BMC genomic data最新文献

{"title":"AgroLD: a knowledge graph for the plant sciences.","authors":"Larmande Pierre, Pittolat Bertrand, Tando Ndomassi, Pomie Yann, Happi Happi Bill Gates, Guignon Valentin, Ruiz Manuel","doi":"10.1186/s12863-025-01359-6","DOIUrl":"10.1186/s12863-025-01359-6","url":null,"abstract":"<p><strong>Background: </strong>The demand for food is expected to grow substantially in the coming years. To address this challenge, especially in the context of climate change, a deeper understanding of genotype-phenotype relationships is crucial for improving crop yields. Recent advances in high-throughput technologies have transformed the landscape of plant science research. However, there is an urgent need to integrate and consolidate complementary data to understand the biological system.</p><p><strong>Results: </strong>We introduce AgroLD, a knowledge graph that uses Semantic Web technologies to seamlessly integrate plant science data. AgroLD is designed to facilitate hypothesis formulation and validation within the scientific community. With approximately 1.08 billion triples, it integrates and annotates data from more than 151 datasets across 19 distinct sources.</p><p><strong>Conclusion: </strong>The overarching goal is to provide a specialized knowledge platform addressing complex biological questions in the plant sciences, including gene participation in plant disease resistance and adaptive responses to climate change.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 Suppl 1","pages":"73"},"PeriodicalIF":2.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gradient responsive regularization: a deep learning framework for codon frequency based classification of evolutionarily conserved genes.","authors":"Anjum Shahzad, Tahir Mehmood, Sheeraz Akram","doi":"10.1186/s12863-025-01358-7","DOIUrl":"10.1186/s12863-025-01358-7","url":null,"abstract":"","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"72"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12490169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of transcriptome and metabolome analysis reveals the genes and pathways regulating flavonoids biosynthesis in Cinnamomum camphora.","authors":"Huiping Huang, Xinnan Yang, Zerui Yang","doi":"10.1186/s12863-025-01364-9","DOIUrl":"10.1186/s12863-025-01364-9","url":null,"abstract":"<p><strong>Backgroud: </strong>Although Cinnamomum camphora's metabolic composition has been well studied, flavonoid distribution across its tissues remains poorly understood. This study combined transcriptome and metabolomic analyses on leaf, stem, and root tissues to uncover the synthesis pathway of flavonoids and to identify key regulatory genes.</p><p><strong>Results: </strong>Metabolomic analysis revealed 2,893 metabolites, which can be divided into secondary metabolite 1,213(41.93%), primary metabolite: 622 (21.50%) and others: 1,058 (36.57%). As for the secondary metabolite, flavonoids were the most abundant (28%), followed by terpenoids (27%) and phenolic acids (12%). Differential metabolites were identified using VIP > 1, |log2 fold change|≥ 1, and p < 0.05 criteria, showing tissue-specific flavonoids distribution. For example, rutin, quercetin 3-o-alpha-l-rhamnoside, and quercetin were abundant in leaves and stems, while 2-hydroxyisoflavanone naringenin, fustin, and catechin were predominant in roots. Transcriptome analysis indicated that a total of 2,043 differentially expressed genes (DEGs) were identified, with the most considerable number found in the leaf-to-root comparison. The KEGG enrichment analysis of DEGs showed significant changes in pathways related to flavonoid and phenylpropanoid biosynthesis. Correlation analysis indicated that key enzyme genes including CcPAL_1, CcF3H_1, CcF3_H, CcCHS_1, CcC4H_2, CcANR_1, Cc4CL_9, Cc4CL_7 and Cc4CL_1 play positive regulatory roles in the accumulation of downstream metabolites, whereas CcPAL_4, CcPAL_2 and CcC4H_1 exert negative regulation on downstream metabolites. In addition, we have identified several bHLH and MYB transcription factors that may regulate flavonoid biosynthesis. Finally, qRT-PCR validation confirmed the RNA sequencing results.</p><p><strong>Conclusions: </strong>This research elucidates the spatial variations in the accumulation profiles of flavonoid metabolites across different tissues and offers crucial insights into the regulatory mechanisms of flavonoid metabolism in C. camphora. Consequently, it laid a foundation for further research on the flavonoid biosynthetic pathway of C. camphora.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"71"},"PeriodicalIF":2.