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  1. Draft Genome Sequence of a Biosurfactant-Producing Bacillus subtilis UMX-103 Isolated from Hydrocarbon-Contaminated Soil in Terengganu, Malaysia
    Abdelhafiz YA, Manaharan T, BinMohamad S, Merican AF
    Curr Microbiol, 2017 Apr 17.
    PMID: 28417189 DOI: 10.1007/s00284-017-1249-3
    The draft genome here presents the sequence of Bacillus subtilis UMX-103. The bacterial strain was isolated from hydrocarbon-contaminated soil from Terengganu, Malaysia. The whole genome of the bacterium was sequenced using Illumina HiSeq 2000 sequencing platform. The genome was assembled using de novo approach. The genome size of UMX-103 is 4,234,627 bp with 4399 genes comprising 4301 protein-coding genes and 98 RNA genes. The analysis of assembled genes revealed the presence of 25 genes involved in biosurfactant production, where 14 of the genes are related to biosynthesis and 11 of the genes are in the regulation of biosurfactant productions. This draft genome will provide insights into the genetic bases of its biosurfactant-producing capabilities.
    Matched MeSH terms: Genome Size
  2. Fulltext Phenotypic and genetic characterizations of Streptococcus dysgalactiae strains isolated from fish collected in Japan and other Asian countries
    Abdelsalam M, Chen SC, Yoshida T
    FEMS Microbiol Lett, 2010 Jan;302(1):32-8.
    PMID: 19895643 DOI: 10.1111/j.1574-6968.2009.01828.x
    Lancefield group C Streptococcus dysgalactiae is an emerging fish pathogen, which was first isolated in 2002 in Japan. Streptococcus dysgalactiae isolates collected from diseased fish in Japan (n=12), Taiwan (n=12), China (n=2), Malaysia (n=3), and Indonesia (n=1) were characterized using biased sinusoidal field gel electrophoresis (BSFGE), sodA gene sequence analysis, and antimicrobial susceptibility. These isolates exhibited high phenotypic homogeneity irrespective of the countries from where the strains were collected. Seventeen isolates were found to be resistant to oxytetracycline and carried the tet(M) gene, except for the strains collected in Taiwan and the PP1564 strain collected in China. The sodA gene sequence analysis revealed that 23 isolates were identical, except for one Japanese isolate (KNH07902), in which a single nucleotide differed from that of the other isolates. Based on BSFGE typing by ApaI macrorestriction, the isolates - including the Japanese, Taiwanese, and Chinese isolates - could be grouped into one main cluster at a 70% similarity level. However, the macrorestriction genotypes of some isolates were apparently distinct from those of the main cluster.
    Matched MeSH terms: Genome, Bacterial
  3. Draft genome sequence of Parvularcula flava strain NH6-79 T, revealing its role as a cellulolytic enzymes producer
    Abdul Karim MH, Lam MQ, Chen SJ, Yahya A, Shahir S, Shamsir MS, et al.
    Arch Microbiol, 2020 Nov;202(9):2591-2597.
    PMID: 32607725 DOI: 10.1007/s00203-020-01967-z
    To date, the genus Parvularcula consists of 6 species and no potential application of this genus was reported. Current study presents the genome sequence of Parvularcula flava strain NH6-79 T and its cellulolytic enzyme analysis. The assembled draft genome of strain NH6-79 T consists of 9 contigs and 7 scaffolds with 3.68 Mbp in size and GC content of 59.87%. From a total of 3,465 genes predicted, 96 of them are annotated as glycoside hydrolases (GHs). Within these GHs, 20 encoded genes are related to cellulosic biomass degradation, including 12 endoglucanases (5 GH10, 4 GH5, and 3 GH51), 2 exoglucanases (GH9) and 6 β-glucosidases (GH3). In addition, highest relative enzyme activities (endoglucanase, exoglucanase, and β-glucosidase) were observed at 27th hour when the strain was cultured in the carboxymethyl cellulose/Avicel®-containing medium for 45 h. The combination of genome analysis with experimental studies indicated the ability of strain NH6-79 T to produce extracellular endoglucanase, exoglucanase, and β-glucosidase. These findings suggest the potential of Parvularcula flava strain NH6-79 T in cellulose-containing biomass degradation and that the strain could be used in cellulosic biorefining process.
