Displaying publications 161 - 180 of 900 in total

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  1. Fulltext Annotated Sequence of Mycobacterium tuberculosis MTBR3/09 Isolated from a Sputum Sample in Malaysia
    Issa R, Seradja VH, Abdullah MK, Abdul H
    Genome Announc, 2016;4(3).
    PMID: 27340055 DOI: 10.1128/genomeA.00517-16
    This is a report of the annotated genome sequence of Mycobacterium tuberculosis MTBR3/09. The organism was isolated from a sputum sample in Malaysia.
    Matched MeSH terms: Genome, Bacterial
  2. Fulltext Genomic data of two Bacillus and two Pseudomonas strains isolated from the acid mine drainage site at Mamut Copper Mine, Ranau, Malaysia
    Low YY, Chin GJWL, Joseph CG, Musta B, Rodrigues KF
    Data Brief, 2020 Dec;33:106486.
    PMID: 33225029 DOI: 10.1016/j.dib.2020.106486
    The genomic data of four bacteria strains isolated from the abandoned Mamut Copper Mine, an Acid Mine Drainage (AMD) site is presented in this report. Two of these strains belong to the genus Bacillus, while the other two belong to the genus Pseudomonas. The draft genome size of Pseudomonas sp. strain MCMY3 was 6,396,595 bp (GC: 63.3%), Bacillus sp. strain MCMY6 was 6,815,573 bp (GC: 35.2%), Bacillus sp. strain MCMY13 was 5,559,059 bp (GC: 35.5%) and Pseudomonas sp. strain MCMY15 was 7,381,777 bp (GC: 64.8%). These four genomes contained 493, 495, 495 and 579 annotated subsystems, respectively. The sequence data are available at GenBank sequence read archive with accessions numbers SRX7859406, SRX7859404, SRX7859405 and SRX7293032 for strains MCMY3, MCMY6, MCMY13 and MCMY15, respectively.
    Matched MeSH terms: Genome Size
  3. Fulltext The complete chloroplast genome sequence of Chengal (Neobalanocarpus heimii, Dipterocarpaceae), a durable tropical hardwood
    Lee SY, Ng WL, Hishamuddin MS, Mohamed R
    Mitochondrial DNA B Resour, 2019;4(1):19-20.
    PMID: 33365402 DOI: 10.1080/23802359.2018.1535848
    Known for its durable timber quality, Neobalanocarpus heimii (King) Ashton is a highly sought after tree species endemic to the Malay Peninsula. Due to its scarcity and high value, the tree is classified under the IUCN Red List categories of Vulnerable. In this study, we assembled the complete chloroplast (cp) genome of N. heimii using data from high-throughput Illumina sequencing. The Chengal cp genome is 151,191 bp in size and includes two inverted repeat regions of 23,721 bp each, which is separated by a large single copy region of 83,801 bp and a small single copy region of 19,948 bp. A total of 130 genes were predicted, including 37 tRNA, 8 rRNA, and 85 protein-coding genes. Phylogenetic analysis placed N. heimii within the order Malvales.
    Matched MeSH terms: Genome, Chloroplast
  4. Fulltext The whole mitochondrial genome and phylogenetic analysis of Lupocycloporus gracilimanus (Stimpson, 1858) (Decapoda, portunidae)
    Guan M, Tan H, Fazhan H, Xie Z, Shi X, Zhang Y, et al.
    Mitochondrial DNA B Resour, 2018 Oct 26;3(2):1244-1245.
    PMID: 33474478 DOI: 10.1080/23802359.2018.1532345
    The mitochondrial genome plays an important role in studies on phylogeography and population genetic diversity. Here we report the complete mitochondrial genome of Lupocycloporus gracilimanus (Stimpson, 1858) which is the first mitochondrial genome reported in genus Lupocycloporus by now. The mitogenome is 15,990 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. The phylogenetic analysis showed that L. gracilimanus was closest to genus Scylla. The present research should provide valuable information for phylogenetic analysis and classification of Portunidae.
    Matched MeSH terms: Genome, Mitochondrial
  5. Fulltext The complete mitochondrial genome of the snakeskin gourami, Trichopodus pectoralis (Regan 1910) (Teleostei: Osphronemidae)
    Gan HM, Amornsakun T, Tan MP
    Mitochondrial DNA B Resour, 2017 Mar 17;2(1):148-149.
    PMID: 33473747 DOI: 10.1080/23802359.2017.1298418
    We sequenced and assembled three whole mitogenome sequences of the commercially important snakeskin gourami Trichopodus pectoralis isolated from Malaysia (introduced), Viet Nam (native) and Thailand (native). The mitogenome length range from 16,397 to 16,420 bp. The final partitioned nucleotide alignment consists of 14,002 bp and supports the monophyly of the genus Trichopodus (95% ultrafast bootstrap support) with T. trichopterus forming a sister group with the members of T. pectoralis.
    Matched MeSH terms: Genome, Mitochondrial
  6. Fulltext Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana
