Displaying publications 381 - 400 of 746 in total

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  1. Genetic variations of the ABCC2 gene in the Chinese, Malay, and Indian populations of Singapore
    Ho WF, Koo SH, Yee JY, Lee JD
    Drug Metab. Pharmacokinet., 2008;23(5):385-91.
    PMID: 18974617
    MRP2 is a drug transporter that is responsible for the gastrointestinal absorption and biliary excretion of a wide variety of endogenous and xenobiotic compounds, including many clinically used drugs. This study aims to identify genetic variations of ABCC2 gene in three distinct ethnic groups of the Singaporean population (n = 288). The coding region of the gene encoding the transporter protein was screened for genetic variations in the study population by denaturing high-performance liquid chromatography and DNA sequencing. Twenty-two genetic variations of ABCC2, including 8 novel ones, were found: 1 in the 5' untranslated region, 10 in the coding exons (8 nonsynonymous and 2 synonymous variations), and 11 in the introns. Three novel nonsynonymous variations: 2686G > A (Glu896Lys), 4240C > T (His1414Tyr) and 4568A > C (Gln1523Pro) were detected in single heterozygous Malay, Chinese, and Indian subjects, respectively. Among the novel nonsynonymous variations, 4240C > T and 4568A > C were predicted to be functionally significant. These data would provide fundamental and useful information for pharmacogenetic studies on drugs that are substrates of MRP2 in Asians.
    Matched MeSH terms: Genetic Variation*
  2. Genetic variations of the SLCO1B1 gene in the Chinese, Malay and Indian populations of Singapore
    Ho WF, Koo SH, Yee JY, Lee EJ
    Drug Metab. Pharmacokinet., 2008;23(6):476-82.
    PMID: 19122343
    OATP1B1 is a liver-specific transporter that mediates the uptake of various endogenous and exogenous compounds including many clinically used drugs from blood into hepatocytes. This study aims to identify genetic variations of SLCO1B1 gene in three distinct ethnic groups of the Singaporean population (n=288). The coding region of the gene encoding the transporter protein was screened for genetic variations in the study population by denaturing high-performance liquid chromatography and DNA sequencing. Twenty-five genetic variations of SLCO1B1, including 10 novel ones, were found: 13 in the coding exons (9 nonsynonymous and 4 synonymous variations), 6 in the introns, and 6 in the 3' untranslated region. Four novel nonsynonymous variations: 633A>G (Ile211Met), 875C>T (Ala292Val), 1837T>C (Cys613Arg), and 1877T>A (Leu626Stop) were detected as heterozygotes. Among the novel nonsynonymous variations, 633A>G, 1837T>C, and 1877T>A were predicted to be functionally significant. These data would provide fundamental and useful information for pharmacogenetic studies on drugs that are substrates of OATP1B1 in Asians.
    Matched MeSH terms: Genetic Variation/genetics*
  3. The geography of diversification in mutualistic ants: a gene's-eye view into the Neogene history of Sundaland rain forests
    Quek SP, Davies SJ, Ashton PS, Itino T, Pierce NE
    Mol Ecol, 2007 May;16(10):2045-62.
    PMID: 17498231
    We investigate the geographical and historical context of diversification in a complex of mutualistic Crematogaster ants living in Macaranga trees in the equatorial rain forests of Southeast Asia. Using mitochondrial DNA from 433 ant colonies collected from 32 locations spanning Borneo, Malaya and Sumatra, we infer branching relationships, patterns of genetic diversity and population history. We reconstruct a time frame for the ants' diversification and demographic expansions, and identify areas that might have been refugia or centres of diversification. Seventeen operational lineages are identified, most of which can be distinguished by host preference and geographical range. The ants first diversified 16-20 Ma, not long after the onset of the everwet forests in Sundaland, and achieved most of their taxonomic diversity during the Pliocene. Pleistocene demographic expansions are inferred for several of the younger lineages. Phylogenetic relationships suggest a Bornean cradle and major axis of diversification. Taxonomic diversity tends to be associated with mountain ranges; in Borneo, it is greatest in the Crocker Range of Sabah and concentrated also in other parts of the northern northwest coast. Within-lineage genetic diversity in Malaya and Sumatra tends to also coincide with mountain ranges. A series of disjunct and restricted distributions spanning northern northwest Borneo and the major mountain ranges of Malaya and Sumatra, seen in three pairs of sister lineages, further suggests that these regions were rain-forest refuges during drier climatic phases of the Pleistocene. Results are discussed in the context of the history of Sundaland's rain forests.
