Displaying publications 121 - 140 of 1094 in total

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  1. Fulltext Prevalence of the CYP2C19*2 (681 G>A), *3 (636 G>A) and *17 (‑806 C>T) alleles among an Iranian population of different ethnicities
    Dehbozorgi M, Kamalidehghan B, Hosseini I, Dehghanfard Z, Sangtarash MH, Firoozi M, et al.
    Mol Med Rep, 2018 03;17(3):4195-4202.
    PMID: 29328413 DOI: 10.3892/mmr.2018.8377
    Polymorphisms in the cytochrome P (CYP) 450 family may cause adverse drug responses in individuals. Cytochrome P450 2C19 (CYP2C19) is a member of the CYP family, where the presence of the 681 G>A, 636 G>A and 806 C>T polymorphisms result in the CYP2C19*2, CYP2C19*3 and CYP2C19*17 alleles, respectively. In the current study, the frequency of the CYP2C19*2, CYP2C19*3 and CYP2C19*17 alleles in an Iranian population cohort of different ethnicities were examined and then compared with previously published frequencies within other populations. Allelic and genotypic frequencies of the CYP2C19 alleles (*2, *3 and *17) were detected using polymerase chain reaction (PCR)‑restriction fragment length polymorphism analysis, PCR‑single‑strand conformation polymorphism analysis and DNA sequencing from blood samples of 1,229 unrelated healthy individuals from different ethnicities within the Iranian population. The CYP2C19 allele frequencies among the Iranian population were 21.4, 1.7, and 27.1% for the CYP2C19*2, CYP2C19*3 and CYP2C19*17 alleles, respectively. The frequency of the homozygous A/A variant of the CYP2C19*2 allele was significantly high and low in the Lur (P<0.001) and Caspian (P<0.001) ethnicities, respectively. However, the frequency of the homozygous A/A variant of the CYP2C19*3 allele was not detected in the Iranian cohort in the current study. The frequency of the heterozygous G/A variant of the CYP2C19*3 allele had the significantly highest and lowest frequency in the Fars (P<0.001) and Lur (P<0.001) groups, respectively. The allele frequency of the homozygous T/T variant of the CYP2C19*17 allele was significantly high in the Caspian (P<0.001) and low in the Kurd (P<0.05) groups. The frequency of the CYP2C19 alleles involved in drug metabolism, may improve the clinical understanding of the ethnic differences in drug responses, resulting in the advancement of the personalized medicine among the different ethnicities within the Iranian population.
    Matched MeSH terms: Genotype*
  2. Fulltext Detection of east/central/south African genotype of chikungunya virus in Myanmar, 2010
    Tun MM, Thant KZ, Inoue S, Nabeshima T, Aoki K, Kyaw AK, et al.
    Emerg Infect Dis, 2014 Aug;20(8):1378-81.
    PMID: 25062511 DOI: 10.3201/eid2008.131431
    In 2010, chikungunya virus of the East Central South African genotype was isolated from 4 children in Myanmyar who had dengue-like symptoms. Phylogenetic analysis of the E1 gene revealed that the isolates were closely related to isolates from China, Thailand, and Malaysia that harbor the A226V mutation in this gene.
    Matched MeSH terms: Genotype*
  3. Fulltext Distribution of alleles, genotypes and haplotypes of the CYP2B6 (rs3745274; rs2279343) and CYP3A4 (rs2740574) genes in the Malian population: Implication for pharmacogenetics
    Kassogue Y, Diakite B, Kassogue O, Konate I, Tamboura K, Diarra Z, et al.
    Medicine (Baltimore), 2021 Jul 23;100(29):e26614.