    Matched MeSH terms: Genome, Bacterial/genetics*
  4. Isolation and characterization of novel microsatellite loci for Asian sea bass, Lates calcarifer from genome sequence survey database
    Abdul Rahman Z, Choay-Hoong L, Mat Khairuddin R, Ab Razak S, Othman AS
    J Genet, 2012 Aug;91(2):e82-5.
    PMID: 22932425
    Matched MeSH terms: Genome*
  5. Fulltext Dataset of complete genome assembly and analysis of mycobacterium tuberculosis strain SIT745/EAI1-MYS
    Abdullah M, Suraiya S, Mohamad S, Harun A
    Data Brief, 2020 Aug;31:105949.
    PMID: 32671154 DOI: 10.1016/j.dib.2020.105949
    In this dataset, we report the genome assembly and data analysis of Mycobacterium tuberculosis strain SIT745/EAI1-MYS. Previously, this strain was isolated from a Malaysian patient with extra-pulmonary tuberculosis, and identification of this strain is done by spoligotype patterns with fifteen known Shared International Type (SITs). Further analysis showed that this strain has a remarkable phylogeographical specificity for Malaysia. Based on the National Center for Biotechnology Information (NCBI) nucleotide database information, the complete genome consists of 150 contigs with various sequence lengths and was not assembled. In this assembly, the aforementioned contigs along with reference sequence from Mycobacterium tuberculosis strain H37Rv and Mycobacterium bovis strain AF2122/97 was used for gap closures, were assembled into a single circular chromosome length of approximately 4.42 Mega bases (Mb) with an average GC content of 65.6%. The single circular chromosome was shown to contain 4,009 protein-coding sequences, 3 ribosomal RNAs, 45 transfer RNAs, and 12 superclasses distributed with 277 subsystems which constitute nearly 1900 genes, respectively. The genome information will provide fundamental knowledge of this organism as well as insight for understanding genomic and proteomic profiling, phylogenetic relationship.
    Matched MeSH terms: Genome
  6. Fulltext Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
    Abdullah-Zawawi MR, Ahmad-Nizammuddin NF, Govender N, Harun S, Mohd-Assaad N, Mohamed-Hussein ZA
    Sci Rep, 2021 10 04;11(1):19678.
    PMID: 34608238 DOI: 10.1038/s41598-021-99206-y
    Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon-intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.
    Matched MeSH terms: Genome-Wide Association Study*
  7. Fulltext Investigation of DNA prepared from human cytomegalovirus infected cells
    AbuBakar S
    JUMMEC, 1996;1:21-24.
    The effects of human cytomegalovirus (HCMV) infection on human fibroblast cell genomes were investigated using agarose gel electrophoresis. At selected intervals post-infection (PI), cellular D N A from mock-treated and HCMV-infected cells were prepared in low melting point agarose plugs. Results obtained following electrophoresis of the cellular D N A indicate that HCMV infection did not result in extensive degradation of the cellular DNA, even in samples obtained from cells which showed > 95% cytopathologic effects. High molecular weight DNA (> 23 Kb) comparable to that of the mock-treated samples were noted in a l l HCMV infected DNA samples. Digestion of the DNA samples with restriction endonucleases, EcoR I, Not I, Sfi I, and Nru I, however, resulted in the appearance of smaller DNA fragments (< 23 Kb) in samples obtained on day 3, 4, and 5 PI. Since these DNA bands appeared only in the infected cells, it was likely that these were the HCMV genomic DNA fragments. Findings presented in this study support the notion that the cellular DNA of HCMVinfected cells could remained intact and functiona. KEYWORDS: Cytomegalovirus, chromosomes, DNA, genomes, restriction enzymes
    Matched MeSH terms: Genome
  8. Isolation and molecular identification of Nipah virus from pigs
    AbuBakar S, Chang LY, Ali AR, Sharifah SH, Yusoff K, Zamrod Z
    Emerg Infect Dis, 2004 Dec;10(12):2228-30.
    PMID: 15663869
    Nipah viruses from pigs from a Malaysian 1998 outbreak were isolated and sequenced. At least two different Nipah virus strains, including a previously unreported strain, were identified. The findings highlight the possibility that the Malaysia outbreaks had two origins of Nipah virus infections.
