Displaying publications 81 - 100 of 407 in total

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  1. Ng ZX, Kuppusamy UR, Tajunisah I, Fong KC, Chua KH
    J Diabetes Complications, 2012 Sep-Oct;26(5):388-92.
    PMID: 22795339 DOI: 10.1016/j.jdiacomp.2012.05.014
    PURPOSE:
    In this study, we aimed to investigate the possible association between SLC2A1 26177A/G polymorphism and diabetic retinopathy (DR) in Malaysian patients with type 2 diabetes.

    METHODS:
    Genomic DNA was extracted from 211 Malaysian type 2 diabetic patients (100 without retinopathy [DNR], 111 with retinopathy) and 165 healthy controls. A high resolution melting assay developed in this study was used to detect SLC2A1 26177A/G polymorphism followed by statistical analysis.

    RESULTS:
    A statistically significant difference in 26177G minor allele frequency between healthy controls (19.7 %) and total patient group (26.1 %) (p<0.05, Odd ratio = 1.437, 95% Confidence interval = 1.015-2.035) as well as between healthy controls (19.7 %) and DNR patients (27.5%) (p<0.05, Odd ratio = 1.546, 95% Confidence interval = 1.024-2.336) was shown in this study. However, when compared between DR and DNR patients, there was no significant difference (p>0.05).

    CONCLUSIONS:
    This is the first study which shows that SLC2A1 26177G allele is associated with type 2 diabetes in Malaysian population but not with DR.
    Matched MeSH terms: Gene Frequency
  2. Ng ZX, Kuppusamy UR, Tajunisah I, Fong KC, Koay AC, Chua KH
    Br J Ophthalmol, 2012 Feb;96(2):289-92.
    PMID: 22116960 DOI: 10.1136/bjophthalmol-2011-300658
    The receptor for advanced glycation end-products (RAGE) has been implicated in the pathogenesis of diabetic microvascular complications. The aim of this study was to investigate the association between 2245G/A gene polymorphism of the RAGE gene and retinopathy in Malaysian type 2 diabetic patients.
    Matched MeSH terms: Gene Frequency
  3. Sirica R, Buonaiuto M, Petrella V, Sticco L, Tramontano D, Antonini D, et al.
    Sci Rep, 2019 03 19;9(1):4843.
    PMID: 30890716 DOI: 10.1038/s41598-019-40360-9
    Natural selection acts on genetic variants by increasing the frequency of alleles responsible for a cellular function that is favorable in a certain environment. In a previous genome-wide scan for positive selection in contemporary humans, we identified a signal of positive selection in European and Asians at the genetic variant rs10180970. The variant is located in the second intron of the ABCA12 gene, which is implicated in the lipid barrier formation and down-regulated by UVB radiation. We studied the signal of selection in the genomic region surrounding rs10180970 in a larger dataset that includes DNA sequences from ancient samples. We also investigated the functional consequences of gene expression of the alleles of rs10180970 and another genetic variant in its proximity in healthy volunteers exposed to similar UV radiation. We confirmed the selection signal and refine its location that extends over 35 kb and includes the first intron, the first two exons and the transcription starting site of ABCA12. We found no obvious effect of rs10180970 alleles on ABCA12 gene expression. We reconstructed the trajectory of the T allele over the last 80,000 years to discover that it was specific to H. sapiens and present in non-Africans 45,000 years ago.
    Matched MeSH terms: Gene Frequency/genetics
  4. Black WC, Hawley WA, Rai KS, Craig GB
    Heredity (Edinb), 1988 Dec;61 ( Pt 3):439-46.
    PMID: 3230033
    The mosquito, Aedes albopictus, has recently become established in a number of cities throughout the United States. An initial survey of allozyme and genotypic frequencies in U.S. populations (Black et al., 1988) revealed an extensive amount of local differentiation of populations and suggested that much genetic drift may have accompanied colonization. A study of gene flow was initiated in native habitats of Ae. albopictus in Malaysia to determine if the result observed in the U.S. was a consequence of colonization or simply followed the natural breeding structure of the species. Allelic and genotypic frequencies were monitored at ten enzymatic loci in 11 populations from peninsular Malaysia and Borneo. Multiple populations were sampled within the districts of Kuala Lumpur and Kuala Trengganu. Peninsular Malaysian and Borneo populations were strongly genetically differentiated. Allele frequencies were significantly different among and within districts in both regions. Variance in allele frequencies among all collections was partitioned into the variance among regions, districts within regions and collections within districts. Almost all of the variance within regions was attributable to local differentiation suggesting that genetic drift is an important component of the natural breeding structure of this species. This indicates that the large amounts of local differentiation found in U.S. populations was not a consequence of recent colonization.