    PMID: 34398016 DOI: 10.1097/MD.0000000000026614
    Cytochrome P450 enzymes play a central role in the phase I biotransformation process of a wide range of compounds, including xenobiotics, drugs, hormones and vitamins. It is noteworthy that these enzymes are highly polymorphic and, depending on the genetic makeup, an individual may have impaired enzymatic activity. Therefore, the identification of genetic variants in these genes could facilitate the implementation of pharmacogenetic studies and genetic predisposition to multifactorial diseases. We have established the frequencies of CYP2B6 (rs3745274; rs2279343) and CYP3A4 (rs2740574) alleles and genotypes in 209 healthy Malian subjects using TaqMan drug metabolism genotyping assays for allelic discrimination. Allele frequencies were 37% for CYP2B6 rs3745274; 38% for CYP2B6 rs2279343; and 75% for CYP3A4 rs2740574 respectively. Overall, the frequencies observed in Mali are statistically comparable to those reported across Africa except North Africa. The major haplotypes in CYP2B6 rs3745274 and CYP2B6 rs2279343 were represented by GA (60.24%) followed by TG (35.36%). We noted a strong linkage disequilibrium between CYP2B6 rs3745274 and CYP2B6 rs2279343 with D' = 0.91 and r2 = 0.9. The frequencies of the genotypic combinations were 43.5% (GT/AG), 37.3% (GG/AA) and 11.5% (TT/GG) in the combination of CYP2B6-rs3745274 and CYP2B6-rs2279343; 26.8% (GT/CC), 25.4%, (GT/CT), 17.2% and GG/CT in the combination CYP2B6-rs3745274-CYP3A4-rs2740574; 26.8% (AG/CC), 23.9% (AA/CC), 19.1% (AG/CT), and 11% (AA/CT) in the combination CYP2B6-rs2279343-CYP3A4-rs2740574, respectively. The most common triple genotype was GT/AG/CC with 24.9%, followed by GG/AA/CC with 23.9%, GT/AG/CT with 16.7%, and GG/AA/CT with 10%. Our results provide new insights into the distribution of these pharmacogenetically relevant genes in the Malian population. Moreover, these data will be useful for studies of individual genetic variability to drugs and genetic predisposition to diseases.
    Matched MeSH terms: Genotype*
  4. Fulltext Distinct genetic clades of Malaysian Copera damselflies and the phylogeny of platycnemine subfamilies
    Lim PE, Tan J, Eamsobhana P, Yong HS
    Sci Rep, 2013 Oct 17;3:2977.
    PMID: 24131999 DOI: 10.1038/srep02977
    The phylogenetic relationships of some taxa in the Platycnemidinae at the species and generic levels have been investigated. Phylogenetic trees were generated from both individual mitochondrial encoded COI, COII, 16S rDNA and nuclear encoded 28S rDNA and also combined sequences; these data indicate that the component taxa of the genus Copera belong to two distinct genetic clades - the marginipes group and the annulata group. There was no distinct genetic difference between the red-legged and yellow-legged morphs of C. vittata. Molecular data showed that the annulata group is considered a member of the genus Platycnemis, as originally proposed. The genus Coeliccia, a member of the subfamily Calicnemiinae (Platycnemididae), is not grouped with the Platycnemidinae. The Disparoneurinae of the 'Protoneuridae' showed a closer relationship to the Platycnemidinae than the Calicnemiinae. The dataset supports the placement of the Disparoneurinae as a subfamily of the Platycnemididae. This resolves the monophyly of Platycnemididae.
    Matched MeSH terms: Genotype*
  5. Fulltext KASP: a genotyping method to rapid identification of resistance in Plasmodium falciparum
    Alvarez-Fernandez A, Bernal MJ, Fradejas I, Martin Ramírez A, Md Yusuf NA, Lanza M, et al.
    Malar J, 2021 Jan 06;20(1):16.
    PMID: 33407529 DOI: 10.1186/s12936-020-03544-7
    BACKGROUND: The emergence and spread of anti-malarial resistance continues to hinder malaria control. Plasmodium falciparum, the species that causes most human malaria cases and most deaths, has shown resistance to almost all known anti-malarials. This anti-malarial resistance arises from the development and subsequent expansion of Single Nucleotide Polymorphisms (SNPs) in specific parasite genes. A quick and cheap tool for the detection of drug resistance can be crucial and very useful for use in hospitals and in malaria control programmes. It has been demonstrated in different contexts that genotyping by Kompetitive Allele Specific PCR (KASP), is a simple, fast and economical method that allows a high-precision biallelic characterization of SNPs, hence its possible utility in the study of resistance in P. falciparum.