    Matched MeSH terms: Genome, Viral*
  9. Fulltext Towards precision medicine: from quantitative imaging to radiomics
    Acharya UR, Hagiwara Y, Sudarshan VK, Chan WY, Ng KH
    J Zhejiang Univ Sci B, 2018 1 9;19(1):6-24.
    PMID: 29308604 DOI: 10.1631/jzus.B1700260
    Radiology (imaging) and imaging-guided interventions, which provide multi-parametric morphologic and functional information, are playing an increasingly significant role in precision medicine. Radiologists are trained to understand the imaging phenotypes, transcribe those observations (phenotypes) to correlate with underlying diseases and to characterize the images. However, in order to understand and characterize the molecular phenotype (to obtain genomic information) of solid heterogeneous tumours, the advanced sequencing of those tissues using biopsy is required. Thus, radiologists image the tissues from various views and angles in order to have the complete image phenotypes, thereby acquiring a huge amount of data. Deriving meaningful details from all these radiological data becomes challenging and raises the big data issues. Therefore, interest in the application of radiomics has been growing in recent years as it has the potential to provide significant interpretive and predictive information for decision support. Radiomics is a combination of conventional computer-aided diagnosis, deep learning methods, and human skills, and thus can be used for quantitative characterization of tumour phenotypes. This paper discusses the overview of radiomics workflow, the results of various radiomics-based studies conducted using various radiological images such as computed tomography (CT), magnetic resonance imaging (MRI), and positron-emission tomography (PET), the challenges we are facing, and the potential contribution of radiomics towards precision medicine.
    Matched MeSH terms: Genome
  10. Fulltext Circulating Metabolic Biomarkers of Screen-Detected Prostate Cancer in the ProtecT Study
    Adams CD, Richmond R, Ferreira DLS, Spiller W, Tan V, Zheng J, et al.
    Cancer Epidemiol Biomarkers Prev, 2019 Jan;28(1):208-216.
    PMID: 30352818 DOI: 10.1158/1055-9965.EPI-18-0079
    BACKGROUND: Whether associations between circulating metabolites and prostate cancer are causal is unknown. We report on the largest study of metabolites and prostate cancer (2,291 cases and 2,661 controls) and appraise causality for a subset of the prostate cancer-metabolite associations using two-sample Mendelian randomization (MR).

    METHODS: The case-control portion of the study was conducted in nine UK centers with men ages 50-69 years who underwent prostate-specific antigen screening for prostate cancer within the Prostate Testing for Cancer and Treatment (ProtecT) trial. Two data sources were used to appraise causality: a genome-wide association study (GWAS) of metabolites in 24,925 participants and a GWAS of prostate cancer in 44,825 cases and 27,904 controls within the Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium.

    RESULTS: Thirty-five metabolites were strongly associated with prostate cancer (P < 0.0014, multiple-testing threshold). These fell into four classes: (i) lipids and lipoprotein subclass characteristics (total cholesterol and ratios, cholesterol esters and ratios, free cholesterol and ratios, phospholipids and ratios, and triglyceride ratios); (ii) fatty acids and ratios; (iii) amino acids; (iv) and fluid balance. Fourteen top metabolites were proxied by genetic variables, but MR indicated these were not causal.

    CONCLUSIONS: We identified 35 circulating metabolites associated with prostate cancer presence, but found no evidence of causality for those 14 testable with MR. Thus, the 14 MR-tested metabolites are unlikely to be mechanistically important in prostate cancer risk.

    IMPACT: The metabolome provides a promising set of biomarkers that may aid prostate cancer classification.

    Matched MeSH terms: Genome-Wide Association Study
  11. Fulltext Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber
    Adedze YMN, Lu X, Xia Y, Sun Q, Nchongboh CG, Alam MA, et al.
    Sci Rep, 2021 02 16;11(1):3872.
    PMID: 33594240 DOI: 10.1038/s41598-021-83313-x
    Insertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line '9930' and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.
    Matched MeSH terms: Genome, Plant*
  12. Fulltext Simple and cost-effective restriction endonuclease analysis of human adenoviruses
    Adhikary AK, Hanaoka N, Fujimoto T
    Biomed Res Int, 2014;2014:363790.