    Biswas MK, Bagchi M, Biswas D, Harikrishna JA, Liu Y, Li C, et al.
    Genes (Basel), 2020 12 09;11(12).
    PMID: 33317074 DOI: 10.3390/genes11121479
    Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
    Matched MeSH terms: Genome, Plant/genetics; Genome-Wide Association Study/methods
  7. Fulltext Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTB221/11 Isolated from a Cerebrospinal Fluid Sample in Malaysia
    Issa R, Seradja VH, Abdullah MK
    Genome Announc, 2016;4(3).
    PMID: 27365342 DOI: 10.1128/genomeA.00376-16
    Here, we report of the annotated genome sequence of Mycobacterium tuberculosis MTB221/11. The organism was isolated from the cerebrospinal fluid of a patient in Malaysia.
    Matched MeSH terms: Genome, Bacterial
  8. 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
  9. Fulltext Molecular conservation strategies for Malaysian endemic species
    Rodrigues, K. F.
    Buletin Persatuan Genetik Malaysia, 2008;14(1):4-8.
    MyJurnal
    Molecular techniques involving the application of DNA based molecular markers for the conservation and management of endemic and endangered species have assumed significance as
    genome sequencing projects have generated an extensive database which can be mined for informative genomic regions. Scientific approaches towards conservation involve several stages, which encompass determination of appropriate genomic regions for characterization, design and testing of specific molecular markers, screening of multiple populations and statistical treatment and
    interpretation of data. Population data can be utilized to develop controlled breeding and relocation programs aimed at ensuring that genetic diversity within populations of endangered species is
    sustained within the context of an overall conservation program. The information derived as a result of this approach can be applied to establish a scientific and legal framework for the conservation of endemic species. Species specific genomic markers can be applied to enforce the implementation of CITES within the guidelines of a national biodiversity conservation policy.
    Matched MeSH terms: Genome
  10. Fulltext Human variome project and launching of it’s Malaysian node; towards a new horizon of genetics in Malaysia
    Atif A. B., Halim-Fikri A H, Zilfalil BA
    Buletin Persatuan Genetik Malaysia, 2010;17(1):9-11.
    MyJurnal
    In the human genome, point variations are most common (Nachman & Crowell, 2000) and well understood. These variations, when existing in more than 1% of the population, is referred to as
    Single Nucleotide Polymorphism (SNP) and can fall in the coding region of a gene, non coding region or intergenic regions.
    Matched MeSH terms: Genome, Human
  11. Integrative Multi-Omics Through Bioinformatics
    Goh HH
    Adv Exp Med Biol, 2018 11 2;1102:69-80.
    PMID: 30382569 DOI: 10.1007/978-3-319-98758-3_5
    This chapter introduces different aspects of bioinformatics with a brief discussion in the systems biology context. Example applications in network pharmacology of traditional Chinese medicine, systems metabolic engineering, and plant genome-scale modelling are described. Lastly, this chapter concludes on how bioinformatics helps to integrate omics data derived from various studies described in previous chapters for a holistic understanding of secondary metabolite production in P. minus.
    Matched MeSH terms: Genome, Plant
  12. Fulltext Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave
    Tan KK, Tan JY, Wong JE, Teoh BT, Tiong V, Abd-Jamil J, et al.
    Sci Rep, 2021 11 11;11(1):22105.
    PMID: 34764315 DOI: 10.1038/s41598-021-01223-4
    The COVID-19 pandemic first emerged in Malaysia in Jan 2020. As of 12th Sept 2021, 1,979,698 COVID-19 cases that occurred over three major epidemic waves were confirmed. The virus contributing to the three epidemic waves has not been well-studied. We sequenced the genome of 22 SARS-CoV-2 strains detected in Malaysia during the second and the ongoing third wave of the COVID-19 epidemic. Detailed phylogenetic and genetic variation analyses of the SARS-CoV-2 isolate genomes were performed using these newly determined sequences and all other available sequences. Results from the analyses suggested multiple independent introductions of SARS-CoV-2 into Malaysia. A new B.1.524(G) lineage with S-D614G mutation was detected in Sabah, East Malaysia and Selangor, Peninsular Malaysia on 7th October 2020 and 14th October 2020, respectively. This new B.1.524(G) group was not the direct descendant of any of the previously detected lineages. The new B.1.524(G) carried a set of genetic variations, including A701V (position variant frequency = 0.0007) in Spike protein and a novel G114T mutation at the 5'UTR. The biological importance of the specific mutations remained unknown. The sequential appearance of the mutations, however, suggests that the spread of the new B.1.524(G) lineages likely begun in Sabah and then spread to Selangor. The findings presented here support the importance of SARS-CoV-2 full genome sequencing as a tool to establish an epidemiological link between cases or clusters of COVID-19 worldwide.