    METHODS: Three SNPs involved in most cases of resistance to the most widespread anti-malarial treatments have been analysed by PCR plus sequencing and by KASP (C580Y of the Kelch13 gene, Y86N of the Pfmdr1 gene and M133I of the Pfcytb gene). A total of 113 P. falciparum positive samples and 24 negative samples, previously analysed by PCR and sequencing, were selected for this assay. Likewise, the samples were genotyped for the MSP-1 and MSP-2 genes, and the Multiplicity of Infection (MOI) and parasitaemia were measured to observe their possible influence on the KASP method.

    RESULTS: The KASP results showed the same expected mutations and wild type genotypes as the reference method, with few exceptions that correlated with very low parasitaemia samples. In addition, two cases of heterozygotes that had not been detected by sequencing were found. No correlation was found between the MOI or parasitaemia and the KASP values of the sample. The reproducibility of the technique shows no oscillations between repetitions in any of the three SNPs analysed.

    CONCLUSIONS: The KASP assays developed in this study were efficient and versatile for the determination of the Plasmodium genotypes related to resistance. The method is simple, fast, reproducible with low cost in personnel, material and equipment and scalable, being able to core KASP arrays, including numerous SNPs, to complete the main pattern of mutations associated to P. falciparum resistance.

    Matched MeSH terms: Genotype*; Genotyping Techniques/methods*
  6. Fulltext Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms
    Auburn S, Getachew S, Pearson RD, Amato R, Miotto O, Trimarsanto H, et al.
    J Infect Dis, 2019 Oct 22;220(11):1738-1749.
    PMID: 30668735 DOI: 10.1093/infdis/jiz016
    The Horn of Africa harbors the largest reservoir of Plasmodium vivax in the continent. Most of sub-Saharan Africa has remained relatively vivax-free due to a high prevalence of the human Duffy-negative trait, but the emergence of strains able to invade Duffy-negative reticulocytes poses a major public health threat. We undertook the first population genomic investigation of P. vivax from the region, comparing the genomes of 24 Ethiopian isolates against data from Southeast Asia to identify important local adaptions. The prevalence of the Duffy binding protein amplification in Ethiopia was 79%, potentially reflecting adaptation to Duffy negativity. There was also evidence of selection in a region upstream of the chloroquine resistance transporter, a putative chloroquine-resistance determinant. Strong signals of selection were observed in genes involved in immune evasion and regulation of gene expression, highlighting the need for a multifaceted intervention approach to combat P. vivax in the region.
    Matched MeSH terms: Genotype*
  7. Fulltext Association of Selenoprotein and Selenium Pathway Genotypes with Risk of Colorectal Cancer and Interaction with Selenium Status
    Fedirko V, Jenab M, Méplan C, Jones JS, Zhu W, Schomburg L, et al.
    Nutrients, 2019 Apr 25;11(4).
    PMID: 31027226 DOI: 10.3390/nu11040935
    Selenoprotein genetic variations and suboptimal selenium (Se) levels may contribute to the risk of colorectal cancer (CRC) development. We examined the association between CRC risk and genotype for single nucleotide polymorphisms (SNPs) in selenoprotein and Se metabolic pathway genes. Illumina Goldengate assays were designed and resulted in the genotyping of 1040 variants in 154 genes from 1420 cases and 1421 controls within the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Multivariable logistic regression revealed an association of 144 individual SNPs from 63 Se pathway genes with CRC risk. However, regarding the selenoprotein genes, only TXNRD1 rs11111979 retained borderline statistical significance after adjustment for correlated tests (PACT = 0.10; PACT significance threshold was P < 0.1). SNPs in Wingless/Integrated (Wnt) and Transforming growth factor (TGF) beta-signaling genes (FRZB, SMAD3, SMAD7) from pathways affected by Se intake were also associated with CRC risk after multiple testing adjustments. Interactions with Se status (using existing serum Se and Selenoprotein P data) were tested at the SNP, gene, and pathway levels. Pathway analyses using the modified Adaptive Rank Truncated Product method suggested that genes and gene x Se status interactions in antioxidant, apoptosis, and TGF-beta signaling pathways may be associated with CRC risk. This study suggests that SNPs in the Se pathway alone or in combination with suboptimal Se status may contribute to CRC development.
