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291 results for “genetic variant”
Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations
<p>The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 7540 complete nucleotide genomes from 51 African nations were obtained and analysed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Utilising a variety of clade and lineage nomenclature schemes, we looked at their diversity, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa after three years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya, and Nigeria as key sources of viral transmissions between Sub-Saharan African nations. These findings provide insight into the viral strains that are circulating in Africa and their evolutionary patterns.</p>
The population genetics of structural variants in grapevine domestication
<p><strong>The genome assembly: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.fa.fasta?versionId=86a512b8-12a6-4f4d-ac5d-acc26d74589f">Chardonnay.fa.fasta</a> </p> <p><strong>The gene annotation: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.annotation_sorted.gff.gz?versionId=2e5878bc-cf53-489b-ac71-2602f9ba4d2e">Chardonnay.annotation_sorted.gff.gz</a></p> <p><strong>The TE annotation: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.annotation_te_sorted.gff3.gz?versionId=95780497-e0e7-4a7b-8860-74072d7f7bb2">Chardonnay.annotation_te_sorted.gff3.gz</a></p>
Sanger sequencing of target and off-target genomic regions for gene-edited iPSC clones with SETBP1 genetic variants
<p>This data set includes chromatograms generated using sanger sequencing of targeted regions of genomic DNA from clonal iPSC lines. The iPSC lines include clones generated using CRISPR/Cas9 homology directed repair to introduce genetic variants into <em>SETBP1,</em> and their wild-type controls. Additional files have been included in the data set to link chromatogram (ab1) files to specific iPSC clones for genomic regions across the variant in <em>SETBP1 (</em>SETBP1 clones genetic variant sanger sequencing.xslx)<em> </em>and top<em> </em>off-target sites (SETBP1 clones off-target sanger sequencing.xlsx). </p>
Data from: A study on genetic variants of Fibroblast Growth Factor Receptor 2 (FGFR2) and the risk of breast cancer from North India
Genome-Wide Association Studies (GWAS) have identified Fibroblast growth factor receptor 2 (FGFR2) as a candidate gene for breast cancer with single nucleotide polymorphisms (SNPs) located in intron 2 region as the susceptibility loci strongly associated with the risk. However, replicate studies have often failed to extrapolate the association to diverse ethnic regions. This hints towards the existing heterogeneity among different populations, arising due to differential linkage disequilibrium (LD) structures and frequencies of SNPs within the associated regions of the genome. It is therefore important to revisit the previously linked candidates in varied population groups to unravel the extent of heterogeneity. In an attempt to investigate the role of FGFR2 polymorphisms in susceptibility to the risk of breast cancer among North Indian women, we genotyped rs2981582, rs1219648, rs2981578 and rs7895676 polymorphisms in 368 breast cancer patients and 484 healthy controls by Polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP) assay. We observed a statistically significant association with breast cancer risk for all the four genetic variants (P<0.05). In per-allele model for rs2981582, rs1219648, rs7895676 and in dominant model for rs2981578, association remained significant after bonferroni correction (P<0.0125). On performing stratified analysis, significant correlations with various clinicopathological as well as environmental and lifestyle characteristics were observed. It was evident that rs1219648 and rs2981578 interacted with exogenous hormone use and advanced clinical stage III (after Bonferroni correction, P<0.000694), respectively. Furthermore, combined analysis on these four loci revealed that compared to women with 0–1 risk loci, those with 2–4 risk loci had increased risk (OR = 1.645, 95%CI = 1.152–2.347, P = 0.006). In haplotype analysis, for rs2981578, rs2981582 and rs1219648, risk haplotype (GTG) was associated with a significantly increased risk compared to the common (ACA) haplotype (OR = 1.365, 95% CI = 1.086–1.717, P = 0.008). Our results suggest that intron 2 SNPs of FGFR2 may contribute to genetic susceptibility of breast cancer in North India population.