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145194066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High exposure variance enables candidate biomarker detection in a small EWAS of methylmercury-exposed Peruvian adults.","authors":"Caren Weinhouse, Luiza Perez, Ian Ryde, Jaclyn M Goodrich, J Jaime Miranda, Heileen Hsu-Kim, Susan K Murphy, Joel N Meyer, William K Pan","doi":"10.1186/s12863-025-01352-z","DOIUrl":"10.1186/s12863-025-01352-z","url":null,"abstract":"<p><strong>Background: </strong>Epigenome-wide association studies (EWAS) are a highly promising approach that can inform precision environmental health. However, current EWAS are underpowered and increasing sample sizes will require substantial resources. Therefore, alternative approaches for identifying candidate biomarkers through EWAS are critical. Here, we provide proof of principle that maximizing exposure variance in EWAS enables effective candidate biomarker detection, even in small sample sizes.</p><p><strong>Methods: </strong>We profiled genome-wide DNA methylation in whole blood from individuals from Madre de Dios, Peru, with either high methylmercury (MeHg) exposure (> 10 µg/g total hair mercury; N = 16) or low MeHg exposure (< 1 µg/g total hair mercury; N = 16).</p><p><strong>Results: </strong>We identified nine differentially methylated CpG sites (FDR < 0.05), which is comparable to the number identified by much larger EWAS. The most significantly different CpG site was in an intronic enhancer of the SLC5A7 gene, which encodes the L-type amino acid transporter 1 (LAT1) that facilitates MeHg transport. Our Gene Ontology and transcription factor motif enrichment analyses identified genes involved in outcomes linked to MeHg toxicity, including immune response, neurotoxicity, and type 2 diabetes (T2D).</p><p><strong>Conclusions: </strong>Similar EWAS in global populations with known high exposure variance can be leveraged to develop targeted, custom sequencing panels and microarrays limited to replicated, validated biomarkers of a given exposure.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"68"},"PeriodicalIF":2.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145194021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence of Streptococcus hominis isolated from subgingival biofilm.","authors":"Seok Bin Yang, Doyun Ku, Ji-Hoi Moon, Jae-Hyung Lee, Sang Wook Kang, Hak Kyun Kim, Kyu Hwan Kwack","doi":"10.1186/s12863-025-01367-6","DOIUrl":"10.1186/s12863-025-01367-6","url":null,"abstract":"<p><strong>Objective: </strong>Streptococcus hominis is a recently described species within the genus Streptococcus, yet its genomic characteristics remain poorly understood, particularly in the context of the oral microbiome. Previously, only two complete genomes from non-oral sources were available. To address this gap, we sequenced and analyzed S. hominis strain KHUD_010, isolated from the subgingival biofilm of a healthy Korean adult.</p><p><strong>Data description: </strong>Genomic DNA from KHUD_010 was extracted and confirmed as S. hominis by 16 S rRNA gene sequencing. Whole-genome sequencing using the PacBio Sequel II platform generated 135,974 HiFi reads (N50: 10,345 bp). De novo assembly with SMRT Link v11.0 produced a single circular chromosome of 1,883,665 bp with 39.04% GC content. Annotation via the NCBI Prokaryotic Genome Annotation Pipeline predicted 1,793 protein-coding genes, four rRNA operons (5 S, 16 S, 23 S), and 120 tRNAs. BUSCO analysis showed 99.1% completeness. Comparative genomics with NSJ-17 and UMB6992B revealed 1,416 core, 223 dispensable, and 398 strain-specific gene clusters. KHUD_010 harbored 18 unique gene clusters comprising 20 genes, mostly assigned to COG category L (replication, recombination, repair). This high-quality genome expands the genomic landscape of S. hominis and provides a valuable reference for future studies on oral microbiome diversity and host adaptation.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"69"},"PeriodicalIF":2.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145193983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome characterization and metabolite accumulation: novel insights into metabolite biosynthesis during Angiopteris fokiensis leaf development.","authors":"Hongyu Chen, Ye Yang, Bo Wang, Ying Yu, Qingwen Sun","doi":"10.1186/s12863-025-01366-7","DOIUrl":"10.1186/s12863-025-01366-7","url":null,"abstract":"<p><strong>Background: </strong>Leafdevelopment represents a crucial stage in the plant life cycle, involving complex morphogenetic and physiological processes governed by evolving molecular mechanisms and metabolite profiles. The growth and maturation of Angiopteris fokiensis Hieron, a species used in traditional Chinese medicine, are characterized by fluctuating metabolite accumulation patterns regulated by largely unknown molecular pathways.