Displaying publications 61 - 80 of 1097 in total

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  1. Wong FL, Wang MK, Boo NY, Hamidah NH, Ainoon BO
    J Clin Lab Anal, 2007;21(3):167-72.
    PMID: 17506482
    The UGT1A1 Taqman MGB probe single nucleotide polymorphism (SNP) genotyping assay was developed to detect nucleotide 211 of the UDP-glucoronocyltransferase 1A1 (UGT1A1) gene. Defects in this enzyme interfere with process of conjugation of bilirubin and cause unconjugated hyperbilirubinemia. Variation at nucleotide 211 in the coding region of the UGT1A1 gene has been shown to be prevalent in Japanese and Chinese. Using an ABI sequence detection system (SDS) 7000, an allele-specific real-time PCR-based genotyping method was established to detect nucleotide G211A. Cord blood from 125 infants without hyperbilirubinemia (controls) were compared with cord blood from 74 infants (cases) with severe hyperbilirubinemia (total serum bilirubin > 300 micromol/L). Homozygous variation of the UGT1A1 gene at nucleotide 211(A/A) is significantly more common in cases (14.9%) than in controls (0.8%) (P<0.001). Direct sequencing from 20 randomly selected samples showed eight samples with homozygous wild type, seven with homozygous variant, and five samples were heterozygous. The result from this assay was in complete concordance with the DNA sequencing result and clearly discriminate wild-type (G/G), homozygous variant (A/A), and heterozygous (G/A). This assay is rapid and robust for screening of SNP G211A to determine if this polymorphism plays a role in causing severe neonatal jaundice in the local context.
    Matched MeSH terms: Genotype
  2. Azlin I, Wong FL, Ezham M, Hafiza A, Ainoon O
    Malays J Pathol, 2011 Dec;33(2):95-100.
    PMID: 22299209 MyJurnal
    A number of genetic risk factors have been implicated in the development of neonatal severe hyperbilirubinaemia. This includes mutations in the uridine glucoronosyl transferase 1A1 (UGT1A1) gene which is responsible for unconjugated hyperbilirubinemia in Gilbert's Syndrome. We studied the prevalence of UGT1A1 gene mutations in a group of Malay neonates to determine whether they are risk factors to severe neonatal jaundice. One hundred and twenty-five Malay neonates with severe hyperbilirubinemia were studied. Ninety-eight infants without severe hyperbilirubinaemia were randomly selected from healthy Malay term infants (controls). DNA from EDTA cord blood samples were examined for UGT1A1 mutations nt211G > A and nt247T > C using established Taqman SNP genotyping assays and the UGT1A1*28 variant was detected by the Agilent 2100 bioanalyzer. All samples were also screened for common Malay G6PD variants using established techniques. The frequency of UGT1A1 211G > A mutation is significantly higher in the severely hyperbilirubinemic group (13%) than the control group (4%; p = 0.015) and all the positive cases were heterozygous for the mutation. There was no significant difference in the frequency of UGT1A1*28 mutation between the severely hyperbilirubinemic (3.5%) and the control group (0.01%; p = 0.09). None of the neonates in both groups carried the nt247 T > C mutation. The prevalence of G6PD mutation was significantly higher in the severely jaundiced group than control (9% vs 4%; p = 0.04). In conclusion, nt 211 G > A alleles constitute at least 12% of UGT1A1 mutations underlying unconjugated hyperbilirubinemia and appears to be a significant independent risk factor associated with severe neonatal hyperbilirubinemia in the Malay newborns.
    Matched MeSH terms: Genotype
  3. Alina MF, Azma RZ, Norunaluwar J, Azlin I, Darnina AJ, Cheah FC, et al.
    J Hum Genet, 2020 Mar;65(3):263-270.