Data for: Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs
<p><span>Hundreds of genetic variants implicated in Mendelian disease have been characterized in dogs and commercial screening is being offered for most of them worldwide. There is typically limited information available regarding the broader population frequency of variants and uncertainty regarding their functional and clinical impact in ancestry backgrounds beyond the discovery breed. Genetic panel screening of disease variants, commercially offered directly to the consumer or via a veterinary clinician, provides an opportunity to establish large-scale cohorts with phenotype data available to address open questions related to variant prevalence and relevance. We screened the largest canine cohort examined in a single study to date (1,054,293 representative dogs from our existing cohort of 3.5 million; a total of 811,628 mixed breed dogs and 242,665 purebreds from more than 150 countries) to examine the prevalence and distribution of a total of 250 genetic disease-associated variants in the general population. Electronic medical records from veterinary clinics were available for 43.5% of the genotyped dogs, enabling the clinical impact of variants to be investigated. We provide detailed frequencies for all tested variants across breeds and find that 57% of dogs carry at least one copy of a studied Mendelian disease-associated variant. Focusing on a subset of variants, we provide evidence of full penetrance for 10 variants, and at minimum plausible evidence for clinical significance of 22 variants, on diverse breed backgrounds. Specifically, we report that inherited hypocatalasia is a notable oral health condition, confirm that factor VII deficiency presents as subclinical bleeding propensity and verify two genetic causes of reduced leg length. We further assess genome-wide heterozygosity levels in over 100 breeds and show that a reduction in genome-wide heterozygosity is associated with an increased Mendelian disease load. The accumulated knowledge represents a resource to guide discussions on genetic test relevance by breed.</span></p>
Genetic Variants Associated With Adolescent Suicide Attempts
ClinicalTrials.gov study NCT02001649. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genetic Variants and Chemotherapy-induced Abnormal Thermal Sensation
ClinicalTrials.gov study NCT03252834. IPD Sharing: NO. Countries: 1. Publications: 0.
Genetic Variants and Oxidative Stress as Links Between Periodontitis and Metabolic Syndrome
ClinicalTrials.gov study NCT03297749. IPD Sharing: NO. Countries: 2. Publications: 1.
Testing of NBIA Genes: Analysis of Genetic Heterogeneity and Validation of Mitochondrial Markers for Assessing Causality of Sequence Variants.
ClinicalTrials.gov study NCT05615571. IPD Sharing: NO. Countries: 1. Publications: 1.
Correlation Between Genetic Variants and Long-term Cardiac Effects Induced by Doxorubicin in Breast Cancer Patients
ClinicalTrials.gov study NCT02078388. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Association Between Genetic Variant Scores and P2Y12 Inhibitor Effects
ClinicalTrials.gov study NCT04580602. IPD Sharing: UNDECIDED. Countries: 1. Publications: 11.
Association Between Genetic Variant Scores and DOACs (DARES2)
ClinicalTrials.gov study NCT04597593. IPD Sharing: UNDECIDED. Countries: 1. Publications: 15.
Consumption of Whole Grains and Legumes Modulates the Genetic Effect of the APOA5 -1131C Variant
ClinicalTrials.gov study NCT01784952. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Genetic Variants and Non-genetic Variables and Postoperative Nausea and Vomiting
ClinicalTrials.gov study NCT03490175. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Moderate Intensity Training in Patients With Truncating Genetic Variants in TTN.
ClinicalTrials.gov study NCT05180188. IPD Sharing: NO. Countries: 1. Publications: 35.
Genetic Variants Modulate Association Between Dietary n-3 LCPUFAs and DHA Proportion in Breast Milk
ClinicalTrials.gov study NCT03842891. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Identification of Genetic Variants Associated With Unexpected Infant Death Syndrome
ClinicalTrials.gov study NCT06244433. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pharmacogenomics Study on IL28B Genetic Variants in Italian Patients With HCV Infection naïve to Treatment.
ClinicalTrials.gov study NCT01437969. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Genetic Variants Associated With Low Back Pain and Their Response to Treatment With Duloxetine or Propranolol
ClinicalTrials.gov study NCT03364075. IPD Sharing: NO. Countries: 1. Publications: 11.
Influence of CYP2C19 Genetic Variants on Clopidogrel in Healthy Subjects
ClinicalTrials.gov study NCT00413608. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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