    Matched MeSH terms: Genotype*
  8. Fulltext ABO blood group alleles and prostate cancer risk: Results from the breast and prostate cancer cohort consortium (BPC3)
    Markt SC, Shui IM, Unger RH, Urun Y, Berg CD, Black A, et al.
    Prostate, 2015 Nov;75(15):1677-81.
    PMID: 26268879 DOI: 10.1002/pros.23035
    BACKGROUND: ABO blood group has been associated with risk of cancers of the pancreas, stomach, ovary, kidney, and skin, but has not been evaluated in relation to risk of aggressive prostate cancer.

    METHODS: We used three single nucleotide polymorphisms (SNPs) (rs8176746, rs505922, and rs8176704) to determine ABO genotype in 2,774 aggressive prostate cancer cases and 4,443 controls from the Breast and Prostate Cancer Cohort Consortium (BPC3). Unconditional logistic regression was used to calculate age and study-adjusted odds ratios and 95% confidence intervals for the association between blood type, genotype, and risk of aggressive prostate cancer (Gleason score ≥8 or locally advanced/metastatic disease (stage T3/T4/N1/M1).

    RESULTS: We found no association between ABO blood type and risk of aggressive prostate cancer (Type A: OR = 0.97, 95%CI = 0.87-1.08; Type B: OR = 0.92, 95%CI =n0.77-1.09; Type AB: OR = 1.25, 95%CI = 0.98-1.59, compared to Type O, respectively). Similarly, there was no association between "dose" of A or B alleles and aggressive prostate cancer risk.

    CONCLUSIONS: ABO blood type was not associated with risk of aggressive prostate cancer.

    Matched MeSH terms: Genotype*
  9. Fulltext Meta-analysis supports GWAS-implicated link between GRM3 and schizophrenia risk
    Saini SM, Mancuso SG, Mostaid MS, Liu C, Pantelis C, Everall IP, et al.
    Transl Psychiatry, 2017 Aug 08;7(8):e1196.
    PMID: 28786982 DOI: 10.1038/tp.2017.172
    Genome-wide association study (GWAS) evidence has identified the metabotropic glutamate receptor 3 (GRM3) gene as a potential harbor for schizophrenia risk variants. However, previous meta-analyses have refuted the association between GRM3 single-nucleotide polymorphisms (SNPs) and schizophrenia risk. To reconcile these conflicting findings, we conducted the largest and most comprehensive meta-analysis of 14 SNPs in GRM3 from a total of 11 318 schizophrenia cases, 13 820 controls and 486 parent-proband trios. We found significant associations for three SNPs (rs2237562: odds ratio (OR)=1.06, 95% confidence interval (CI)=1.02-1.11, P=0.017; rs13242038: OR=0.90, 95% CI=0.85-0.96, P=0.016 and rs917071: OR=0.94, 95% CI=0.91-0.97, P=0.003). Two of these SNPs (rs2237562, rs917071) were in strong-to-moderate linkage disequilibrium with the top GRM3 GWAS significant SNP (rs12704290) reported by the Schizophrenia Working Group of the Psychiatric Genomics Consortium. We also found evidence for population stratification related to rs2237562 in that the 'risk' allele was dependent on the population under study. Our findings support the GWAS-implicated link between GRM3 genetic variation and schizophrenia risk as well as the notion that alleles conferring this risk may be population specific.