    Matched MeSH terms: Gene Frequency
  5. Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, et al.
    Nat Genet, 2013 Oct;45(10):1160-7.
    PMID: 23974870 DOI: 10.1038/ng.2745
    Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ł0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation.
    Matched MeSH terms: Gene Frequency
  6. Matsuo M, Nishiyama K, Shirakawa T, Padilla CD, San LP, Suryantoro P, et al.
    PMID: 15906715
    Glucose-6-phosphate dehydrogenase (G6PD) deficiency is common in malaria endemic regions and is estimated to affect more than 400 million people worldwide. Deficient subjects are mostly asymptomatic but clinical manifestations range from neonatal jaundice due to acute hemolytic anemia to chronic non-spherocytic hemolytic anemia. To date, biochemical parameters allowed more than 400 different G6PD variants to be distinguished thereby suggesting a vast genetic heterogeneity. So far, only a small portion of this heterogeneity has been confirmed at the DNA level with the identification of about 90 different point mutations in the G6PD coding sequence. To determine the molecular background of G6PD deficiency in Southeast Asian countries, we conducted molecular analyses of G6PD patients from the Philippines, Malaysia, Singapore, Vietnam and Indonesia. The most prevalent mutation identified differs from country to country, thus suggesting independent mutational events of the G6PD gene.
    Matched MeSH terms: Gene Frequency*
  7. Yahya NK, Afzal N, Daud KM
    Objectives: To evaluate the frequency of HLA Class II antigens in Malays with SLE in order to determine their role in disease susceptibility and association with clinical manifestations.
    Design: Cross-sectional study
    Methods: Fifty-four SLE patients from Malay ethnic attending Physician Clinic at Hospital Universiti Sains Malaysia were enrolled into the study. Demographic and clinical findings were obtained from medical records. HLA typing of class II antigens were carried out using MicroSSP Class II generic (DRB/ DQB) from One Lambda Inc. Controls were from ethnically matched healthy individuals.
    Results: A univariate analysis confirmed the association between HLA-DR15 with SLE compared to healthy control group; and was maintained using multiple logistic regression model (P corr = 0.002, adjusted OR = 5.513). There was a weak decrease of HLA-DR4 which was not significant after corrections for multiple comparisons made. DR7 was found to be significantly increased in patients with malar rash. There was positive association of DR15 with arthritis in patients compare to those without.
    Conclusion: Our data support the role of HLA Class II genes in conferring SLE susceptibility.
    Study site: Physician Clinic, Hospital Universiti Sains Malaysia (HUSM), Kelantan, Malaysia
    Matched MeSH terms: Gene Frequency
  8. Simons MJ, Wee GB, Day NE, Morris PJ, Shanmugaratnam K, De-Thé GB
    Int J Cancer, 1974 Jan 15;13(1):122-34.
    PMID: 4131857
    Matched MeSH terms: Gene Frequency
  9. Varma SL, Chary TV, Singh S, Azhar MZ, Dharap AS
    Acta Psychiatr Scand, 1995 Mar;91(3):213-5.
    PMID: 7625199
    Schizophrenics (n = 250) and normal controls (n = 90) were studied to investigate and compare their dermatoglyphic patterns. Their fingerprint patterns were studied. The frequency of arches in the patient and control groups was similar. The frequency of loops in the control group was higher than in the patient group, and the trend was consistent in all the digits. The whorls in the patient group showed an increase over the control group in all the digits, although this finding was not statistically significant.
    Matched MeSH terms: Gene Frequency/genetics
  10. McInerney-Leo AM, Harris JE, Leo PJ, Marshall MS, Gardiner B, Kinning E, et al.
    Clin Genet, 2015 Dec;88(6):550-7.