    PMID: 31863082 DOI: 10.1038/s10038-019-0700-7
    G6PD deficiency is the commonest enzyme deficiency found in humans. Current diagnostic methods lack sensitivity to detect all cases of G6PD deficiency. We evaluated the reverse dot blot flow-through hybridisation assay designed to detect simultaneously multiple known G6PD mutations in a group of Malaysian neonates. Archival DNA samples from 141 G6PD-deficient neonates were subjected to reverse dot blot flow-through hybridisation assay using the GenoArray Diagnostic Kit (Hybribio Limited, Hong Kong) and DNA sequencing. The method involved PCR amplification of 5 G6PD exons using biotinylated primers, hybridisation of amplicons to a membrane containing oligoprobes designed for G6PD mutations known to occur in the Malaysian population and colour detection by enzyme immunoassay. The assay detected 13 of the 14 G6PD mutations and genotyped 133 (94.3%) out of 141 (102 males, 39 females) cases. Among the 39 female G6PD-deficient neonates, there were 7 homozygous and 6 compound heterozygous cases. The commonest alleles were G6PD Viangchan 871G > A (21%) and G6PD Mahidol 487G > A(20%) followed by G6PD Mediterranean 563C > T, (14%), G6PD Vanua Lava 383T > C (12%), G6PD Canton 1376G > T (10%), G6PD Orissa 131C > G (6.3%) G6PD Coimbra 592C > T (5.6%) plus 6 other mutations. DNA sequencing of remaining cases revealed 6 cases of intron 11 nt 93C > T not previously reported in Malaysia and two novel mutations, one case each of nt 1361G > T and nt 1030G > A. We found the reverse dot blot assay easy to perform, rapid, accurate and reproducible, potentially becoming an improved diagnostic test for G6PD deficiency.
    Matched MeSH terms: Genotype
  4. Hatta FH, Aklillu E
    OMICS, 2015 Dec;19(12):777-81.
    PMID: 26669712 DOI: 10.1089/omi.2015.0159
    CYP2C9 enzyme contributes to the metabolism of several pharmaceuticals and xenobiotics and yet displays large person-to-person and interethnic variation. Understanding the mechanisms of CYP2C9 variation is thus of immense importance for personalized medicine and rational therapeutics. A genetic variant of P450 (cytochrome) oxidoreductase (POR), a CYP450 redox partner, is reported to influence CYP2C9 metabolic activity in vitro. We investigated the impact of a common variant, POR*28, on CYP2C9 metabolic activity in humans. 148 healthy Swedish and 146 healthy Korean volunteers were genotyped for known CYP2C9 defective variant alleles (CYP2C9*2, *3). The CYP2C9 phenotype was determined using a single oral dose of 50 mg losartan. Excluding oral contraceptive (OC) users and carriers of 2C9*2 and *3 alleles, 117 Korean and 65 Swedish were genotyped for POR*5, *13 and *28 using Taqman assays. The urinary losartan to its metabolite E-3174 metabolic ratio (MR) was used as an index of CYP2C9 metabolic activity. The allele frequency of the POR*28 variant allele in Swedes and Koreans was 29% and 44%, respectively. POR*5 and *13 were absent in both study populations. Considering the CYP2C9*1/*1 genotypes only, the CYP2C9 metabolic activity was 1.40-fold higher in carriers of POR*28 allele than non-carriers among Swedes (p = 0.02). By contrast, no influence of the POR*28 on CYP2C9 activity was found in Koreans (p = 0.68). The multivariate analysis showed that ethnicity, POR genotype, and smoking were strong predictors of CYP2C9 MR (p < 0.05). This is the first report to implicate the importance of POR*28 genetic variation for CYP2C9 metabolic activity in humans. These findings contribute to current efforts for global personalized medicine and using medicines by taking into account pharmacogenetic and phenotypic variations.
    Matched MeSH terms: Genotype
  5. Ahmad F, Hanafi MM, Hakim MA, Rafii MY, Arolu IW, Akmar Abdullah SN
    PLoS One, 2015;10(9):e0138246.