    Matched MeSH terms: Genetic Variation*
  4. Comparative genome analysis of Ureaplasma parvum clinical isolates
    Momynaliev K, Klubin A, Chelysheva V, Selezneva O, Akopian T, Govorun V
    Res. Microbiol., 2007 May;158(4):371-8.
    PMID: 17363224
    Ureaplasma parvum colonizes human mucosal surfaces, primarily in the respiratory and urogenital tracts, causing a wide spectrum of diseases, from non-gonococcal urethritis to pneumonitis in immunocompromised hosts. Although the basis for these diverse clinical outcomes is not yet understood, more severe disease may be associated with strains harboring a certain set of strain-specific genes. To investigate this, whole genome DNA macroarrays were constructed and used to assess genomic diversity in 10 U. parvum clinical strains. We found that 7.6% of U. parvum genes were dispersed into one or more strains, thus defining a minimal functional core of 538 U. parvum genes. Most of the strain-specific genes (79%) were of unknown function and were unique to U. parvum. Four hypervariable plasticity regions were identified in the genome containing 93% of the variability in the gene pool (UU32-UU33, UU145-UU170, UU440-UU447 and UU527-UU529). We hypothesized that one of them (UU145-UU170) was a pathogenicity island in U. parvum and we characterized it. Thus, we propose that the clinical outcome of U. parvum infection is probably associated with this newly identified pathogenicity island.
    Matched MeSH terms: Genetic Variation*
  5. Genetic diversity of chicken anemia virus following cell culture passaging in MSB-1 cells
    Hasmah MS, Omar AR, Wan KF, Hair-Bejo M, Aini I
    Acta Virol., 2004;48(2):85-9.
    PMID: 15462283
    It has been shown that a chicken anemia virus (CAV) isolates which had undergone 60 passages in MSB-1 cells (SMSC-1/P60, 3-1/P60) acquired 33-66 nucleotide substitutions at the coding region resulting in 13-16 amino acid changes as compared to the CAV isolates passaged only 5 times in MSB-1 cells (SMSC-1 and 3-1) (Chowdhury et al., Arch. Virol. 148, 2437-2448, 2003). In this study we found that a low CAV (BL-5) and a high CAV passage (BL-5/P90) differed by only 15 nucleotide substitutions resulting in 11 amino acid changes. Phylogenetic analysis based on VP1 also revealed that both isolates were close to each other but not to other CAV isolates from Malaysia, namely SMSC-1 and 3-1.
    Matched MeSH terms: Genetic Variation*
  6. Impact of leptin receptor gene variants on risk of non-alcoholic fatty liver disease and its interaction with adiponutrin gene
    Zain SM, Mohamed Z, Mahadeva S, Cheah PL, Rampal S, Chin KF, et al.
    J Gastroenterol Hepatol, 2013 May;28(5):873-9.
    PMID: 23278404 DOI: 10.1111/jgh.12104
    Genetic polymorphism has been implicated as a factor for the occurrence of non-alcoholic fatty liver disease (NAFLD). This study attempted to assess whether polymorphisms in the leptin receptor (LEPR) gene and its combined effect with patatin-like phospholipase domain-containing protein 3 (PNPLA3/adiponutrin) are associated with risk of NAFLD.
    Matched MeSH terms: Genetic Variation/genetics*
  7. Genetic variation among methicillin-resistant Staphylococcus aureus isolates from cancer patients in Saudi Arabia
    Alreshidi MA, Alsalamah AA, Hamat RA, Neela V, Alshrari AS, Atshan SS, et al.
    Eur J Clin Microbiol Infect Dis, 2013 Jun;32(6):755-61.