    Matched MeSH terms: Genotype*
  10. Fulltext Genotyping of the Duffy blood group among Plasmodium knowlesi-infected patients in Malaysia
    De Silva JR, Lau YL, Fong MY
    PLoS One, 2014;9(9):e108951.
    PMID: 25268233 DOI: 10.1371/journal.pone.0108951
    The Duffy blood group is of major interest in clinical medicine as it plays an important role in Plasmodium knowlesi and Plasmodium vivax infection. In the present study, the distribution of Duffy blood group genotypes and allelic frequencies among P. knowlesi infected patients as well as healthy individuals in Peninsular Malaysia were determined. The blood group of 60 healthy blood donors and 51 P. knowlesi malaria patients were genotyped using allele specific polymerase chain reaction (ASP-PCR). The data was analyzed using Fisher's exact test in order to assess the significance of the variables. Our results show a high proportion of the FY*A/FY*A genotype (>85% for both groups) and a high frequency of the FY*A allele (>90% for both groups). The FY*A/FY*A genotype was the most predominant genotype in both infected and healthy blood samples. The genotype frequency did not differ significantly between the donor blood and the malaria patient groups. Also, there was no significant correlation between susceptibility to P. knowlesi infection with any Duffy blood genotype.
    Matched MeSH terms: Genotype*; Genotyping Techniques
  11. Epidemiology and characteristics of the dengue outbreak in Guangdong, Southern China, in 2014
    Huang L, Luo X, Shao J, Yan H, Qiu Y, Ke P, et al.
    Eur J Clin Microbiol Infect Dis, 2016 Feb;35(2):269-77.
    PMID: 26700953 DOI: 10.1007/s10096-015-2540-5
    Dengue is a rapidly spreading mosquito-borne disease caused by the dengue virus (DENV) and has emerged as a severe public health problem around the world. Guangdong, one of the southern Chinese provinces, experienced a serious outbreak of dengue in 2014, which was believed to be the worst dengue epidemic in China over the last 20 years. To better understand the epidemic, we collected the epidemiological data of the outbreak and analyzed 14,594 clinically suspected dengue patients from 25 hospitals in Guangdong. Dengue cases were then laboratory-confirmed by the detection of DENV non-structural protein 1 (NS1) antigen and/or DENV RNA. Afterwards, clinical manifestations of dengue patients were analyzed and 93 laboratory-positive serum specimens were chosen for the DENV serotyping and molecular analysis. Our data showed that the 2014 dengue outbreak in Guangdong had spread to 20 cities and more than 45 thousand people suffered from dengue fever. Of 14,594 participants, 11,387 were definitively diagnosed. Most manifested with a typical non-severe clinical course, and 1.96 % developed to severe dengue. The strains isolated successfully from the serum samples were identified as DENV-1. Genetic analyses revealed that the strains were classified into genotypes I and V of DENV-1, and the dengue epidemic of Guangdong in 2014 was caused by indigenous cases and imported cases from the neighboring Southeast Asian countries of Malaysia and Singapore. Overall, our study is informative and significant to the 2014 dengue outbreak in Guangdong and will provide crucial implications for dengue prevention and control in China and elsewhere.
    Matched MeSH terms: Genotype
  12. Fulltext Heritability and genetic advance among chili pepper genotypes for heat tolerance and morphophysiological characteristics
    Usman MG, Rafii MY, Ismail MR, Malek MA, Abdul Latif M
    ScientificWorldJournal, 2014;2014:308042.