    PMID: 26393807 DOI: 10.1371/journal.pone.0138246
    Coloured rice genotypes have greater nutritious value and consumer demand for these varieties is now greater than ever. The documentation of these genotypes is important for the improvement of the rice plant. In this study, 42 coloured rice genotypes were selected for determination of their genetic divergence using 25 simple sequence repeat (SSR) primers and 15 agro-morphological traits. Twenty-one out of the 25 SSR primers showed distinct, reproducible polymorphism. A dendrogram constructed using the SSR primers clustered the 42 coloured rice genotypes into 7 groups. Further, principle component analysis showed 75.28% of total variations were explained by the first-three components. All agro-morphological traits showed significant difference at the (p≤0.05) and (p≤0.01) levels. From the dendrogram constructed using the agro-morphological traits, all the genotypes were clustered into four distinct groups. Pearson's correlation coefficient showed that among the 15 agro-morphological traits, the yield contributing factor had positive correlation with the number of tillers, number of panicles, and panicle length. The heritability of the 15 traits ranged from 17.68 to 99.69%. Yield per plant and harvest index showed the highest value for both heritability and genetic advance. The information on the molecular and agro-morphological traits can be used in rice breeding programmes to improve nutritional value and produce higher yields.
    Matched MeSH terms: Genotype*
  6. Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M
    Sci Rep, 2021 04 07;11(1):7597.
    PMID: 33828137 DOI: 10.1038/s41598-021-87039-8
    As a crop for the new millennium Bambara groundnut (Vigna subterranea [L.] Verdc.) considered as leading legumes in the tropical regions due to its versatile advantages. The main intent of this study was to find out the high yielding potential genotypes and considering these genotypes to develop pure lines for commercial cultivation in Malaysia. Considering the 14 qualitative and 27 quantitative traits of fifteen landraces the variation and genetic parameters namely, variability, heritability, genetic advance, characters association, and cluster matrix were determined. ANOVA revealed significant variation for all the agronomic traits (except plant height). Among the accessions, highly significant differences (P ≤ 0.01) were found for almost all the traits excluding fifty percent flowering date, seed length, seed width. The 16 traits out of the 27 quantitative traits had a coefficient of variation (CV) ≥ 20%. A positive and intermediate to perfect highly significant association (r = 0.23 to 1.00; P 
    Matched MeSH terms: Genotype
  7. Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M
    Sci Rep, 2022 09 19;12(1):15658.
    PMID: 36123374 DOI: 10.1038/s41598-022-19003-z
    This investigation was carried out to explore G × E interaction for yield and its associated attributes in 30 Bambara groundnut genotypes across four environments in tropical Malaysia. Such evaluations are essential when the breeding program's objective is to choose genotypes with broad adaption and yield potential. Studies of trait relationships, variance components, mean performance, and genetic linkage are needed by breeders when designing, evaluating, and developing selection criteria for improving desired characteristics in breeding programs. The evaluation of breeding lines of Bambara groundnut for high yield across a wide range of environments is important for long-term production and food security. Each site's experiment employed a randomized complete block design with three replicates. Data on vegetative and yield component attributes were recorded. The analysis of variance revealed that there were highly significant (p ≤ 0.01) differences among the 30 genotypes for all variables evaluated. A highly significant and positive correlation was identified between yield per hectare and dry seed weight (0.940), hundred seed weight (0.844), fresh pod weight (0.832), and total pod weight (0.750); the estimated correlation between dry weight of pods and seed yield was 1.0. The environment was more important than genotype and G × E in determining yield and yield components.A total of 49% variation is covered by PC1 (33.9%) and PC2 (15.1%) and the genotypes formed five distinct clusters based on Ward hierarchical clustering (WHC) method. The genotypes S5G1, S5G3, S5G5, S5G6, S5G8, S5G7, S5G2, S5G4, S5G10, S5G13, S5G11, and S5G14 of clusters I, II, and III were closest to the ideal genotype with superior yield across the environments. The PCA variable loadings revealed that an index based on dry pod weight, hundred seed weight, number of total pods and fresh pod weight could be used as a selection criteria to improve seed yield of Bambara groundnut.
    Matched MeSH terms: Genotype
  8. Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M
    Sci Rep, 2021 Nov 23;11(1):22791.
