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opencc-by-4.0Dec 2021View details →

Functional genomics analysis to disentangle the role of genetic variants in major depression - Supplementary Tables

This entry contains the data generated by the study "Functional genomics analysis to disentangle the role of genetic variants in major depression" that are part of the Supplementary information of the article describing the study. The entry contains the following data: Supplementary Tables S1-S7 Supplementary Table S1. Summary of resources. Supplementary Table S2. Causal GVs for MD. Supplementary Table S3. pGenes functional and disease enrichment analysis. Supplementary Table S4. Fine-mapped MD causal GVs disease enrichment analysis. Supplementary Table S5. Colocalizing GWAS-eQTLs association to disease. Supplementary Table S6. TFBS analysis. Supplementary Table S7. GVs state annotation.

opencc-by-4.0Jun 2024View details →

Genetic Variants Representation Learning (GV-Rep)

This dataset is used for Genetic Variants (GV) representation learning.

opencc-by-4.0Sep 2021View details →

Dataset related to article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant".

The files contain raw data related to the article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant", available from <a href="https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/full">https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/ful</a>l. File "Genetic and clinical data": <ul> <li>In the sheet "485 aHUS patients" are reported data obtained from the screening of 485 unrelated patients with aHUS including rare variants (RVs) in complement disease-associated genes (CFH, CD46, CFI, C3, CFB and THBD), the presence of CFH-CFHR genomic rearrangements and/or anti-FH antibodies.</li> <li>In the sheet "Pedigrees with c.286+2T>G" are listed all pedigrees carrying the c.286+2T>G variant, the diseases status of all subjects and the age of disease onset of patients. In bold are indicated pedigrees (n=7) used to study the penetrance of aHUS in c.286+2T>G carriers.</li> <li>In the sheet "Haplotypes" are reported genotypes used to evaluate the association between the presence of CFH-H3 and CD46GGAAC risk haplotypes and aHUS. Results of this analysis are reported in Table 3 of the published paper.</li> <li>In the sheet "Raw data Fig.2" are reported data of "platelet count" and "serum creatinine" of the proband used to elaborate Figure 2.</li> </ul> In the file "C3 and C5b-9 deposition" is reported the quantification of serum-induced C3 and C5b-9 deposition on human microvascular endothelial cell line (HMEC-1). The fluorescent staining was evaluated with Image J and expressed as pixel2 per field analyzed. The fields with the lowest and highest values were excluded from calculation. These values were used to elaborate data included in Table 2 and in Figure 5. In the file "CD46 protein expression" are reported data of CD46 expression on peripheral blood mononuclear cells (PBMCs) isolated from the proband, his relatives and healthy volunteers. Data of specific expression of CD46 (evaluated for SCR1 or for SCR4 as reported in the materials and methods section) are indicated as median fluorescence intensity (MFI) percentage compared with the control. In the ppt file "cDNA amplification and sequencing results" is reported: <ul> <li>the agarose gel image of the amplified cDNA from the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> <li>Electropherograms obtained from the cDNA sequencing of the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> </ul> Additional data will be made available by the authors, without undue reservation, to any qualified researcher.

opencc-by-4.0May 2019View details →

Genetic variants (chr. 6) from Old World Schistosoma mansoni exomes

Variant calling file (VCF) produced from exome libraries of Schistosoma mansoni (bloodfluke) samples from the Old Wold (West Africa (Senegal, Niger), East Africa (Tanzania), and Middle East (Oman)). One sample form the New World (Caribbean (HR9)) was added for comparison. The variants were called on the 3 Mb of chromosome 6 centered on the SmSULT-OR gene. This gene is involved in resistance to the drug oxamniquine  (OXA). The aim of the related article was to investigate the origin of OXA resistant mutations in the New Wolrd by identifying sequence variation in SmSULT-OR in S. mansoni from the Old World, where OXA has seen minimal usage.

opencc-zeroJan 2016View details →

Common Genetic Variants in FOXP2 are Not Associated with Individual Differences in Language Development