    PMID: 25478590 DOI: 10.1155/2014/308042
    High temperature tolerance is an important component of adaptation to arid and semiarid cropping environment in chili pepper. Two experiments were carried out to study the genetic variability among chili pepper for heat tolerance and morphophysiological traits and to estimate heritability and genetic advance expected from selection. There was a highly significant variation among the genotypes in response to high temperature (CMT), photosynthesis rate, plant height, disease incidence, fruit length, fruit weight, number of fruits, and yield per plant. At 5% selection intensity, high genetic advance as percent of the mean (>20%) was observed for CMT, photosynthesis rate, fruit length, fruit weight, number of fruits, and yield per plant. Similarly, high heritability (>60%) was also observed indicating the substantial effect of additive gene more than the environmental effect. Yield per plant showed strong to moderately positive correlations (r = 0.23-0.56) at phenotypic level while at genotypic level correlation coefficient ranged from 0.16 to 0.72 for CMT, plant height, fruit length, and number of fruits. Cluster analysis revealed eight groups and Group VIII recorded the highest CMT and yield. Group IV recorded 13 genotypes while Groups II, VII, and VIII recorded one each. The results showed that the availability of genetic variance could be useful for exploitation through selection for further breeding purposes.
    Matched MeSH terms: Genotype
  13. Fulltext Antigen expression pattern of acute promyelocytic leukaemia cases in Malaysia
    Ambayya A, Zainina S, Salmiah MS, Sabariah MN
    Med J Malaysia, 2014 Apr;69(2):64-9.
    PMID: 25241814 MyJurnal
    INTRODUCTION: Acute Promyelocytic Leukaemia (APL) is associated with devastating coagulopathy and life threatening condition which requires immediate medical attention. It is crucial to establish an expedited diagnosis as early therapeutic intervention has led to optimal patient management. In this study, we assessed the type and frequency of antigen expressions in APL and correlated these findings with genetic studies.

    METHODS: Multiparametric immunophenotyping was performed on 30 samples and findings were correlated with karyotypes, FISH for t(15;17) translocation and RT-PCR for PML-RARΑ for detection of breakpoint cluster regions (bcr1,bcr2 and bcr3).

    RESULTS: On SSC/CD45, APL cells displayed high to moderate SSC, with the expression of CD33 (100%), CD13 (96.8%), cMPO (71%) but lacked CD34 (3.2%) and HLA-DR (9.7%). Aberrant expression of CD4 was seen in 12.9% and CD56 in 6.5% of the cases. A significant association between cumulative aberrant antigen expression and bcr1 were observed bcr1 (X2(2) =6.833,p.05) and (X2(2)=4.599,p>.05) respectively.

    CONCLUSIONS: Flow cytometry is a rapid and effective tool in detecting APL. It is interesting to note that there is significant association between cumulative aberrant antigen expression and genotype analysis. Further validation is required to corroborate this relationship.
    Matched MeSH terms: Genotype
  14. Fulltext Isolation and Characterisation of PRSV-P Resistance Genes in Carica and Vasconcellea
    Razean Haireen MR, Drew RA
    Int J Genomics, 2014;2014:145403.
    PMID: 25184131 DOI: 10.1155/2014/145403
    Papaya (Carica papaya L.) is one of the major tropical fruit crops worldwide, but it is limited throughout its range by papaya ringspot virus type P (PRSV-P). Previous genetic studies identified a functional PRSV-P resistance marker in a mapping population of F2 plants of Vasconcellea pubescens (resistant to PRSV-P) × Vasconcellea parviflora (susceptible to PRSV-P) and showed that the marker exhibited homology to a serine threonine protein kinase (STK) gene. Full length cDNAs of putative PRSV-P resistance genes designated CP_STK from C. papaya and VP_STK1 and VP_STK2 from V. pubescens were cloned by rapid amplification of cDNA ends (RACE). Due to a frame-shift mutation, the two homologous sequences are transcribed and edited differently such that the gene product in V. pubescens is two separate transcripts, whereas in C. papaya they are fused into a single message. A peroxisomal targeting signal (PTS2) present in VP_STK2 but absent in the other transcripts may be the functional source of PRSV resistance in V. pubescens. The STK gene from V. pubescens may have been derived from an alternative splicing to confer resistance. The putative resistance gene, VP_STK2, that was identified in this study is a potential new source of PRSV-P resistance for papaya genotypes.