    PMID: 25492405 DOI: 10.1111/cge.12550
    Short-rib thoracic dystrophies (SRTDs) are congenital disorders due to defects in primary cilium function. SRTDs are recessively inherited with mutations identified in 14 genes to date (comprising 398 exons). Conventional mutation detection (usually by iterative Sanger sequencing) is inefficient and expensive, and often not undertaken. Whole exome massive parallel sequencing has been used to identify new genes for SRTD (WDR34, WDR60 and IFT172); however, the clinical utility of whole exome sequencing (WES) has not been established. WES was performed in 11 individuals with SRTDs. Compound heterozygous or homozygous mutations were identified in six confirmed SRTD genes in 10 individuals (IFT172, DYNC2H1, TTC21B, WDR60, WDR34 and NEK1), giving overall sensitivity of 90.9%. WES data from 993 unaffected individuals sequenced using similar technology showed two individuals with rare (minor allele frequency <0.005) compound heterozygous variants of unknown significance in SRTD genes (specificity >99%). Costs for consumables, laboratory processing and bioinformatic analysis were gene discovery in SRTDs and can be considered a first-line methodology for mutation identification in affected individuals.
    Matched MeSH terms: Gene Frequency
  11. Norhalifah HK, Syafawati WU, Che Mat NF, Chambers GK, Edinur HA
    Hum Immunol, 2016 Apr;77(4):338-9.
    PMID: 26820937 DOI: 10.1016/j.humimm.2016.01.015
    Cytokines are involved in immune responses and the pathogenesis of various diseases. Allelic variations within the genes coding for various ∼30kDa cytokine protein/glycoproteins have been reported for many populations and have been the subjects of many ancestry and health analyses. In this study, we typed 22 single nucleotide polymorphisms (SNPs) in 13 cytokine genes of 165 Orang Asli individuals by using sequence specific primer-polymerase chain reaction (SSP-PCR) assay. The volunteers came from all across the Peninsular of Malaysia and belong to six Orang Asli subgroups; Batek, Kensiu, Lanoh, Che Wong, Semai and Orang Kanaq. Here we report our general findings and original genotype data and their associated analyses (Hardy-Weinberg proportions, estimation of allele and haplotype frequencies) can be found in the supplementary files and will be held at Allele Frequency Net Database (AFND).
    Matched MeSH terms: Gene Frequency
  12. Norhalifah HK, Zafarina Z, Sundararajulu P, Norazmi MN, Edinur HA
    Int. J. Immunogenet., 2015 Jun;42(3):200-3.
    PMID: 25809422 DOI: 10.1111/iji.12189
    In this survey, we have successfully genotyped 22 single nucleotide polymorphisms in the 13 cytokine genes for five Malay subethnic groups (Kelantan, Acheh, Mandailing, Minangkabau and Patani Malays) using polymerase chain reaction-sequence-specific primer cytokine genotyping kit (Invitrogen, Carlsbad, CA, USA). Most of the cytokine genes showed similar pattern of allelic spectra with wild-type alleles (e.g. ILIa-889/C, ILIB+3962/C and IL6 nt565/G) that represent more than 80% in the studied Malay subethnic groups. These newly observed cytokine alleles and subsequent analyses clearly indicate genetic contribution from Asia in the studied Malay subethnic groups with evidence of admixture from neighbouring populations in Patani Malays. The cytokine data sets for the five Malay subethnic groups deposited in this report can also be used as reference standard for searching suitable donor for allograft transplant and diseases association study. This is particularly relevance as our analyses showed differences between the Malay subethnic groups and other populations screened for cytokine genes.
    Matched MeSH terms: Gene Frequency
  13. Kofi AE, Hakim HM, Khan HO, Ismail SA, Ghansah A, David AA, et al.
    Int J Legal Med, 2020 Jul;134(4):1313-1315.
    PMID: 31154498 DOI: 10.1007/s00414-019-02099-w
    In this study, 268 samples for unrelated males belonging to the five major human subpopulation groups in Ghana (Akan, Ewe, Mole-Dagbon, Ga-Dangme and Guang) were genetically characterised for 23 Y chromosome short tandem repeat (STR) loci using the Powerplex® Y23 STR kit. A total of 263 complete haplotypes were recorded of which 258 were unique. The haplotype diversity, discriminating capacity and match probability for the pooled population data were 0.9998, 0.9627 and 0.0039, respectively. The pairwise genetic distance (RST) for the Ghanaian datasets and other reference populations deposited in the Y-STR Haplotype Reference Database (YHRD) were estimated and mapped using multidimensional scaling (MDS) plot. The Guang and Ewe were significantly different from the Akan, Mole-Dagbon and Ga-Dangme. However, the five Ghanaian datasets were all plotted close together with other African populations in the MDS data mapping.
    Matched MeSH terms: Gene Frequency*
  14. Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Nelson BR, et al.