</p><p><strong>Results: </strong>Touncover these pathways, we employed next-generation sequencing to construct the A. fokiensis leaf transcriptome at two distinct developmental stages, allowing for a comprehensive analysis of gene expression dynamics while emphasizing the identification of genes that regulate leaf development and metabolite synthesis. The de novo assembly of high-quality sequencing reads generated 117,627 unigenes averaging 1,308 base pairs in length. FPKM analysis uncovered significant transcriptomic alterations during leaf development. Additionally, non-targeted metabolomics identified 1,494 distinct analytes, with lipids representing the most abundant metabolite class in both A. fokiensis samples. In the 'phenylalanine, tyrosine and tryptophan biosynthesis' pathway, two downregulated arogenate dehydrogenase (NADP+) genes (Unigene23378-S4 and Unigene47537-S2) in Stage1 correlated with reduced L-tyrosine levels. In the 'galactose metabolism' pathway, the upregulation of three beta-galactosidase genes (Unigene43641-S6, Unigene43648-S6, Unigene47074-S1) and the downregulation of one (Unigene28294-S2) corresponded to decreased alpha-lactose levels.</p><p><strong>Conclusions: </strong>This study provides an in-depth examination of the dynamic transcriptomic and metabolomic changes occurring during A. fokiensis leaf development, revealing key regulatory networks and enhancing the annotation of theA. fokiensis genome. These findings lay a crucial groundwork for future research on this medicinal plant.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"70"},"PeriodicalIF":2.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145194041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of QTNs and candidate genes in Ethiopian sorghum (Sorghum bicolor (L.) moench) landraces using SNP-based approaches.","authors":"Addisu Getahun, Habte Nida, Adugna Abdi Woldesemayat","doi":"10.1186/s12863-025-01350-1","DOIUrl":"10.1186/s12863-025-01350-1","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Sorghum, a diploid C4 cereal (2n = 2x = 20) with a 750 Mbp genome, is widely adaptable to tropical and temperate climates. As its center of origin and diversity, Ethiopia holds valuable genetic variation for improving yield and nutritional traits. This study aimed to identify and functionally characterize quantitative trait nucleotides (QTNs) linked to key agronomic and yield-related traits and their associated candidate genes.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Two hundred sixteen sorghum genotypes were evaluated over two seasons in northwestern Ethiopia using an alpha lattice design. Agronomic traits assessed included days to flowering, days to maturity, plant height, seed number per plant, seed yield, and thousand-seed weight. Genotyping-by-sequencing (GBS) generated 351,692 SNPs, with 50,165 high-quality markers retained. Candidate gene identification and functional characterization were carried out using a combination of bioinformatics tools and publicly available databases. Data normalization and analysis were conducted using META-R and SAS JMP. Linkage disequilibrium was assessed via TASSEL 5.0, and multi-locus genome-wide association study (ML-GWAS) identified significant QTNs (LOD ≥ 4.0) associated with phenotypic traits.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Result: &lt;/strong&gt;This study investigates the genetic basis of key agronomic and yield related traits in sorghum by identifying QTNs associated with phenotypic variation. Descriptive statistics revealed notable variability in traits such as days to flowering (101 days), days to maturity (145.77 days), plant height (357.47 cm), seed number per plant (1808.92 count), seed yield (45.07 g), and thousand-seed weight (23.44 g). Correlation analysis showed strong relationships, particularly between days to flowering and maturity (r = 0.7058). ML-GWAS detected 176 QTNs across all 10 chromosomes, with 34 considered reliable Due to their consistent identification across multiple models. 117 candidate genes were mapped to these QTNs, associated with six major traits: 20 for flowering time, 16 for maturity, 16 for plant height, 17 for seed number per plant, 38 for seed yield, and 10 for seed weight. Key genes included Sobic.001G196700 (flowering time) and Sobic.005G176100 (stress responses). Two important regulatory genes, SbMADS1 and SbFT, were highlighted for their roles in flowering regulation. SbMADS1 influences days to flowering, while SbFT acts as a mobile signal integrating photoperiod cues. These genes are involved in starch and sucrose metabolism pathways, essential for energy storage and mobilization, thereby supporting improved growth and yield in sorghum.