    PMID: 24734232 DOI: 10.1155/2014/363790
    Restriction endonuclease analyses (REAs) constitute the only inexpensive molecular approach capable of typing and characterizing human adenovirus (HAdV) strains based on the entire genome. However, the application of this method is limited by the need for time-consuming and labor-intensive procedures. We herein developed a simple and cost-effective REA for assessing HAdV. The method consists of (1) simple and cost-effective DNA extraction, (2) fast restriction endonuclease (RE) digestion, and (3) speedy mini agarose gel electrophoresis. In this study, DNA was isolated according to the kit-based method and 21.0 to 28.0  μg of viral DNA was extracted from prototypes (HAdV-1, HAdV-3, HAdV-4, and HAdV-37) in each flask. The amount of DNA ranged from 11.4 to 57.0  μg among the HAdV-3 (n=73) isolates. The obtained viral DNA was found to be applicable to more than 10 types of REAs. Fast-cut restriction endonucleases (REs) were able to digest the DNA within 15 minutes, and restriction fragments were easily separated via horizontal mini agarose gel electrophoresis. The whole procedure for 10 samples can be completed within approximately six hours (the conventional method requires at least two days). These results show that our REA is potentially applicable in many laboratories in which HAdVs are isolated.
    Matched MeSH terms: Genome; Genome, Viral
  13. Genomic diversity of human adenovirus type 3 isolated in Fukui, Japan over a 24-year period
    Adhikary AK
    J Med Microbiol, 2017 Nov;66(11):1616-1622.
    PMID: 29068283 DOI: 10.1099/jmm.0.000625
    Recently, human adenovirus type 3 (HAdV-3) has become the most isolated HAdV worldwide. Restriction endonuclease analysis of globally isolated strains of HAdV-3 has uncovered 51 genome types to date. Information on the genome type is important to the epidemiological study of HAdV-3. In this study, analysis of 75 isolates of HAdV- 3 collected over a 24-year period in Fukui revealed: (1) the emergence of three novel genome types (HAdV-3a52, HAdV-3a53 and HAdV-3a54) and two known genome types (HAdV-3a and HAdV-3a54); (2) the spectrum of diseases caused by individual genome types and their major involvement in the paediatric age population; and (3) the co-circulation and replacement of genome types as a usual phenomenon. The rising number of HAdV-3 genome types indicates that the genetic variation of HAdV-3 is more than other HAdVs. Considering the clinical importance of HAdV-3 infection, its genetic diversity underscores the need for its continuous surveillance and genetic characterization.
    Matched MeSH terms: Genome, Viral*
  14. Fulltext Macrogenomic evidence for the origin of the black fly Simulium suzukii (Diptera: Simuliidae) on Okinawa Island, Japan
    Adler PH, Huang YT, Reeves WK, Kim SK, Otsuka Y, Takaoka H
    PLoS One, 2013;8(8):e70765.
    PMID: 23951001 DOI: 10.1371/journal.pone.0070765
    To determine the geographic origin of the black fly Simulium suzukii on Okinawa Island, Japan, macrogenomic profiles derived from its polytene chromosomes were compared with those of mainland and other insular populations of S. suzukii and of the isomorphic Simulium tani species complex. The Okinawan population is a chromosomally unique cytoform, designated 'D,' which is essentially monomorphic and differs by about 27 fixed rearrangements from the chromosomal standard sequence for the subgenus Simulium and by two fixed differences from its nearest known relative, representing the type of S. suzukii, on the main islands of Japan. Chromosomal band sequences revealed two additional, sympatric cytoforms of S. suzukii, designated 'A' and 'B,' each with species status, in Korea, and a third cytoform, designated 'C,' on Hokkaido, Japan. A new cytoform, 'K,' of S. tani from Malaysia, representing the type of S. tani, is more closely related to cytoforms in Thailand, as are populations from Taiwan previously treated as S. suzukii but more closely aligned with S. tani and newly recognized as cytoform 'L' of the latter nominal species. Rooting of chromosomal band sequences by outgroup comparisons allowed directionality of chromosomal rearrangements to be established, enabling phylogenetic inference of cytoforms. Of 41 macrogenomic rearrangements discovered in the five new cytoforms, four provide evidence for a stepwise origin of the Okinawan population from populations characteristic of the main islands of Japan. The macrogenomic approach applied to black flies on Okinawa Island illustrates its potential utility in defining source areas for other species of flies including those that might pose medical and veterinary risks.