    PMID: 23318757 DOI: 10.1007/s10096-012-1801-9
    One hundred and twenty methicillin-resistant Staphylococcus aureus (MRSA) isolated from cancer and non-cancer patients in Saudi Arabia were investigated for antibiotic resistance, virulence determinants and genotypes. The majority of MRSA isolates from cancer (n = 44, 73.3 %) and non-cancer patients (n = 34, 56.7 %) were multi-resistant to more than four classes of antibiotics. Virulence gene profiling showed that all strains were commonly positive for adhesin genes, except ebps and bbp genes, which were not detected in any isolate. Although the presence of adhesin genes varied slightly among MRSA isolates from cancer and non-cancer patients, these variations were not found to be statistically significant. In contrast, the presence of the toxin genes seb, sec, seg and sei was significantly elevated in MRSA strains isolated from cancer patients. Multilocus sequence typing (MLST) detected six and nine sequence types (STs) among isolates from cancer and non-cancer patients, respectively. Using spa typing, 12 and 25 types were detected, including four new types. The ability of different MRSA clones to become multi-resistant and their ability to acquire different virulence factors may contribute to their success as pathogens in individual groups of patients.
    Matched MeSH terms: Genetic Variation*
  8. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes
    Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, et al.
    Science, 2005 May 13;308(5724):1034-6.
    PMID: 15890885
    A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated "relict" populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia approximately 65,000 years ago was rapid, most likely taking only a few thousand years.
    Matched MeSH terms: Genetic Variation*
  9. Three Taxa in One: Cryptic Diversity in the Black Fly Simulium nobile (Diptera: Simuliidae) in Southeast Asia
    Low VL, Takaoka H, Pramual P, Adler PH, Ya'cob Z, Chen CD, et al.
    J Med Entomol, 2016 07;53(4):972-976.
    PMID: 27208009
    We access the molecular diversity of the black fly Simulium nobile De Mejiere, using the universal cytochrome c oxidase subunit I (COI) barcoding gene, across its distributional range in Southeast Asia. Our phylogenetic analyses recovered three well-supported mitochondrial lineages of S. nobile, suggesting the presence of cryptic species. Lineage A is composed of a population from Sabah, East Malaysia (Borneo); lineage B represents the type population from Java, Indonesia; and lineage C includes populations from the mainland of Southeast Asia (Peninsular Malaysia and Thailand). The genetic variation of lineage C on the mainland is greater than that of lineages A and B on the islands of Borneo and Java. Our study highlights the value of a molecular approach in assessing species status of simuliids in geographically distinct regions.
    Matched MeSH terms: Genetic Variation*
  10. Fulltext Genetic Diversity, Natural Selection and Haplotype Grouping of Plasmodium knowlesi Gamma Protein Region II (PkγRII): Comparison with the Duffy Binding Protein (PkDBPαRII)
    Fong MY, Rashdi SA, Yusof R, Lau YL
    PLoS One, 2016;11(5):e0155627.
    PMID: 27195821 DOI: 10.1371/journal.pone.0155627
    BACKGROUND: Plasmodium knowlesi is a simian malaria parasite that has been reported to cause malaria in humans in Southeast Asia. This parasite invades the erythrocytes of humans and of its natural host, the macaque Macaca fascicularis, via interaction between the Duffy binding protein region II (PkDBPαRII) and the Duffy antigen receptor on the host erythrocytes. In contrast, the P. knowlesi gamma protein region II (PkγRII) is not involved in the invasion of P. knowlesi into humans. PkγRII, however, mediates the invasion of P. knowlesi into the erythrocytes of M. mulata, a non-natural host of P. knowlesi via a hitherto unknown receptor. The haplotypes of PkDBPαRII in P. knowlesi isolates from Peninsular Malaysia and North Borneo have been shown to be genetically distinct and geographically clustered. Also, the PkDBPαRII was observed to be undergoing purifying (negative) selection. The present study aimed to determine whether similar phenomena occur in PkγRII.

