiency diseases. However, the definite diagnosis was not clear due to complex disease phenotypes. The objective of this study was to identify the causative gene mutation in these patients.
Methods: Lymphocyte subset enumeration test and whole exome sequencing were performed.
Results: We identified a compound heterozygous CR2 mutation (c.1916G>A and c.2012G>A) in both patients. These variants were then confirmed using Sanger sequencing.
Conclusion: Whole exome sequencing analysis of the monozygotic twins revealed compound heterozygous missense mutations in CR2.

Matched MeSH terms: Mutation; Mutation, Missense
Somatic mitochondrial DNA mutations in different grades of glioma

Soon BH, Abu N, Abdul Murad NA, Then SM, Abu Bakar A, Fadzil F, et al.

Per Med, 2022 01;19(1):25-39.
PMID: 34873928 DOI: 10.2217/pme-2021-0033

Aim: Mitochondrial DNA (mtDNA) alterations play an important role in the multistep processes of cancer development. Gliomas are among the most diagnosed brain cancer. The relationship between mtDNA alterations and different grades of gliomas are still elusive. This study aimed to elucidate the profile of somatic mtDNA mutations in different grades of gliomas and correlate it with clinical phenotype. Materials & methods: Forty histopathologically confirmed glioma tissue samples and their matched blood were collected and subjected for mtDNA sequencing. Results & conclusion: About 75% of the gliomas harbored at least one somatic mutation in the mtDNA gene, and 45% of these mutations were pathogenic. Mutations were scattered across the mtDNA genome, and the commonest nonsynonymous mutations were located at complex I and IV of the mitochondrial respiratory chain. These findings may have implication for future research to determine the mitochondrial energetics and its downstream metabolomics on gliomas.

Matched MeSH terms: Mutation/genetics

Filters

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links