    PMID: 34815427 DOI: 10.1038/s41598-021-01411-2
    The stability and high yielding of Vigna subterranea L. Verdc. genotype is an important factor for long-term development and food security. The effects of G × E interaction on yield stability in 30 Bambara groundnut genotypes in four different Malaysian environments were investigated in this research. The experiment used a randomized complete block design with three replications in each environment. Over multiple harvests, yield component traits such as the total number of pods per plant, fresh pods weight (g), hundred seeds weight (g), and yield per hectare were evaluated in the main and off-season in 2020 and 2021. Stability tests for multivariate stability parameters were performed based on analyses of variance. For all the traits, the pooled analysis of variance revealed highly significant (p 
    Matched MeSH terms: Genotype
  9. Al-Kubaisy WA, Obaid KJ, Noor NA, Ibrahim NS, Al-Azawi AA
    Asian Pac J Cancer Prev, 2014;15(18):7725-30.
    PMID: 25292053
    Hepatocellular carcinoma (HCC) is the third most common cause for cancer death in the world, now being especially linked to chronic hepatitis C virus (HCV) infection. This case-control study consisting of 65 HCC patients and 82 patients with other malignant tumours as controls was conducted to determine the association of HCV markers with HCC. Serum of each participant was obtained for detection of HCV Ab and RNA by DNA enzyme immunoassay (DEIA). Twenty six per cent (26.0%) of HCC patients had positive anti-HCV which was significantly greater than the control group (p=0.001). HCC patients significantly have a risk of exposure to HCV infection almost 3 times than the control group (OR=2.87, 95% C.I=1.1-7). Anti-HCV seropositive rate was significantly (p=0.03) higher among old age HCC patients and increases with age. Males with HCC significantly showed to have more than 9 times risk of exposure to HCV infection (OR=9.375, 95 % CI=1.299-67.647) than females. HCV-RNA seropositive rate was (70.8%) significantly higher among HCC patients compared to (22.2%) the control group (p=0.019). The most prevalent genotype (as a single or mixed pattern of infection) was HCV- 1b. This study detected a significantly higher HCV seropositive rate of antibodies and RNA in HCC patients.
    Matched MeSH terms: Genotype
  10. Atroosh WM, Lau YL, Snounou G, Azzani M, Al-Mekhlafi HM
    Malar J, 2022 Jan 04;21(1):2.
    PMID: 34983529 DOI: 10.1186/s12936-021-04014-4
    BACKGROUND: Genotyping of the three Plasmodium falciparum polymorphic genes, msp1, msp2 and glurp, has been adopted as a standard strategy to distinguish recrudescence from new infection in drug efficacy clinical trials. However, the suitability of a particular gene is compromised in areas where its allelic variants distribution is significantly skewed, a phenomenon that might occur in isolated parasite populations or in areas of very low transmission. Moreover, observation of amplification bias has diminished the value of glurp as a marker.

    METHODS: The suitability of the polymorphic P. falciparum histidine-rich protein 2 (pfhrp2) gene was assessed to serve as an alternative marker using a PCR-sequencing or a PCR-RFLP protocol for genotyping of samples in drug efficacy clinical trials. The value of pfhrp2 was validated by side-by-side analyses of 5 admission-recrudescence sample pairs from Yemeni malaria patients.

    RESULTS: The outcome of the single pfhrp2 gene discrimination analysis has been found consistent with msp1, msp2 and glurp pool genotyping analysis for the differentiation of recrudescence from new infection.

    CONCLUSION: The findings suggest that under the appropriate circumstances, pfhrp2 can serve as an additional molecular marker for monitoring anti-malarials efficacy. However, its use is restricted to endemic areas where only a minority of P. falciparum parasites lack the pfhrp2 gene.

    Matched MeSH terms: Genotype
  11. Al-Khateeb, A, Al-Talib, H
    JUMMEC, 2016;19(2):1-11.