    Matched MeSH terms: Genome, Viral
  13. Fulltext Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations
    Teo YY, Sim X, Ong RT, Tan AK, Chen J, Tantoso E, et al.
    Genome Res, 2009 Nov;19(11):2154-62.
    PMID: 19700652 DOI: 10.1101/gr.095000.109
    The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.
    Matched MeSH terms: Genome, Human/genetics*; Genome-Wide Association Study/methods
  14. Fulltext Draft Genome Sequence of Rhizoctonia solani Anastomosis Group 1 Subgroup 1A Strain 1802/KB Isolated from Rice
    Nadarajah K, Mat Razali N, Cheah BH, Sahruna NS, Ismail I, Tathode M, et al.
    Genome Announc, 2017 Oct 26;5(43).
    PMID: 29074665 DOI: 10.1128/genomeA.01188-17
    Sheath blight, caused by Rhizoctonia solani anastomosis group 1 subgroup 1A (AG1-1A), is one of the most devastating rice diseases worldwide. Here, we report the draft genome sequence of R. solani AG1-1A strain 1802/KB isolated from a popular Malaysian rice variety. To the best of our knowledge, this is the second reported representative genome from AG1-1A.
    Matched MeSH terms: Genome
  15. Fulltext Phenotypic Characterization and Comparative Genomic Analysis of Novel Salmonella Bacteriophages Isolated from a Tropical Rainforest
    Mutusamy P, Banga Singh KK, Su Yin L, Petersen B, Sicheritz-Ponten T, Clokie MRJ, et al.
    Int J Mol Sci, 2023 Feb 12;24(4).
    PMID: 36835084 DOI: 10.3390/ijms24043678
    Salmonella infections across the globe are becoming more challenging to control due to the emergence of multidrug-resistant (MDR) strains. Lytic phages may be suitable alternatives for treating these multidrug-resistant Salmonella infections. Most Salmonella phages to date were collected from human-impacted environments. To further explore the Salmonella phage space, and to potentially identify phages with novel characteristics, we characterized Salmonella-specific phages isolated from the Penang National Park, a conserved rainforest. Four phages with a broad lytic spectrum (kills >5 Salmonella serovars) were further characterized; they have isometric heads and cone-shaped tails, and genomes of ~39,900 bp, encoding 49 CDSs. As the genomes share a <95% sequence similarity to known genomes, the phages were classified as a new species within the genus Kayfunavirus. Interestingly, the phages displayed obvious differences in their lytic spectrum and pH stability, despite having a high sequence similarity (~99% ANI). Subsequent analysis revealed that the phages differed in the nucleotide sequence in the tail spike proteins, tail tubular proteins, and portal proteins, suggesting that the SNPs were responsible for their differing phenotypes. Our findings highlight the diversity of novel Salmonella bacteriophages from rainforest regions, which can be explored as an antimicrobial agent against MDR-Salmonella strains.
    Matched MeSH terms: Genome, Viral
  16. Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus
    Tajuddin S, Khan AM, Chong LC, Wong CL, Tan JS, Ina-Salwany MY, et al.
    Appl Microbiol Biotechnol, 2023 Feb;107(2-3):749-768.
    PMID: 36520169 DOI: 10.1007/s00253-022-12312-3
    Vibrio alginolyticus is a Gram-negative bacterium commonly associated with mackerel poisoning. A bacteriophage that specifically targets and lyses this bacterium could be employed as a biocontrol agent for treating the bacterial infection or improving the shelf-life of mackerel products. However, only a few well-characterized V. alginolyticus phages have been reported in the literature. In this study, a novel lytic phage, named ΦImVa-1, specifically infecting V. alginolyticus strain ATCC 17749, was isolated from Indian mackerel. The phage has a short latent period of 15 min and a burst size of approximately 66 particles per infected bacterium. ΦImVa-1 remained stable for 2 h at a wide temperature (27-75 °C) and within a pH range of 5 to 10. Transmission electron microscopy