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;This study highlights the complexity of trait inheritance shaped by diverse genetic factors and underscores the significance of major, stable, and unique QTNs for marker-assisted selection. Functional genome annotation revealed that candidate genes are involved in key biological processes and ","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"67"},"PeriodicalIF":2.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145180591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Staphylococcus aureus.","authors":"Andrey Shelenkov, Anna Slavokhotova, Mariyam Yunusova, Vladimir Kulikov, Yulia Mikhaylova, Vasiliy Akimkin","doi":"10.1186/s12863-025-01363-w","DOIUrl":"10.1186/s12863-025-01363-w","url":null,"abstract":"<p><strong>Background: </strong>Bacterial infections pose a global health threat across clinical and community settings. Over the past decade, the alarming expansion of antimicrobial resistance (AMR) has progressively narrowed therapeutic options, particularly for healthcare-associated infections. This critical situation has been formally recognized by the World Health Organization as a major public health concern. Epidemiological studies have demonstrated that the dissemination of AMR is frequently mediated by specific high-risk bacterial lineages, often designated as \"global clones\" or \"clonal complexes.\" Consequently, surveillance of these epidemic clones and elucidation of their pathogenic mechanisms and AMR acquisition pathways have become essential research priorities. The advent of whole genome sequencing has revolutionized these investigations, enabling comprehensive epidemiological tracking and detailed analysis of mobile genetic elements responsible for resistance gene transfer. However, despite the exponential increase in available bacterial genome sequences, significant challenges persist. Current genomic datasets often suffer from uneven representation of clinically relevant strains and inconsistent availability of accompanying metadata. These limitations create substantial obstacles for large-scale comparative studies and hinder effective surveillance efforts.</p><p><strong>Description: </strong>This database represents a comprehensive genomic analysis of 98,950 Staphylococcus aureus isolates, a high-priority bacterial pathogen of global clinical significance. We provide detailed isolate characterization through several established typing schemes including multilocus sequence typing (MLST), clonal complex (CC) assignments, spa typing results, and core genome MLST (cgMLST) profiles. The dataset also documents the presence of CRISPR-Cas systems in these isolates. Beyond fundamental typing data, our resource incorporates the distribution of antimicrobial resistance determinants, virulence factors, and plasmid replicons. These systematically curated genomic features offer researchers valuable insights into isolate epidemiology, resistance mechanisms, and horizontal gene transfer patterns in this highly concerning pathogen.</p><p><strong>Conclusion: </strong>This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.14833440 . The data provided enables researchers to identify optimal reference isolates for various genomic studies, supporting critical investigations into S. aureus epidemiology and antimicrobial resistance evolution. This resource will ultimately inform the development of more effective prevention and control measures against this high-priority pathogen.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"65"},"PeriodicalIF":2.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145180607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics mediation pipeline reveals differential pathways of maternal SNPs affecting newborn adiposity outcomes.","authors":"Nathan P Gill, Alan Kuang, Denise M Scholtens","doi":"10.1186/s12863-025-01355-w","DOIUrl":"10.1186/s12863-025-01355-w","url":null,"abstract":"<p><strong>Background: </strong>A great deal of previous research describes the impact of the maternal metabolic and genetic milieu on newborn adiposity outcomes. However, much of this research does not focus on all aspects of the problem simultaneously. Studies focusing on metabolic factors may not distinguish between maternal and fetal genetic pathways, while studies that do focus on these different genetic pathways may not incorporate metabolic information into effect estimates or variant classifications. In this paper, we introduce a novel multi-omics pipeline for maternal genetic variant selection and mediation effect testing that can handle all these pathways, and use it to investigate broad patterns in the effects of maternal genetic variants on newborn adiposity outcomes.