Three data sets used in” Common Genetic Variants in FOXP2 Are Not Associated with Individual Differences in Language Development” are provided.  The discovery data set was comprised of 834 children who were members of a Longitudinal sample and children who were members of a School sample.  Both samples are contained in the Iowa data set.  The Iowa data set contains a quantitative variable LCOMP that represents a composite z-score representing oral language ability.  The data set also identifies which sample the children belonged to and the allele calls for 13 tag SNPs located across FOXP2.  A second data file, ELVS, contains data from a separate sample of children who were used to test for replication of inconsistent evidence of an association between language and the SNP rs1916988.  The ELVS file provides a composite oral language score scaled in standard score units (mean=100, SD=15) and the genotype calls for the  SNP rs1916988.

opencc-by-4.0Nov 2021View details →

Summary statistics for association tests between human and Plasmodium falciparum genetic variants in 3,346 severe malaria cases from The Gambia and Kenya

This dataset contains summary statistics for association tests between human and Plasmodium falciparum malaria parasite genetic variants, using data from 3,346 severe malaria cases from The Gambia and Kenya.  These results underlie the analysis described in our paper: "Malaria protection due to sickle haemoglobin depends on parasite genotype" Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy Nguyen, Sónia M. Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor, David J. Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski Nature (2021) doi: <a href="https://doi.org/10.1038/s41586-021-04288-3">10.1038/s41586-021-04288-3</a> bioRxiv link:: <a href="https://doi.org/10.1101/2021.03.30.437659">doi.org/10.1101/2021.03.30.437659</a> The genotype data underlying these summary statistics has also been deposited on Zenodo (<a href="https://zenodo.org/record/4973477">doi:10.5281/zenodo.4973477</a>).  The <a href="https://www.well.ox.ac.uk/~gav/hptest)">HPTEST software</a> used to generate these results has also been deposited (<a href="https://doi.org/10.5281/zenodo.5685580">doi:10.5281/zenodo.5685580</a>).  Please see the <a href="https://www.malariagen.net/resource/32">MalariaGEN website</a> for a full list of datasets which have been released with this manuscript. Data contents. The dataset consists of a single <a href="http://sqlite.org">sqlite database file</a> containing the results, and an accompanying README file in markdown and html format.  Please see the README file for full details of the data contents.

opencc-by-4.0Jul 2024View details →

Tissue-aware interpretation of genetic variants advances the etiology of rare diseases

Pathogenic variants underlying Mendelian diseases often disrupt the normal physiology of a few tissues and organs. However, variant effect prediction tools that aim to identify pathogenic variants are typically oblivious to tissue contexts. Here we report a machine- learning framework, denoted ‘Tissue Risk Assessment of Causality by Expression for variants’ (TRACEvar, https://netbio.bgu.ac.il/TRACEvar/), that offers two advancements. First, TRACEvar predicts pathogenic variants that disrupt the normal physiology of specific tissues. This was achieved by creating 14 tissue-specific models that were trained on over 14,000 variants and combined 84 attributes of genetic variants with 495 attributes derived from tissue omics. TRACEvar outperformed 10 well-established and tissue-oblivious variant effect prediction tools. Second, the resulting models are interpretable, thereby illuminating variants' mode-of-action. Application of TRACEvar to variants of 52 rare-disease patients highlighted pathogenicity mechanisms and relevant disease processes. Lastly, interpretation of large-scale models revealed that top-ranking determinants of pathogenicity included attributes of disease-affected tissues, particularly cellular process activities. Hence, tissue contexts and interpretable machine-learning models can greatly enhance the etiology of rare diseases. Article link: https://www.embopress.org/doi/full/10.1038/s44320-024-00061-6

opencc-by-4.0Sep 2021View details →

dataset related to article "Multiple Genetic Rare Variants in Autism Spectrum Disorders: A Single-Center Targeted NGS Study"

dataset contains: NGS data (.vcf; .bam; .bam.bai) of all 40 ASD patients analysed in the study at title

opencc-by-4.0Dec 2022View details →

Rice genetic variants with dbSNP and pseudoDB

Rice genetic variants with dbSNP and pseudoDB

opencc-by-4.0Dec 2022View details →

Chickpea genetic variants with dbSNP and pseudoDB

Chickpea genetic variants with dbSNP and pseudoDB

dryad40/100

In search of the genetic variants of human sex ratio at birth: Was Fisher wrong about sex ratio evolution?