    Int J Legal Med, 2020 Jul;134(4):1335-1337.
    PMID: 31897667 DOI: 10.1007/s00414-019-02237-4
    Genetic polymorphisms at 23 Y chromosome short tandem repeat (STRs) loci included in the Powerplex® Y23 PCR kit were successfully scored in 128 unrelated Kedayan individuals living in Sabah, East Malaysia. Complete haplotypes were recorded for all individuals and included 92 different types with 72 being unique to single male subjects. Three important forensic statistics were calculated from these data; haplotype diversity = 0.993, discriminating capacity = 0.719, and match probability = 0.015. The Kedayan appear to be most closely related to Malays and Filipinos in a multidimensional scaling plot and are separated from other mainland Asia populations including Thais and Hakka Han. These new data for Kedayan have been deposited in the YHRD database (accession number: YA004621). Our statistical analyses showed the reliability of Y-STR loci for geographically extended use in forensic casework and for studying human population history.
    Matched MeSH terms: Gene Frequency*
  15. Hajar CGN, Zefarina Z, Md Riffin NS, Mohammad THT, Hassan MN, Dafalla AM, et al.
    Ann Lab Med, 2020 11;40(6):493-499.
    PMID: 32539307 DOI: 10.3343/alm.2020.40.6.493
    Matched MeSH terms: Gene Frequency
  16. Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Abdullah MT, et al.
    Data Brief, 2020 Aug;31:105909.
    PMID: 32642519 DOI: 10.1016/j.dib.2020.105909
    This data article provides population frequencies for 21 autosomal and two sex determining short tandem repeat (STR) loci in unrelated Kedayan individuals. This article is related to the research paper entitled "Forensic parameters and ancestral fraction in the Kedayan population inferred using 21 autosomal STR loci" [1] where these same data were subjected to ancestry and forensic analyses. We have collected 200 blood samples consisting of 128 male and 72 female volunteer representatives from Kedayan people residing in various parts of Borneo. All 23 STR loci were simultaneously amplified using Globalfiler™ Express PCR and amplicons were separated using an ABI 3500xl Genetic Analyzer. The STR allele calls at each locus were called using GeneMapperⓇ ID-X Software v1.4, while several algorithms in Arlequin software version 3.5 were used to estimate Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) between pairs of STR loci.
    Matched MeSH terms: Gene Frequency
  17. Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Aziz MY, et al.
    Int J Legal Med, 2021 Jul;135(4):1433-1435.
    PMID: 33782746 DOI: 10.1007/s00414-021-02577-0
    DNA profiling of X-chromosomal short tandem repeats (X-STR) has exceptional value in criminal investigations, especially for complex kinship and incest cases. In this study, Investigator® Argus X-12 Quality Sensor (QS) kits were successfully used to characterize 12 X-STR loci in 199 unrelated healthy Kedayan individuals living in Sabah and Sarawak, Malaysia. The LG1 haplogroup (DXS8378 - DXS10135 - DXS10148) has the largest HD (0.9799) as compared with all other closely linked haplotype groups examined (LG2; DXS7132-DXS10074-DXS10079, LG3; DXS10103-DXS10101-HPRTB and LG4; DXS10134-DXS7423-DXS10146). Data from statistical analysis showed that high combined of PDM, PDF, MEC_Krüger, MEC_Kishida, MEC_Desmarais, and MEC_Desmarais_duo values (0.999999994405922, 0.99999999999999, 0.999990463834938, 0.999999975914808, 0.999999975985006, and 0.999996491927194, respectively) in the Kedayan. In a two-dimensional scaling (MDS) plot and dendrogram constructed using allele frequencies at the 12 X-STR loci, Kedayan appear to be most closely related to their other Austronesian populations including the Malays and Filipinos as compared with other reference population groups. Findings from the present study thus demonstrate high genetic variability across the 12 tested X-STR loci and can be used for population studies and forensic applications.
    Matched MeSH terms: Gene Frequency
  18. Hajar CGN, Zulkafli Z, Md Riffin NS, Tuan Mohammad TH, Safuan S, Nelson BR, et al.
    Transfus Apher Sci, 2020 Apr;59(2):102651.
    PMID: 31606336 DOI: 10.1016/j.transci.2019.09.004
    BACKGROUND: Human neutrophil antigens (HNAs) are implicated in several clinical disorders and their allelic variations have been reported for many populations. This new study was aimed to report the genotype and alleles frequencies of HNA-1, -3, -4 and -5 loci in Malays, Chinese and Indians in Peninsular Malaysia.