    Matched MeSH terms: Genotype
  15. Fulltext Haemoglobin Sickle D Punjab: - a case report
    Rahimah A, Syahira Lazira O, Siti Hida HM, Faidatul Syazlin AH, Nur Aisyah A, Nik Hafidzah NM, et al.
    Med J Malaysia, 2014 Feb;69(1):42-3.
    PMID: 24814631 MyJurnal
    Haemoglobin S D-Punjab is a rare compound heterozygous haemoglobinopathy characterised by the presence of two β globin gene variants: Β6(GAG→GTG) and Β121(GAA→CAA). These patients' clinical and haematological features mimic haemoglobin S disease. We describe the first case of doubly heterozygous HbSD-Punjab from Malaysia managed with regular blood transfusion at the age of one. This case highlights the propensity for occurrence of rare phenotypes within our multi-ethnic population and emphasises the importance of accurate genotyping to avoid erroneous counselling, and to plan an effective patient management strategy before complication evolves.
    Matched MeSH terms: Genotype
  16. Fulltext Ethnic variation in interleukin-6 -174 (g/c) polymorphism in the malaysian population
    Gan GG, Subramaniam R, Lian LH, Nadarajan V
    Balkan J. Med. Genet., 2013 Dec;16(2):53-8.
    PMID: 24778564 DOI: 10.2478/bjmg-2013-0032
    Interleukin-6 (IL-6) is one of the cytokines that has been well studied and implicated in many diseases including cancers. The frequency of the IL-6 -174 (G/C) polymorphism had been proven to differ in various populations. Malaysia is a country with three major ethnic populations, Malays, Chinese and Indians. In this study, we proposed to determine the G or C allele frequency of the IL-6 -174 polymorphism in these three populations. A total of 348 blood samples were available for analysis. The median age for the subjects was 31 years. There were a total of 245 males and 103 females. A total of 86 Malays (25.0%), 122 Chinese (33.0%) and 140 Indians (40.0%) were genotyped. The result showed a significant difference in the G or C allele frequency of the -174 polymorphism. The total frequencies for the G and C alleles were 91.0 and 9.0%, respectively. In the Malays, the allele frequency of the C allele was 4.0% compared with 19.0% in the Indians. The C allele was not detected in the Chinese population. This finding is the first reported on the Malaysian population and may be important in determining risk of diseases associated with the IL-6 polymorphism in these three populations.
    Matched MeSH terms: Genotype
  17. Fulltext The efficacy of molecular markers analysis with integration of sensory methods in detection of aroma in rice
    Yeap HY, Faruq G, Zakaria HP, Harikrishna JA
    ScientificWorldJournal, 2013;2013:569268.
    PMID: 24222741 DOI: 10.1155/2013/569268
    Allele Specific Amplification with four primers (External Antisense Primer, External Sense Primer, Internal Nonfragrant Sense Primer, and Internal Fragrant Antisense Primer) and sensory evaluation with leaves and grains were executed to identify aromatic rice genotypes and their F1 individuals derived from different crosses of 2 Malaysian varieties with 4 popular land races and 3 advance lines. Homozygous aromatic (fgr/fgr) F1 individuals demonstrated better aroma scores compared to both heterozygous nonaromatic (FGR/fgr) and homozygous nonaromatic (FGR/FGR) individuals, while, some F1 individuals expressed aroma in both leaf and grain aromatic tests without possessing the fgr allele. Genotypic analysis of F1 individuals for the fgr gene represented homozygous aromatic, heterozygous nonaromatic and homozygous nonaromatic genotypes in the ratio 20:19:3. Genotypic and phenotypic analysis revealed that aroma in F1 individuals was successfully inherited from the parents, but either molecular analysis or sensory evaluation alone could not determine aromatic condition completely. The integration of molecular analysis with sensory methods was observed as rapid and reliable for the screening of aromatic genotypes because molecular analysis could distinguish aromatic homozygous, nonaromatic homozygous and nonaromatic heterozygous individuals, whilst the sensory method facilitated the evaluation of aroma emitted from leaf and grain during flowering to maturity stages.