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publicSep 2024View details →

opencc-zeroNov 2020View details →

Genetic variants beyond amyloid and tau associated cognitive decline: a cohort study

Objective: To identify single nucleotide polymorphisms (SNPs) associated with cognitive decline independent of amyloid &[beta] (A&[beta]) and tau pathology in Alzheimer's disease (AD). Methods: Discovery and replication datasets consisting of 414 subjects (94 cognitively normal control [CN), 185 with mild cognitive impairment [MCI], and 135 AD) and 72 subjects (22 CN, 39 MCI, and 11 AD), respectively, were obtained from the Alzheimer's Disease Neuroimaging Initiative database. Genome-wide association analysis was conducted to identify SNPs associated with individual cognitive function (measured using the MMSE and ADAS-cog) while controlling for the level of A&[beta] and tau (measured as CSF p-tau/A&[beta]1-42). Gene ontology analysis was performed on SNP associated genes. Results: We identified one significant (rs55906536, &[beta]=-1.91,standard error 0.34, P =4.07×10-8) and four suggestive variants on chromosome 6, which were associated with poorer cognitive function. Congruent results were found in the replication data. A structural equation model showed that the identified SNP deteriorated cognitive function partially through cortical thinning of the brain in a region-specific manner. Furthermore, a bioinformatics analysis showed that the identified SNPs were associated with genes related to glutathione metabolism. Conclusions: In this study, we identified SNPs related to cognitive decline, in a manner which could not be explained by A&[beta] and tau levels. Our findings provide insight into the complexity of AD pathogenesis and support the growing literature on the role of glutathione in AD. This study suggests anti-oxidative agents may serve therapeutic for AD subjects with the identified SNPs.

opencc-zeroOct 2023View details →

Identification of genetic variants associated with anterior cruciate ligament rupture and AKC standard coat color in the Labrador Retriever

Canine anterior cruciate ligament (ACL) rupture is a common complex disease. Prevalence of ACL rupture is breed-dependent. In an epidemiological study, yellow coat color was associated with increased risk of ACL rupture in the Labrador Retriever. ACL rupture risk variants may be linked to coat color through genetic selection or through linkage with coat color genes. To investigate these associations, Labrador Retrievers were phenotyped as ACL rupture cases or controls and for coat color and were single nucleotide polymorphism (SNP) genotyped. After filtering, ~697K SNPs were analyzed using GEMMA and mvBIMBAM for multivariate association. Functional annotation clustering analysis with DAVID was performed on candidate genes. A large 8Mb region on chromosome 5 that included ACSF3, as well as 32 additional SNPs, met genome-wide significance at P<6.07E-7 or Log10(BF) = 3.0 for GEMMA and mvBIMBAM, respectively. On chromosome 23, SNPs were located within or near PCCB and MSL2. On chromosome 30, a SNP was located within IGDCC3. SNPs associated with coat color were also located within ADAM9, FAM109B, SULT1C4,RTDR1, BCR, and RGS7. DZIP1L was associated with ACL rupture. Several significant SNPs on chromosomes 2, 3, 7, 24, and 26 were located within uncharacterized regions or long non-coding RNA sequences. This study validates associations with the previous ACL rupture candidate genes ACSF3 and DZIP1L and identifies novel candidate genes. These variants could act as targets for treatment or as factors in disease prediction modeling. The study highlighted the importance of regulatory SNPs in the disease, as several significant SNPs were located within non-coding regions.

opencc-zeroOct 2023View details →

Raw data for the association of genetic variants of ErbB4 gene and gestational diabetes mellitus