    METHODS: A total of 222 blood samples were collected from healthy, unrelated Malay, Chinese and Indian individuals. Their HNA-1, -3 and -4 and HNA-5 loci were genotyped using polymerase chain reaction-sequence specific primer (PCR-SSP) or PCR-restriction fragment length polymorphism (RFLP) assays.

    RESULTS: All HNA loci are polymorphic, except for HNA -4. Geneotypes HNA-1a/1b, -3a/3b and -4a/4a were observed most frequently at these three loci in all three ethnic groups. In contrast, HNA-5a/5b and -5a/5a were observed as the predominant genotypes in Malays vs. Chinese and Indians, respectively. The Malays, Chinese and Indians shared HNA -3a (0.505-0.527), HNA -4a (1.000) and -5a (0.676-0.854) as the most frequent alleles. However, HNA-1a was found to be the most common in Malays (0.506) and Chinese (0.504) and HNA-1b for Indians (0.525).

    CONCLUSION: Combined with HNA data that have been published for Malay subethnic and Orang Asli groups, this study provides the first fully comprehensive HNA dataset for populations to be found in Peninsular Malaysia. Overall, our findings provide further evidence of genetic complexity in the region. This now publicly available HNA dataset can be used as a reliable reference source for improving medical outcomes.

    Matched MeSH terms: Gene Frequency/immunology*
  19. Kofi AE, Hakim HM, Khan HO, Ismail SA, Ghansah A, Haslindawaty ARN, et al.
    Data Brief, 2020 Aug;31:105746.
    PMID: 32490095 DOI: 10.1016/j.dib.2020.105746
    Short tandem repeat (STR) loci are widely used as genetic marker for ancestral and forensic analyses. The latter application includes for paternity testing and DNA profiling of samples collected from scenes of crime and suspects. This survey provides the first dataset for 21 STR loci across the Akan population in Ghana by genotyping of 109 unrelated healthy individuals using Investigator 24plex kit. None of the STR loci screened deviated from Hardy-Weinberg equilibrium after applying Bonferroni correction. Overall, 224 unique alleles were observed with allele frequencies ranging from 0.005 to 0.518. The combined match probability, combined power of exclusion and combined power discrimination were 1 in 4.07 × 10-25, 0.999999999 and 1, respectively. Principal coordinate analysis carried out using 21 STR allele frequency data mapped the Akans with Nigerian subpopulation groups (Hausa, Igbo and Yoruba), but separated from Thais of Thailand, Chechen of Jordan and Tijuana of Mexico.
    Matched MeSH terms: Gene Frequency
  20. Kofi AE, Agyemang DA, Ghansah A, Awandare GA, Hakim HM, Khan HO, et al.
    Biochem Genet, 2023 Oct;61(5):1850-1866.
    PMID: 36869999 DOI: 10.1007/s10528-023-10347-3
    Autosomal short tandem repeat (STR) population data collected from a well characterized population are needed to correctly assigning the weight of DNA profiles in the courtroom and widely used for ancestral analyses. In this study, allele frequencies for the 15 autosomal short tandem repeat (STR) loci included in the AmpFlSTR® Identifiler® plus kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) were obtained by genotyping 332 unrelated individuals of Ghanaian origin. Statistical tests on STR genotype data showed no significant departure from Hardy-Weinberg equilibrium (HWE). The overall match probability, combined power of exclusion and combined power of discrimination for these loci were 1 in 3.85 × 1017, 0.99999893 and 0.99999998, respectively. Polymorphic information content (PIC) greater than 0.70 was observed for all loci except TH01 and D13S317. These statistical parameters confirm that this combination of loci is valuable for forensic identification and parentage analysis. Our results were also compared with those for 20 other human populations analyzed for the same set of markers. We observed that the Ghanaian population grouped with other African populations in two-dimensional principal coordinate (PCO) and a neighbor-joining (N-J) data mapping and placed closest to Nigerians. This observation reflects cultural similarities and geographical factors, coupled with the long history of migration and trading activities between Ghana and Nigeria. Our report provides what we believe to be the first published autosomal STR data for the general Ghanaian population using 15 loci genotyped using the AmpFlSTR® Identifiler® plus kit methodology. Our data show that the loci tested have sufficient power to be used reliably for DNA profiling in forensic casework and help to elucidate the genetic history of people living in the country.
    Matched MeSH terms: Gene Frequency
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