    MyJurnal
    Background:
    Familial hypercholesterolaemia (FH) is one of the most frequent inherited metabolic disorders that can lead
    to a risk of premature cardiovascular disease. Publications on FH are mainly from western patients as there is
    little research on Asians, including Malaysians. The aim of this review is to provide an up-to- date information
    on Malaysian studies on FH genotyping and its relation to the phenotype of the affected patients.
    Method:
    A search was conducted for data from online databases on FH in Malaysia.
    Results:
    The mutation spectrum for FH among Malaysian patients was extremely broad. The gene variants were located
    mainly in the low-density lipoprotein receptor (LDLR) and apolipoprotein B-100 (APOB-100) genes rather than
    in the proprotein convertase subtilisin kexin type 9 (PCSK9) gene. The exon 9 and 14 were the hotspots in the
    LDLR gene. The most frequent mutation was p.Cys255Ser, at 12.5%, followed by p.Arg471Gly, at 11%, and the
    most common single nucleotide polymorphism (SNP) was c.1060+7 T>C at 11.7%. The LDLR gene variants were
    more common compared to the APOB-100 gene variants, while variants in the PCSK9 gene were very few.
    Phenotype-genotype associations were identified. Subjects with LDLR and APOB-100 genes mutations had a
    higher frequency of cardiovascular disease, a family history of hyperlipidaemia and tendon xanthoma and a
    higher low-density lipoprotein cholesterol (LDL-C) level than non-carriers.
    Conclusion:
    Research on Malaysian familial hypercholesterolaemic patients by individual groups is encouraging. However,
    more extensive molecular studies on FH on a national scale, with a screening of the disease-causing mutations
    together with a comprehensive genotype-phenotype association study, can lead to a better outcome for
    patients with the disease.
    Matched MeSH terms: Genotype
  12. 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: Genotype
  13. Yazici Z, Gumusova S, Tamer C, Muftuoglu B, Ozan E, Arslan S, et al.
    Trop Biomed, 2019 Sep 01;36(3):803-809.
    PMID: 33597501
    Bovine parainfluenza 3 virus (BPI3V)is one of the most important respiratory pathogens and a leading cause of serious respiratory illnesses in cattle, both independent of and in connection with other pathogens involved in the bovine respiratory disease complex (BRDC). In this study, we aimed to identify the historical circulation of genotype C bovine BPI3V (BPI3Vc) in Turkey using the archival serum samples of domestic ruminants that had been collected from six provinces of northern Anatolia in Turkey between 2009-2010. A total of 896 sera from cattle (n=442), sheep (n=330), and goats (n=124) were randomly selected and screened with a virus neutralization test in order to detect antibodies for BPI3Vc. The overall seropositivity rate was 21.09%, with seropositivity rates for cattle, sheep, and goats of 21.04%, 20.00%, and 24.19%, respectively. Neutralizing antibody titers for selected samples ranged between 1/4 to 1/512. This study represents the first serological study conducted using the first BPI3V isolate of Turkey.
    Matched MeSH terms: Genotype
  14. Rahman M, Wong K, Ishak I, Rashid Z, Alfizah H
    Sains Malaysiana, 2014;43:739-744.
    Human respiratory syncytial virus (RSV) is an important cause of acute respiratory tract infection in infants and young children. Phylogenetic analysis for RSV in Malaysia has not been reported before. We investigated the genetic features of RSV in respiratory specimens from March to August 2011 with molecular methods. From a total of 130 throat swab and nasopharyngeal aspirate specimens, 54 (41.5%) were positive with RSV, identified by in-house real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay. Thirty-four out of 54 (63.0%) RSV positive patients were children below two years old and two (1.4%) were adults. Phylogenetic analysis showed 39 isolates were genotype GA5, 13 genotypes GA2, one genotype GA1 and one genotype GA7. The findings indicated four genotypes of RSV circulating in the country and the predominant genotype is GA5.
    Matched MeSH terms: Genotype
  15. Vasudevan R, Ismail P, Stanslas J, Shamsudin N, Ali AB
    Int J Biol Sci, 2008;4(6):362-7.