    Matched MeSH terms: Genotype
  18. Fulltext Distribution of alpha thalassaemia gene variants in diverse ethnic populations in malaysia: data from the institute for medical research
    Ahmad R, Saleem M, Aloysious NS, Yelumalai P, Mohamed N, Hassan S
    Int J Mol Sci, 2013;14(9):18599-614.
    PMID: 24025420 DOI: 10.3390/ijms140918599
    Alpha thalassaemia is highly prevalent in the plural society of Malaysia and is a public health problem. Haematological and molecular data from 5016 unrelated patients referred from various hospitals to the Institute for Medical Research for α thalassaemia screening from 2007 to 2010 were retrieved. The aims of this retrospective analysis were to describe the distribution of various alpha thalassaemia alleles in different ethnic groups, along with their genotypic interactions, and to illustrate the haematological changes associated with each phenotype. Amongst the patients, 51.2% (n = 2567) were diagnosed with α thalassaemia. Of the 13 α thalassaemia determinants screened, eight different deletions and mutations were demonstrated: three double gene deletions, --(SEA), --(THAI), --(FIL); two single-gene deletions, α-³·⁷ and -α⁴·²; and three non-deletion mutations, Cd59G > A (haemoglobin [Hb] Adana), Cd125T > C (Hb Quong Sze) and Cd142 (Hb Constant Spring). A high incidence of α-³·⁷ deletion was observed in Malays, Indians, Sabahans, Sarawakians and Orang Asli people. However, the --SEA deletion was the most common cause of alpha thalassaemia in Chinese, followed by the α-³·⁷ deletion. As many as 27 genotypic interactions showed 1023 α thalassaemia silent carriers, 196 homozygous α⁺ thalassaemia traits, 973 heterozygous α⁰ thalassaemia carriers and 375 patients with Hb H disease. Statistical analysis showed a significant difference in the distribution of α thalassaemia determinants amongst the various ethnic groups. Hence, the heterogeneous distribution of common determinants indicated that the introduction of an ethnicity-targeted hierarchical α thalassaemia screening approach in this multi-ethnic Malaysian population would be effective.
    Matched MeSH terms: Genotype
  19. Fulltext Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene
    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: Genotype
  20. Fulltext Stability analysis of oil yield in oil palm (Elaeis guineensis) progenies in different environments
    Rafii MY, Jalani BS, Rajanaidu N, Kushairi A, Puteh A, Latif MA
    Genet. Mol. Res., 2012;11(4):3629-41.
    PMID: 23096688 DOI: 10.4238/2012.October.4.10
    We evaluated 38 dura x pisifera (DP) oil palm progenies in four locations in Malaysia for genotype by environment interaction and genotypic stability studies. The DP progenies derived from crosses between pisifera palms of AVROS, Serdang S27B, Serdang 29/36, and Lever Cameroon were chosen to be the males' parent and Deli dura palms designated as females' parent. All the locations differed in terms of soil physical and chemical properties, and the soil types ranged from coastal clay to inland soils. The genotype by environment interaction and stability of the individual genotypes were analyzed for oil yield trait using several stability techniques. A genotype by environment interaction was detected for oil yield and it had a larger variance component than genotypic variance (σ(2)(gl)/σ(2)(g) = 139.7%). Genotype by environment interaction of oil yield was largely explained by a non-linear relationship between genotypic and environmental values. Overall assessment of individual genotypic stability showed that seven genotypes were highly stable and had consistent performance over the environments for the oil yield trait [total individual genotype stability scored more than 10 and mean oil yielded above the average of the environment (genotype means are more than 34.37 kg·palm(-1)·year(-1))]. These genotypes will be useful for oil palm breeding and tissue culture programs for developing high oil yielding planting materials with stable performance.
    Matched MeSH terms: Genotype
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