revealed that ΦImVa-1 has an icosahedral head of approximately 60 nm in diameter with a short tail, resembling those in the Schitoviridae family. High throughput sequencing and bioinformatics analysis elucidated that ΦImVa-1 has a linear dsDNA genome of 77,479 base pairs (bp), with a G + C content of ~ 38.72% and 110 predicted gene coding regions (106 open reading frames and four tRNAs). The genome contains an extremely large virion-associated RNA polymerase gene and two smaller non-virion-associated RNA polymerase genes, which are hallmarks of schitoviruses. No antibiotic genes were found in the ΦImVa-1 genome. This is the first paper describing the biological properties, morphology, and the complete genome of a V. alginolyticus-infecting schitovirus. When raw mackerel fish flesh slices were treated with ΦImVa-1, the pathogen loads reduced significantly, demonstrating the potential of the phage as a biocontrol agent for V. alginolyticus strain ATCC 17749 in the food. KEY POINTS: • A novel schitovirus infecting Vibrio alginolyticus ATCC 17749 was isolated from Indian mackerel. • The complete genome of the phage was determined, analyzed, and compared with other phages. • The phage is heat stable making it a potential biocontrol agent in extreme environments.
    Matched MeSH terms: Genome, Viral
  17. Fulltext Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus
    Ge F, Guo R, Liang Y, Chen Y, Shao H, Sung YY, et al.
    Virus Res, 2023 Oct 15;336:199226.
    PMID: 37739268 DOI: 10.1016/j.virusres.2023.199226
    Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.
    Matched MeSH terms: Genome, Viral
  18. Fulltext Association of polygenic score for major depression with response to lithium in patients with bipolar disorder
    Amare AT, Schubert KO, Hou L, Clark SR, Papiol S, Cearns M, et al.
    Mol Psychiatry, 2021 Jun;26(6):2457-2470.
    PMID: 32203155 DOI: 10.1038/s41380-020-0689-5
    Lithium is a first-line medication for bipolar disorder (BD), but only one in three patients respond optimally to the drug. Since evidence shows a strong clinical and genetic overlap between depression and bipolar disorder, we investigated whether a polygenic susceptibility to major depression is associated with response to lithium treatment in patients with BD. Weighted polygenic scores (PGSs) were computed for major depression (MD) at different GWAS p value thresholds using genetic data obtained from 2586 bipolar patients who received lithium treatment and took part in the Consortium on Lithium Genetics (ConLi+Gen) study. Summary statistics from genome-wide association studies in MD (135,458 cases and 344,901 controls) from the Psychiatric Genomics Consortium (PGC) were used for PGS weighting. Response to lithium treatment was defined by continuous scores and categorical outcome (responders versus non-responders) using measurements on the Alda scale. Associations between PGSs of MD and lithium treatment response were assessed using a linear and binary logistic regression modeling for the continuous and categorical outcomes, respectively. The analysis was performed for the entire cohort, and for European and Asian sub-samples. The PGSs for MD were significantly associated with lithium treatment response in multi-ethnic, European or Asian populations, at various p value thresholds. Bipolar patients with a low polygenic load for MD were more likely to respond well to lithium, compared to those patients with high polygenic load [lowest vs highest PGS quartiles, multi-ethnic sample: OR = 1.54 (95% CI: 1.18-2.01) and European sample: OR = 1.75 (95% CI: 1.30-2.36)]. While our analysis in the Asian sample found equivalent effect size in the same direction: OR = 1.71 (95% CI: 0.61-4.90), this was not statistically significant. Using PGS decile comparison, we found a similar trend of association between a high genetic loading for MD and lower response to lithium. Our findings underscore the genetic contribution to lithium response in BD and support the emerging concept of a lithium-responsive biotype in BD.
    Matched MeSH terms: Genome-Wide Association Study
  19. Reassortment and genomic analysis of a G9P[8]-E2 rotavirus isolated in China
    Peng R, Li D, Wang J, Xiong G, Wang M, Liu D, et al.
    Virol J, 2023 Jun 22;20(1):135.
    PMID: 37349792 DOI: 10.1186/s12985-023-02064-5
    OBJECTIVE: To isolate a prevalent G9P[8] group A rotavirus (RVA) (N4006) in China and investigate its genomic and evolutionary characteristics, with the goal of facilitating the development of a new rotavirus vaccine.