    PMID: 18953403
    An insertion/deletion (I/D) polymorphism of Alpha2B-Adrenoceptor (ADRA2B) gene located on chromosome 2 has been studied extensively in related to cardiovascular diseases. The main aim of the present study was to examine the potential association of D allele frequency of I/D polymorphism of ADRA2B gene in Malaysian essential hypertensive subjects with or without type 2 diabetes mellitus (T2DM). This study includes 70 hypertensive subjects without T2DM, 65 hypertensive subjects with T2DM and 75 healthy volunteers as control subjects. Genotyping of I/D polymorphism was performed by conventional PCR method. There was significant difference found in age, body mass index, systolic/diastolic blood pressure and high density lipoprotein cholesterol level between the case and control subjects. DD genotypic frequency of I/D polymorphism was significantly higher in hypertensive subjects (42.84% vs. 29.33%; P-=0.029) and in hypertensive with T2DM subjects (46.15% vs. 29.33%; P=0.046) than control group. D allele frequency was higher in hypertensive group (67.41%) than control subjects (52.67%). However, no significant difference was found between the three genotypes of I/D polymorphism of ADRA2B gene and the clinical characteristics of the subjects. The result obtained in this study show D allele of ADRA2B gene was associated with essential hypertension with or without T2DM in Malaysian subjects.
    Matched MeSH terms: Genotype
  16. Alshahrani MY, Alanazi AD, Alouffi AS, Abdullah HHAM, Allam AM, Mahmoud MS, et al.
    Trop Biomed, 2020 Sep 01;37(3):587-598.
    PMID: 33612774 DOI: 10.47665/tb.37.3.587
    Knowledge of molecular identification of tick-borne pathogens in camels in Saudi Arabia is very limited; few molecular epidemiological studies have been under taken. This study was to detect Anaplasma spp. and Piroplasma spp. in camels from Asir Province, Saudi Arabia. A total of 150 blood samples were collected from camels in Asir Province and investigated by polymerase chain reaction (PCR) that targeted 18S rRNA and 23S rRNA to detect the DNA of Piroplasma spp. and Anaplasma spp., respectively. The positive samples for 23S rRNA were assayed again by PCR targeting the 16S rRNA. All the blood samples were free from Piroplasma spp. infection. Three camels (2%) were found to be positive for Anaplasma infection through use of PCR that targeted the 23S rRNA gene. There were no significant differences between ages or sexes in the camels that tested positive for Anaplasma. All positive Anaplasma infections were recorded in camels that were infested by ticks. Two Anaplasma sequences for the16S rRNA gene were deposited in GenBank with accession numbers MN882724 and MN882725. They recorded 99.16% and 99.34% similarities (respectively) with KF843825.1 (Candidatus Anaplasma camelii reported in Unizah, Saudi Arabia). Phylogenetic analyses revealed that the two sequences recorded in this study were close to each other; both were located in one cluster with Candidatus Anaplasma camelii isolates that were recorded before in the adjacent areas of Unizah in Saudi Arabia and Iran. In conclusion: two new Anaplasma genotypes close to Candidatus Anaplasma camelii were found in camels in Asir Province, Saudi Arabia for the first time. The camels in this province were found to be free of Piroplasma infection.
    Matched MeSH terms: Genotype
  17. Maddirevula S, AlZahrani F, Anazi S, Almureikhi M, Ben-Omran T, Abdel-Salam GMH, et al.
    Genet Med, 2018 01;20(1):64-68.