<div>Gestational diabetes (GDM) is one of the common complications of female pregnancy, which seriously affects the health of patients and their offspring. So far, the etiology has not yet been fully clarified. To clarify the relationship of Erb-b2 receptor tyrosine kinase 4 (ErbB4) genetic variants and GDM risk in a Chinese population, ErbB4 variants (rs1595064, rs1595065, rs1595066 and rs6719645) were selected and genotyped in 554 GDM cases and 641 healthy controls. The associations between variants and GDM risk were evaluated with the odds ratios (ORs) and their corresponding 95% confidence intervals (CIs). The false-positive reporting probability (FPRP), multi-factor dimension reduction (MDR) and bioinformatics analysis were adopted to confirm the significant associations. A nomogram model was constructed to predict the risk of GDM. Association analysis demonstrated that the rs1595066 genotype performed a protective effect on GDM risk among whole subjects. Meanwhile, stratified analysis showed that rs1595066 was significantly associated with GDM risk in various subgroups, such as age>30.09 years old, pre-pregnancy BMI>22.23 Kg/m2 ,SBP≤110.08 mmHg, etc. Further, interactions between rs1595066 and DBP (Pinteraction=0.01), FPG (Pinteraction<0.001) and HbA1c (Pinteraction< 0.001) were detected. The FPRP analysis confirmed that association of rs1595066 and GDM risk in subjects of FPG≤4.79 mmol/L (P=0.199) is true at a prior probability of 0.1. The MDR analysis suggested that rs1595066 was the best single locus model, while the 4-loci model was considered the best multiple factors model to predict GDM risk. Functional prediction revealed that rs1595066 may disturb the microRNA binding sites to influence the stability of miRNA-mRNA binding. The predictive nomogram model has a good consistency and acceptable discriminative ability with a diagnosed AUC of 0.813.ErbB4 rs1595066 was significantly associated with GDM risk and underlying mechanism causing GDM may be the interaction of gene-gene, gene-environment and the changes in the regulatory effects of miRNAs on ERBB4 expression. The nomogram model has a good prospect for GDM prediction.</div>

opencc-by-4.0Nov 2023View details →

Genetic variants regulating the immune response improve the prediction of COVID-19 severity provided by clinical variables

Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and their clinical outcome.

opencc-zeroDec 2023View details →

Data for: Genetic variants underlying human bisexual behavior are reproductively advantageous

Because human same-sex sexual behavior (SSB) is heritable and leads to fewer offspring, how SSB-associated alleles have persisted and whether they will remain in human populations are of interest. Using the UK Biobank, we address these questions separately for bisexual behavior (BSB) and exclusive SSB (eSSB) after confirming their genetic distinction. We discover that male BSB is genetically positively correlated with the number of offspring. This unexpected phenomenon is attributable to the horizontal pleiotropy of male risk-taking behavior-associated alleles, because male risk-taking behavior is genetically positively correlated with both BSB and the number of offspring and because genetically controlling male risk-taking behavior abolishes the genetic correlation between male BSB and the number of offspring. By contrast, eSSB is genetically negatively correlated with the number of offspring. Our results suggest that male BSB-associated alleles are likely reproductively advantageous, which may explain their past persistence and predict their future maintenance, and that eSSB-associated alleles are likely being selected against at present.

opencc-by-4.0Dec 2023View details →

Genetic variants affecting NQO1 protein levels impact on efficacy of idebenone treatment in Leber hereditary optic neuropathy

Fastq files with complete sequencing of NQO1 gene after PCR amplification for cell lines harboring m.11778G>A/MT-ND4 or m.3460A>G/MT-ND1 and controls.

opencc-zeroAug 2022View details →

Raw data: Association and functional analysis of angiotensin-converting enzyme 2 gene genetic variants with the pathogenesis of pre-eclampsia

These data were generated to investigate the association and functional analysis of angiotensin-converting enzyme 2 genetic variants with the pathogenesis of pre-eclampsia(PE). This study conducted a case-control study involving 327 PE patients and 591 healthy pregnant women to explore the associations between candidate variants in the ACE2 gene variants and the pathogenesis of PE.This study collected clinical samples and data, and used logistic regression, false positive report rate, multi factor dimension reduction, functional analysis and other analysis methods to process the research data. Potential functional ACE2 gene variants (rs2106809 A>G, rs6632677 G>C, and rs2074192 C>T) were selected and genotyped using kompetitive allele-specific PCR. The strength of the associations between the studied genetic variants and the risk of PE were evaluated using odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Finally,it showed that the rs2106809 A>Gis significantly associated with the risk of PE via individual locus effects and/or complex gene-gene and gene-environment interactions.

opencc-by-4.0Jun 2024View details →

Identification of genetic variants associated with clinical features of sickle cell disease

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