    METHODS: Blood samples from 78 knowlesi malaria patients were used. Forty-eight of the samples were from Peninsular Malaysia, and 30 were from Malaysia Borneo. The genomic DNA of the samples was extracted and used as template for the PCR amplification of the PkγRII. The PCR product was cloned and sequenced. The sequences obtained were analysed for genetic diversity and natural selection using MEGA6 and DnaSP (version 5.10.00) programmes. Genetic differentiation between the PkγRII of Peninsular Malaysia and North Borneo isolates was estimated using the Wright's FST fixation index in DnaSP (version 5.10.00). Haplotype analysis was carried out using the Median-Joining approach in NETWORK (version 4.6.1.3).

    RESULTS: A total of 78 PkγRII sequences was obtained. Comparative analysis showed that the PkγRII have similar range of haplotype (Hd) and nucleotide diversity (π) with that of PkDBPαRII. Other similarities between PkγRII and PkDBPαRII include undergoing purifying (negative) selection, geographical clustering of haplotypes, and high inter-population genetic differentiation (FST index). The main differences between PkγRII and PkDBPαRII include length polymorphism and no departure from neutrality (as measured by Tajima's D statistics) in the PkγRII.

    CONCLUSION: Despite the biological difference between PkγRII and PkDBPαRII, both generally have similar genetic diversity level, natural selection, geographical haplotype clustering and inter-population genetic differentiation index.

    Matched MeSH terms: Genetic Variation*
  11. Fulltext Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders
    Arloth J, Bogdan R, Weber P, Frishman G, Menke A, Wagner KV, et al.
    Neuron, 2015 Jun 03;86(5):1189-202.
    PMID: 26050039 DOI: 10.1016/j.neuron.2015.05.034
    Depression risk is exacerbated by genetic factors and stress exposure; however, the biological mechanisms through which these factors interact to confer depression risk are poorly understood. One putative biological mechanism implicates variability in the ability of cortisol, released in response to stress, to trigger a cascade of adaptive genomic and non-genomic processes through glucocorticoid receptor (GR) activation. Here, we demonstrate that common genetic variants in long-range enhancer elements modulate the immediate transcriptional response to GR activation in human blood cells. These functional genetic variants increase risk for depression and co-heritable psychiatric disorders. Moreover, these risk variants are associated with inappropriate amygdala reactivity, a transdiagnostic psychiatric endophenotype and an important stress hormone response trigger. Network modeling and animal experiments suggest that these genetic differences in GR-induced transcriptional activation may mediate the risk for depression and other psychiatric disorders by altering a network of functionally related stress-sensitive genes in blood and brain.
    Matched MeSH terms: Genetic Variation/genetics*
  12. Genetic diversity of enterovirus 71 isolated from cases of hand, foot and mouth disease in Yokohama City between 1982 and 2000
    Munemura T, Saikusa M, Kawakami C, Shimizu H, Oseto M, Hagiwara A, et al.
    Arch Virol, 2003 Feb;148(2):253-63.
    PMID: 12556991
    Enterovirus 71 (EV71) is known as one of the major causative agents of hand, foot and mouse disease (HFMD) and is also associated with neurological manifestations such as aseptic meningitis, polio-like paralysis and encephalitis. Recently, large HFMD outbreaks, involving severe neurological complications, have been experienced in Malaysia, Taiwan and some other countries in the Western-Pacific region. To investigate the genetic diversity of EV71 isolates in a single community in Japan, nucleotide sequences of the VP4 region of 52 EV71 isolates in Yokohama City from 1982 to 2000 were determined and the phylogenetic relationship was compared with other referential EV71 strains in Japan and in the world. There were two major genotypes of EV71 in Yokohama City through the 1980's and 1990's. Six EV71 isolates in the early 1980's in Yokohama City were closely related to those from HFMD outbreaks in Japan and from outbreaks of polio-like paralysis in Europe in the 1970's. During recent HFMD outbreaks in 1997 and 2000, two distinct genotypes of EV71 were co-circulating in Yokohama City as in HFMD outbreaks in Malaysia and Taiwan. However, the genetic diversity of EV71 in Yokohama City was not directly correlated with the severity of HFMD. The results confirmed the circulation of two distinct genotypes of EV71 over the past 20 years in Japan.