    PMID: 28640246 DOI: 10.1038/gim.2017.78
    PurposeGenome-wide association studies (GWAS) have been instrumental to our understanding of the genetic risk determinants of complex traits. A common challenge in GWAS is the interpretation of signals, which are usually attributed to the genes closest to the polymorphic markers that display the strongest statistical association. Naturally occurring complete loss of function (knockout) of these genes in humans can inform GWAS interpretation by unmasking their deficiency state in a clinical context.MethodsWe exploited the unique population structure of Saudi Arabia to identify novel knockout events in genes previously highlighted in GWAS using combined autozygome/exome analysis.ResultsWe report five families with homozygous truncating mutations in genes that had only been linked to human disease through GWAS. The phenotypes observed in the natural knockouts for these genes (TRAF3IP2, FRMD3, RSRC1, BTBD9, and PXDNL) range from consistent with, to unrelated to, the previously reported GWAS phenotype.ConclusionWe expand the role of human knockouts in the medical annotation of the human genome, and show their potential value in informing the interpretation of GWAS of complex traits.
    Matched MeSH terms: Genotype
  18. Candotti D, Lin CK, Belkhiri D, Sakuldamrongpanich T, Biswas S, Lin S, et al.
    Gut, 2012 Dec;61(12):1744-53.
    PMID: 22267593 DOI: 10.1136/gutjnl-2011-301281
    To investigate the molecular basis of occult hepatitis B virus (HBV) infection (OBI) in Asian blood donors.
    Matched MeSH terms: Genotype
  19. Meldal BH, Bon AH, Prati D, Ayob Y, Allain JP
    J Viral Hepat, 2011 Feb;18(2):91-101.
    PMID: 20196797 DOI: 10.1111/j.1365-2893.2010.01282.x
    Malaysia is a medium endemic country for hepatitis B virus (HBV) infection but little is known about HBV strains circulating in Malaysian blood donors. Viral load, HBsAg concentrations and nested PCR products from 84 HBV surface antigen (HBsAg) positive samples were analysed in detail. Median viral load was 3050 IU/mL and median HBsAg 1150 IU/mL. Fifty-six full genome, 20 pre-S/S, 1 S gene and six basic core promoter/precore-only sequences were obtained. Genotypes B and C were present at a ratio of 2:1, and two genotype D samples were obtained, both from donors of Indian background. Phylogenetically, genotype B was more diverse with subgenotypes B2-5, B7 and B8 present, while most genotype C strains were from subgenotype C1. Genotypes B and C were equally frequent in ethnic Malays, but 80% of strains from Chinese were genotype B. HBsAg concentrations were higher in genotype C than in genotype B, in Chinese than Malays and in donors under the age of 30. HBV vaccine escape substitutions (P120S/T, I126N and G145G) were present in six strains. In the large surface protein, immuno-inactive regions were more mutated than CD8 epitopes and the major hydrophilic region. Strains of genotype B or from ethnic Malays had higher genetic diversity than strains of genotype C or from Chinese donors. Hence HBV strains circulating in Malaysia are phylogenetically diverse reflecting the ethnic mix of its population. Ethnic Malays carry lower HBsAg levels and higher genetic diversity of the surface antigen, possibly resulting in more effective immune control of the infection.
    Matched MeSH terms: Genotype
  20. Nair S, Schreiber E, Thong KL, Pang T, Altwegg M
    J Microbiol Methods, 2000 Jun;41(1):35-43.
    PMID: 10856775
    Amplified fragment length polymorphism (AFLP) is a recently developed, PCR-based high resolution fingerprinting method that is able to generate complex banding patterns which can be used to delineate intraspecific genetic relationships among bacteria. In the present study, AFLP was evaluated for its usefulness in the molecular typing of Salmonella typhi in comparison to ribotyping and pulsed-field gel electrophoresis (PFGE). Six S. typhi isolates from diverse geographic areas (Malaysia, Indonesia, India, Chile, Papua New Guinea and Switzerland) gave unique, heterogeneous profiles when typed by AFLP, a result which was consistent with ribotyping and PFGE analysis. In a further study of selected S. typhi isolates from Papua New Guinea which caused fatal and non-fatal disease previously shown to be clonally related by PFGE, AFLP discriminated between these isolates but did not indicate a linkage between genotype with virulence. We conclude that AFLP (discriminatory index=0.88) has a higher discriminatory power for strain differentiation among S. typhi than ribotyping (DI=0.63) and PFGE (DI=0.74).
    Matched MeSH terms: Genotype
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