    METHODS: The RVA G9P[8] genotype from a diarrhea sample was passaged in MA104 cells. The virus was evaluated by TEM, polyacrylamide gel electrophoresis, and indirect immunofluorescence assay. The complete genome of virus was obtained by RT-PCR and sequencing. The genomic and evolutionary characteristics of the virus were evaluated by nucleic acid sequence analysis with MEGA ver. 5.0.5 and DNASTAR software. The neutralizing epitopes of VP7 and VP4 (VP5* and VP8*) were analyzed using BioEdit ver. 7.0.9.0 and PyMOL ver. 2.5.2.

    RESULTS: The RVA N4006 (G9P[8] genotype) was adapted in MA104 cells with a high titer (105.5 PFU/mL). Whole-genome sequence analysis showed N4006 to be a reassortant rotavirus of Wa-like G9P[8] RVA and the NSP4 gene of DS-1-like G2P[4] RVA, with the genotype constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2). Phylogenetic analysis indicated that N4006 had a common ancestor with Japanese G9P[8]-E2 rotavirus. Neutralizing epitope analysis showed that VP7, VP5*, and VP8* of N4006 had low homology with vaccine viruses of the same genotype and marked differences with vaccine viruses of other genotypes.

    CONCLUSION: The RVA G9P[8] genotype with the G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2) constellation predominates in China and may originate from reassortment between Japanese G9P[8] with Japanese DS-1-like G2P[4] rotaviruses. The antigenic variation of N4006 with the vaccine virus necessitates an evaluation of the effect of the rotavirus vaccine on G9P[8]-E2 genotype rotavirus.

    Matched MeSH terms: Genome, Viral
  20. Fulltext Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors
    Mullins N, Kang J, Campos AI, Coleman JRI, Edwards AC, Galfalvy H, et al.
    Biol Psychiatry, 2022 Feb 01;91(3):313-327.
    PMID: 34861974 DOI: 10.1016/j.biopsych.2021.05.029
    BACKGROUND: Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders.

    METHODS: We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors.

    RESULTS: Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged.

    CONCLUSIONS: Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.

    Matched MeSH terms: Genome-Wide Association Study
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