</p><p><strong>Results: </strong>A Bayesian network model is used to incorporate both metabolomic and genomic data into an initial filter for maternal variants likely to affect newborn adiposity outcomes through a direct maternal genetic effect, an indirect fetal genetic effect, a maternal metabolic effect, or some combination of these pathways. A mediation model is then fit to these candidate variants and associated outcomes to identify which of these pathways, if any, mediate the total effect. We then group maternal genetic variants according to the relative magnitudes of these three effect pathways. In an application to existing mother-newborn data from the HAPO study, we find that of 78 candidate variants, the majority influence newborn birthweight solely through either a direct maternal or indirect fetal genetic effect (37% and 40%, respectively), a smaller number through both of these (14%), relatively few exclusively through the maternal metabolic pathway (6%), and almost none through a combination of the maternal metabolic pathway with either of the two genetic pathways (3%). We also find that these overall patterns of mediation effects are similar across outcomes.</p><p><strong>Conclusions: </strong>Our results reveal broad patterns in the effects of maternal genetic variants on newborn adiposity, and identify both new genetic loci and loci known from previous literature to influence newborn adiposity. These results demonstrate the potential for scientific discovery enabled by our multi-omics mediation pipeline, and the approach is broadly applicable for untangling path-specific contributions in the modern integrated multi-omics landscape.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"66"},"PeriodicalIF":2.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12466079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145180589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association study meta-analysis uncovers novel genetic variants associated with olfactory dysfunction.","authors":"Mohammed Aslam Imtiaz, Konstantinos Melas, Adrienne Tin, Valentina Talevi, Honglei Chen, Myriam Fornage, Srishti Shrestha, Martin Gögele, David Emmert, Cristian Pattaro, Peter Pramstaller, Franz Förster, Katrin Horn, Thomas H Mosley, Christian Fuchsberger, Markus Scholz, Monique M B Breteler, N Ahmad Aziz","doi":"10.1186/s12863-025-01360-z","DOIUrl":"10.1186/s12863-025-01360-z","url":null,"abstract":"<p><strong>Background: </strong>Olfactory dysfunction is among the earliest signs of many age-related neurodegenerative diseases and has been associated with increased mortality in older adults; however, its genetic basis remains largely unknown. Therefore, here we aimed to elucidate its genetic architecture through a genome-wide association study meta-analysis (GWMA).</p><p><strong>Methods: </strong>This GWMA included the participants of European ancestry (N = 22,730) enrolled in four different large population-based studies followed by a multi-ancestry GWMA including participants of African ancestry (N = 1,030). Olfactory dysfunction was assessed using a 12-item smell identification test.</p><p><strong>Results: </strong>GWMA revealed a novel genome-wide significant locus (tagged by single nucleotide polymorphism rs11228623 at the 11q12 locus) associated with olfactory dysfunction. Gene-based analysis revealed a high enrichment for olfactory receptor genes in this region. Phenome-wide association studies demonstrated associations between genetic variants related to olfactory dysfunction and blood cell counts, kidney function, skeletal muscle mass, cholesterol levels and cardiovascular disease. Using individual-level data, we also confirmed and quantified the strength of these associations on a phenotypic level. Moreover, employing two-sample Mendelian Randomization analyses, we found evidence for causal associations between olfactory dysfunction and these phenotypes.</p><p><strong>Conclusions: </strong>Our findings provide novel insights into the genetic architecture of the sense of smell and highlight its importance for many aspects of human health. Moreover, these findings could facilitate the identification and monitoring of individuals at increased risk of olfactory dysfunction and associated diseases.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"64"},"PeriodicalIF":2.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145082371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}