    Matched MeSH terms: Genome, Insect*
  15. Fulltext The Conserved Molecular Determinants of Virulence in Dengue Virus
    Ahmad Z, Poh CL
    Int J Med Sci, 2019;16(3):355-365.
    PMID: 30911269 DOI: 10.7150/ijms.29938
    Dengue virus belongs to the Flaviviridae family which also includes viruses such as the Zika, West Nile and yellow fever virus. Dengue virus generally causes mild disease, however, more severe forms of the dengue virus infection, dengue haemorrhagic fever (DHF) and dengue haemorrhagic fever with shock syndrome (DSS) can also occur, resulting in multiple organ failure and even death, especially in children. The only dengue vaccine available in the market, CYD-TDV offers limited coverage for vaccinees from 9-45 years of age and is only recommended for individuals with prior dengue exposure. A number of mutations that were shown to attenuate virulence of dengue virus in vitro and/or in vivo have been identified in the literature. The mutations which fall within the conserved regions of all four dengue serotypes are discussed. This review hopes to provide information leading to the construction of a live attenuated dengue vaccine that is suitable for all ages, irrespective of the infecting dengue serotype and prior dengue exposure.
    Matched MeSH terms: Genome, Viral
  16. Effects of different mycotoxins on humans, cell genome and their involvement in cancer (Review)
    Ahmed Adam MA, Tabana YM, Musa KB, Sandai DA
    Oncol Rep, 2017 Mar;37(3):1321-1336.
    PMID: 28184933 DOI: 10.3892/or.2017.5424
    The chemical nature of most of the mycotoxins makes them highly liposoluble compounds that can be absorbed from the site of exposure such as from the gastrointestinal and respiratory tract to the blood stream where it can be dissimilated throughout the body and reach different organs such as the liver and kidneys. Mycotoxins have a strong tendency and ability to penetrate the human and animal cells and reach the cellular genome where it causes a major mutagenic change in the nucleotide sequence which leads to strong and permanent defects in the genome. This defect will eventually be transcribed, translated and lead to the development of cancer. In this review, the chemical and physical nature of mycotoxins, the action of mycotoxins on the cellular genome and its effect on humans, mycotoxins and their carcinogenicity and mycotoxins research gaps are discussed, and new research areas are suggested. The research review posed various questions. What are the different mycotoxins that can cause cancer, what is the role of mycotoxins in causing cancer and what types of cancers can be caused by mycotoxins? These questions have been selected due to the significant increase in the mycotoxin contamination and the cancer incidence rate in the contemporary world. By revealing and understanding the role of mycotoxins in developing cancer, measures to reduce the risks and incidents of cancer could be taken.
    Matched MeSH terms: Genome, Human/drug effects*; Genome, Human/genetics
  17. Helicobacter pylori in 2013: multiplying genomes, emerging insights
    Ahmed N, Loke MF, Kumar N, Vadivelu J
    Helicobacter, 2013 Sep;18 Suppl 1:1-4.
    PMID: 24011237 DOI: 10.1111/hel.12069
    We describe features of key additions to the existing pool of publicly accessible Helicobacter pylori genome sequences and sequences of Helicobacter pylori phages from April 2012 to March 2013. In addition, important studies involving H. pylori genomes, especially those pertaining to genomic diversity, disease outcome, H. pylori population structure and evolution are reviewed. High degree of homologous recombination contributes to increased diversity of H. pylori genomes. New methods of resolving H. pylori population structure to an ultrafine level led to the proposal of new subpopulations. As the magnitude of diversity in the H. pylori gene pool becomes more and more clear, geographic and demographic factors should be brought to analysis while identifying disease-specific biomarkers and defining new virulence mechanisms.
    Matched MeSH terms: Genome, Bacterial*
  18. Contributions of IKZF1, DDC, CDKN2A, CEBPE, and LMO1 Gene Polymorphisms to Acute Lymphoblastic Leukemia in a Yemeni Population
    Al-Absi B, Razif MFM, Noor SM, Saif-Ali R, Aqlan M, Salem SD, et al.