    Matched MeSH terms: Genetic Variation/genetics*
  13. Genetic diversity of Asian water buffalo (Bubalus bubalis): mitochondrial DNA D-loop and cytochrome b sequence variation
    Lau CH, Drinkwater RD, Yusoff K, Tan SG, Hetzel DJ, Barker JS
    Anim. Genet., 1998 Aug;29(4):253-64.
    PMID: 9745663
    Swamp and river buffalo mitochondrial DNA (mtDNA) was sequenced for 303 bp of the cytochrome b gene for 54 animals from 14 populations, and for 158 bp of the D-loop region for 80 animals from 11 populations. Only one cytochrome b haplotype was found in river buffalo. Of the four haplotypes identified in swamp buffalo, one found in all populations is apparently ancestral both to the other swamp haplotypes and to the river haplotype. The phylogenetic relationships among the 33 D-loop haplotypes, with a cluster of 11 found in swamp buffalo only, also support the evolution of domesticated swamp and river buffalo from an ancestral swamp-like animal, most likely represented today by the wild Asian buffalo (Bubalus arnee). The time of divergence of the swamp and river types, estimated from the D-loop data, is 28,000 to 87,000 years ago. We hypothesise that the species originated in mainland south-east Asia, and that it spread north to China and west to the Indian subcontinent, where the rive type evolved and was domesticated. Following domestication in China, the domesticated swamp buffalo spread through two separate routes, through Taiwan and the Philippines to the eastern islands of Borneo and Sulawesi, and south through mainland south-east Asia and then to the western islands of Indonesia.
    Matched MeSH terms: Genetic Variation*
  14. Nucleoprotein gene analysis of fixed and street rabies virus variants using RT-PCR
    Arai YT, Yamada K, Kameoka Y, Horimoto T, Yamamoto K, Yabe S, et al.
    Arch Virol, 1997;142(9):1787-96.
    PMID: 9672637
    A simple and rapid single-step reverse transcriptase-polymerase chain reaction (RT-PCR) was used to investigate the nucleoprotein (N) gene of 11 rabies viruses. A conserved set of RT-PCR primers was designed to amplify the most variable region in the N gene. N gene regions were amplified from 6 fixed laboratory viruses, 4 street viruses from dogs in Thailand, and a horse in Zambia. Sequences of the amplified products, together with the database of 91 additional sequences, were analyzed by using PILEUP program of the GCG package. The rabies viruses grouped into at least 9 distinct clusters by < 90% nucleotide similarity of the N gene region: I (4 isolates, USA), II (2 isolates, South America), III (3 isolates, Africa), IV (52 strains, Europe, Middle East, Africa and South America), V (16 isolates, North America and Arctic), VI (17 isolates, Africa), VII (1 isolate, Africa), VIII (6 isolates, Thailand and Malaysia) and IX (1 isolate, Sri Lanka). A unique group of rabies viruses from Thailand and clusters of isolates corresponding to their geographic origin also were determined. The simple and rapid single-step RT-PCR proved to be useful for identifying rabies viruses, and for grouping the viruses into clades by sequence analysis.
    Matched MeSH terms: Genetic Variation*
  15. HIV-1 variants in South and South-East Asia
    Tsuchie H, Saraswathy TS, Sinniah M, Vijayamalar B, Maniar JK, Monzon OT, et al.
    Int J STD AIDS, 1995 Mar-Apr;6(2):117-20.
    PMID: 7779924 DOI: 10.1177/095646249500600211
    HIV spread in South and South-East Asia is most alarming, and genetic variability of HIV-1 is an important consideration in vaccine development. In this study, we examined the third variable (V3) region of env gene of HIV-1 variants prevalent in Thailand, Malaysia, India, and the Philippines. By phylogenetic tree analyses, an HIV-1 variant from an injecting drug user (IDU) in Thailand belonged to subtype B, and HIV-1 variants from 2 IDUs in Malaysia were classified into 2 subtypes, B and E. One HIV-1 variant from a male homosexual in the Philippines belonged to subtype B. Out of 8 HIV-1 variants from sexually transmitted disease patients in India, 7 belonged to subtype C, and one to subtype A. Although the total number of individuals examined in this study was limited, 4 HIV-1 subtypes were found in South and South-East Asia and large international movements of HIV-1-infected individuals in this region could induce global dissemination of these HIV-1 variants.