    Genet Test Mol Biomarkers, 2017 Oct;21(10):592-599.
    PMID: 28768142 DOI: 10.1089/gtmb.2017.0084
    BACKGROUND: Genome-wide and candidate gene association studies have previously revealed links between a predisposition to acute lymphoblastic leukemia (ALL) and genetic polymorphisms in the following genes: IKZF1 (7p12.2; ID: 10320), DDC (7p12.2; ID: 1644), CDKN2A (9p21.3; ID: 1029), CEBPE (14q11.2; ID: 1053), and LMO1 (11p15; ID: 4004). In this study, we aimed to conduct an investigation into the possible association between polymorphisms in these genes and ALL within a sample of Yemeni children of Arab-Asian descent.

    METHODS: Seven single-nucleotide polymorphisms (SNPs) in IKZF1, three SNPs in DDC, two SNPs in CDKN2A, two SNPs in CEBPE, and three SNPs in LMO1 were genotyped in 289 Yemeni children (136 cases and 153 controls), using the nanofluidic Dynamic Array (Fluidigm 192.24 Dynamic Array). Logistic regression analyses were used to estimate ALL risk, and the strength of association was expressed as odds ratios with 95% confidence intervals.

    RESULTS: We found that the IKZF1 SNP rs10235796 C allele (p = 0.002), the IKZF1 rs6964969 A>G polymorphism (p = 0.048, GG vs. AA), the CDKN2A rs3731246 G>C polymorphism (p = 0.047, GC+CC vs. GG), and the CDKN2A SNP rs3731246 C allele (p = 0.007) were significantly associated with ALL in Yemenis of Arab-Asian descent. In addition, a borderline association was found between IKZF1 rs4132601 T>G variant and ALL risk. No associations were found between the IKZF1 SNPs (rs11978267; rs7789635), DDC SNPs (rs3779084; rs880028; rs7809758), CDKN2A SNP (rs3731217), the CEBPE SNPs (rs2239633; rs12434881) and LMO1 SNPs (rs442264; rs3794012; rs4237770) with ALL in Yemeni children.

    CONCLUSION: The IKZF1 SNPs, rs10235796 and rs6964969, and the CDKN2A SNP rs3731246 (previously unreported) could serve as risk markers for ALL susceptibility in Yemeni children.

    Matched MeSH terms: Genome-Wide Association Study/methods
  19. Initiating a Human Variome Project Country Node
    AlAama J, Smith TD, Lo A, Howard H, Kline AA, Lange M, et al.
    Hum Mutat, 2011 May;32(5):501-6.
    PMID: 21305654 DOI: 10.1002/humu.21463
    Genetic diseases are a pressing global health problem that requires comprehensive access to basic clinical and genetic data to counter. The creation of regional and international databases that can be easily accessed by clinicians and diagnostic labs will greatly improve our ability to accurately diagnose and treat patients with genetic disorders. The Human Variome Project is currently working in conjunction with human genetics societies to achieve this by establishing systems to collect every mutation reported by a diagnostic laboratory, clinic, or research laboratory in a country and store these within a national repository, or HVP Country Node. Nodes have already been initiated in Australia, Belgium, China, Egypt, Malaysia, and Kuwait. Each is examining how to systematically collect and share genetic, clinical, and biochemical information in a country-specific manner that is sensitive to local ethical and cultural issues. This article gathers cases of genetic data collection within countries and takes recommendations from the global community to develop a procedure for countries wishing to establish their own collection system as part of the Human Variome Project. We hope this may lead to standard practices to facilitate global collection of data and allow efficient use in clinical practice, research and therapy.
    Matched MeSH terms: Genome, Human/genetics*
  20. Current Genetic and Epigenetic Insights into Type 2 Diabetes Mellitus
    Alam F, Kamal MA, Islam MA, Banu S
    Endocr Metab Immune Disord Drug Targets, 2019;19(6):717-718.
    PMID: 31530259 DOI: 10.2174/187153031906190724104004
    Matched MeSH terms: Genome-Wide Association Study/methods; Genome-Wide Association Study/trends
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