    Matched MeSH terms: Genetic Variation*
  16. Fulltext Genome-wide mosaicism in divergence between zoonotic malaria parasite subpopulations with separate sympatric transmission cycles
    Divis PCS, Duffy CW, Kadir KA, Singh B, Conway DJ
    Mol Ecol, 2018 02;27(4):860-870.
    PMID: 29292549 DOI: 10.1111/mec.14477
    Plasmodium knowlesi is a significant cause of human malaria transmitted as a zoonosis from macaque reservoir hosts in South-East Asia. Microsatellite genotyping has indicated that human infections in Malaysian Borneo are an admixture of two highly divergent sympatric parasite subpopulations that are, respectively, associated with long-tailed macaques (Cluster 1) and pig-tailed macaques (Cluster 2). Whole-genome sequences of clinical isolates subsequently confirmed the separate clusters, although fewer of the less common Cluster 2 type were sequenced. Here, to analyse population structure and genomic divergence in subpopulation samples of comparable depth, genome sequences were generated from 21 new clinical infections identified as Cluster 2 by microsatellite analysis, yielding a cumulative sample size for this subpopulation similar to that for Cluster 1. Profound heterogeneity in the level of intercluster divergence was distributed across the genome, with long contiguous chromosomal blocks having high or low divergence. Different mitochondrial genome clades were associated with the two major subpopulations, but limited exchange of haplotypes from one to the other was evident, as was also the case for the maternally inherited apicoplast genome. These findings indicate deep divergence of the two sympatric P. knowlesi subpopulations, with introgression likely to have occurred recently. There is no evidence yet of specific adaptation at any introgressed locus, but the recombinant mosaic types offer enhanced diversity on which selection may operate in a currently changing landscape and human environment. Loci responsible for maintaining genetic isolation of the sympatric subpopulations need to be identified in the chromosomal regions showing fixed differences.
    Matched MeSH terms: Genetic Variation*
  17. Fulltext De Novo Truncating Variants in the Last Exon of SEMA6B Cause Progressive Myoclonic Epilepsy
    Hamanaka K, Imagawa E, Koshimizu E, Miyatake S, Tohyama J, Yamagata T, et al.
    Am J Hum Genet, 2020 04 02;106(4):549-558.
    PMID: 32169168 DOI: 10.1016/j.ajhg.2020.02.011
    De novo variants (DNVs) cause many genetic diseases. When DNVs are examined in the whole coding regions of genes in next-generation sequencing analyses, pathogenic DNVs often cluster in a specific region. One such region is the last exon and the last 50 bp of the penultimate exon, where truncating DNVs cause escape from nonsense-mediated mRNA decay [NMD(-) region]. Such variants can have dominant-negative or gain-of-function effects. Here, we first developed a resource of rates of truncating DNVs in NMD(-) regions under the null model of DNVs. Utilizing this resource, we performed enrichment analysis of truncating DNVs in NMD(-) regions in 346 developmental and epileptic encephalopathy (DEE) trios. We observed statistically significant enrichment of truncating DNVs in semaphorin 6B (SEMA6B) (p value: 2.8 × 10-8; exome-wide threshold: 2.5 × 10-6). The initial analysis of the 346 individuals and additional screening of 1,406 and 4,293 independent individuals affected by DEE and developmental disorders collectively identified four truncating DNVs in the SEMA6B NMD(-) region in five individuals who came from unrelated families (p value: 1.9 × 10-13) and consistently showed progressive myoclonic epilepsy. RNA analysis of lymphoblastoid cells established from an affected individual showed that the mutant allele escaped NMD, indicating stable production of the truncated protein. Importantly, heterozygous truncating variants in the NMD(+) region of SEMA6B are observed in general populations, and SEMA6B is most likely loss-of-function tolerant. Zebrafish expressing truncating variants in the NMD(-) region of SEMA6B orthologs displayed defective development of brain neurons and enhanced pentylenetetrazole-induced seizure behavior. In summary, we show that truncating DNVs in the final exon of SEMA6B cause progressive myoclonic epilepsy.
    Matched MeSH terms: Genetic Variation/genetics*
  18. Genetic abnormalities in a large cohort of Coffin-Siris syndrome patients
    Sekiguchi F, Tsurusaki Y, Okamoto N, Teik KW, Mizuno S, Suzumura H, et al.
    J Hum Genet, 2019 Dec;64(12):1173-1186.
    PMID: 31530938 DOI: 10.1038/s10038-019-0667-4
    Coffin-Siris syndrome (CSS, MIM#135900) is a congenital disorder characterized by coarse facial features, intellectual disability, and hypoplasia of the fifth digit and nails. Pathogenic variants for CSS have been found in genes encoding proteins in the BAF (BRG1-associated factor) chromatin-remodeling complex. To date, more than 150 CSS patients with pathogenic variants in nine BAF-related genes have been reported. We previously reported 71 patients of whom 39 had pathogenic variants. Since then, we have recruited an additional 182 CSS-suspected patients. We performed comprehensive genetic analysis on these 182 patients and on the previously unresolved 32 patients, targeting pathogenic single nucleotide variants, short insertions/deletions and copy number variations (CNVs). We confirmed 78 pathogenic variations in 78 patients. Pathogenic variations in ARID1B, SMARCB1, SMARCA4, ARID1A, SOX11, SMARCE1, and PHF6 were identified in 48, 8, 7, 6, 4, 1, and 1 patients, respectively. In addition, we found three CNVs including SMARCA2. Of particular note, we found a partial deletion of SMARCB1 in one CSS patient and we thoroughly investigated the resulting abnormal transcripts.
    Matched MeSH terms: Genetic Variation/genetics*
  19. Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes
    Yan CZY, Austin CM, Ayub Q, Rahman S, Gan HM
    FEMS Microbiol Lett, 2019 09 01;366(17).
    PMID: 31589302 DOI: 10.1093/femsle/fnz211
    The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.
    Matched MeSH terms: Genetic Variation*
  20. Genetic variability of classical swine fever virus
    Vilcek S, Stadejek T, Ballagi-Pordány A, Lowings JP, Paton DJ, Belák S
    Virus Res, 1996 Aug;43(2):137-47.
    PMID: 8864203
    The genetic variability of classical swine fever virus was studied by comparative nucleotide sequence analysis of 76 virus isolates, collected during a half century from three continents. Parts of the E2 (gp55) and the polymerase gene coding regions of the viral genome were amplified by RT-PCR and DNA fragments of 254 and 207 bp, respectively, were sequenced. The comparative sequence analysis of the E2 region revealed two main phylogenetic groups of CSFV, indicating that the virus apparently evolved from two ancestor nodes. Group I (represented by Brescia strain) consisted of old and recent American and Asian viruses, as well as old English isolates from the 1950s. This group was subdivided into three subgroups, termed I.A-I.C. Group II (represented by Alfort strain) consisted of relatively recent isolates from Europe, together with strain Osaka, which was isolated in Japan from a pig of European origin. Based on genetic distances the group was divided into subgroups II.A and II.B. Malaysian isolates were branched into both groups, indicating multiple origins for contemporaneous outbreaks in that country. All ten vaccine strains tested were branched in group I, implying a common ancestor. The Japanese Kanagawa strain, isolated in 1974, and the British Congenital Tremor strain from 1964 were the most distinct variants of CSFV in our collection. The comparison of the nucleotide sequences of the polymerase coding region of 32 European strains distinguished subgroups II.A and II.B which were similar to the corresponding subgroups of the E2 phylogenetic tree. Thus, the results revealed that the E2 region and the polymerase coding regions seem to be appropriate for the grouping of CSFV isolates from all over the world, distinguishing two major groups of the virus. The reliability of these regions for phylogenetic analysis is indicated by the similarity of the results obtained from the two separate parts of the CSFV genome.
    Matched MeSH terms: Genetic Variation*
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