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Archaic variants from Altai, Vindija, Chagyrskaya and Denisova (hg38)
<p>This is the variants for Altai, Vindija, Chagyrskaya and Denisova lifted over from hg19 to hg38.</p> <p>Liftover with CrossMap.py</p> <p>CrossMap.py vcf {chain} {vcffile} {refgenome} {outfile} --no-comp-alleles</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>
Source data for the manuscript "Time-Variant Parity-Time Symmetry in Frequency-Scanning Systems"
Open the record for dataset details and reuse information.
Lunn 2024_Variants in Lrrk2 and Snca deficiency do not alter the course of primary encephalitis due to neurotropic reovirus T3D in newborn mice
<p>This dataset is associated with the manuscript 'Variants in Lrrk2 and Snca deficiency do not alter the course of primary encephalitis due to neurotropic reovirus T3D in newborn mice'; Lunn et al., 2024; BioRxiv <a href="https://doi.org/10.1101/2024.09.28.615578">https://doi.org/10.1101/2023.12.18.572180</a></p> <p> </p> <p>Each tab of the .xlsx file corresponds to a Figure, as indicated. </p>
FIGURE 12. Salmacis spp. A. S. bicolor. Red color variant. B. S in New Ecological Observations and Occurrence for Asteroidea and Echinoidea in Hong Kong
FIGURE 12. Salmacis spp. A. S. bicolor. Red color variant. B. S. sphaeroides. In situ observation of S. sphaeroides. C. S. sphaeroides. Showing individuals scavenging on a dead fish. Photographer: A. Josy Lai; B. and C. Sam King Fung Yiu.
Natural selection at PRKAA1 variant in Andeans is associated with improved ventilation and sleep phenotypes in highlanders and lowlanders
<h2><span>Overview</span></h2> <p><span>This repository contains data files and scripts related to the study titled "Natural selection at PRKAA1 variant in Andeans is associated with improved ventilation and sleep phenotypes in highlanders and lowlanders." This study explores genetic selection on the PRKAA1 gene in Andean populations and investigates how it impacts physiological responses to high altitude. The data includes genotype-phenotype associations, whole-genome sequences, and selection scans that contribute to understanding how PRKAA1 variants support adaptation to high-altitude environments.</span></p> <h2><span>Repository Structure</span></h2> <h3><span>Main Directory</span></h3> <ul> <li> <p><span><strong><span>README.md</span></strong></span><span>: This document.</span></p> </li> </ul> <h3><span>Subdirectories and Files</span></h3> <ol> <li> <p><span><strong><span>SNP Genotyping</span></strong></span></p> <ul> <li> <p><span><strong><span>prkaa1 association results.xlsx</span></strong></span><span>: Contains statistical results for associations between PRKAA1 SNPs and respiratory and sleep-related phenotypes.</span></p> </li> <li> <p><span><strong><span>prkaa1 genotype and cdp phenotype.csv</span></strong></span><span>: Dataset with PRKAA1 genotypes linked to phenotypic data, particularly ventilation and sleep metrics, in Cerro de Pasco, Peru.</span></p> </li> <li> <p><span><strong><span>summary table.xlsx</span></strong></span><span>: Summary statistics for SNP association tests, including sample sizes and effect sizes for each phenotype.</span></p> </li> </ul> </li> <li> <p><span><strong><span>Large Genome Summary Statistics</span></strong></span></p> <ul> <li> <p><span>FHS</span></p> <p><span>: Data from the Framingham Heart Study (FHS), a cohort of European descent.</span></p> <ul> <li> <p><span><strong><span>dbgap variables.xlsx</span></strong></span><span>: Description of phenotype and covariate variables in FHS.</span></p> </li> <li> <p><span><strong><span>fhs stats.xlsx</span></strong></span><span>: Summary statistics for PRKAA1 SNPs in FHS, including sleep-related phenotypes.</span></p> </li> <li> <p><span><strong><span>prkaa1 variant.csv</span></strong></span><span>: Genotype data for PRKAA1 SNPs in FHS participants.</span></p> </li> </ul> </li> <li> <p><span>HCHS</span></p> <p><span>: Data from the Hispanic Community Health Study/Study of Latinos (HCHS), focusing on the Latino population.</span></p> <ul> <li> <p><span><strong><span>HCHS top results annotated.xlsx</span></strong></span><span>: Annotated top results from association tests with PRKAA1 variants.</span></p> </li> <li> <p><span><strong><span>HCHS variable explained.xlsx</span></strong></span><span>: Explanation of phenotype variables in the HCHS dataset.</span></p> </li> <li> <p><span><strong><span>prkaa1 variant.csv</span></strong></span><span>: Genotype data for PRKAA1 SNPs in HCHS participants.</span></p> </li> </ul> </li> </ul> </li> <li> <p><span><strong><span>Luciferase</span></strong></span></p> <ul> <li> <p><span><strong><span>prkaa1 luciferase.csv</span></strong></span><span>: Contains results from luciferase assays assessing transcriptional activity related to PRKAA1 variants. These assays were conducted in HEK293T cells to determine the regulatory effect of the rs10035235 variant.</span></p> </li> </ul> </li> <li> <p><span><strong><span>Selection Scan</span></strong></span></p> <ul> <li> <p><span><strong><span>selection scan results part1.csv.gz</span></strong></span><span> & </span><span><strong><span>selection scan results part2.csv.gz</span></strong></span><span>: Compressed CSV files with selection scan results for PRKAA1 across the Andean genome. These files contain scores and metrics derived from the Composite of Multiple Signals (CMS) test to identify regions under selection.</span></p> </li> </ul> </li> <li> <p><span><strong><span>Whole Genome Sequencing</span></strong></span></p> <ul> <li> <p><span><strong><span>andean_prkaa1_region.vcf</span></strong></span><span>: A VCF file of high-coverage whole-genome sequences from Andean individuals, focused on the PRKAA1 region. Used in selection scans to assess allele frequencies and LD (linkage disequilibrium) patterns.</span></p> </li> </ul> </li> </ol> <h2><span>Data Use and Citation</span></h2> <p><span>Please cite the original manuscript when using this data for publications, presentations, or analyses. Data access is intended for research purposes only and requires proper attribution.</span></p> <p><span>For further information or questions about the data, please contact the repository authors: Wanjun Gu (</span><span><a href="mailto:wanjun.gu@ucsf.edu">wanjun.gu@ucsf.edu</a></span><span>) and Elijah Lawrence (</span><span><a href="mailto:elijah.lawrence@duke.edu">elijah.lawrence@duke.edu</a></span><span>) or the corresponding author Dr. Tatum Simonson (</span><span><a href="mailto:tsimonson@ucsd.edu">tsimonson@ucsd.edu</a></span><span>).</span></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 from: Stepwise colonization of the Andes by Ruddy Ducks and the evolution of novel β-globin variants
Andean uplift played a key role in Neotropical bird diversification, yet past dispersal and genetic adaptation to high-altitude environments remain little understood. Here we use multilocus population genetics to study population history and historical demographic processes in the ruddy duck (Oxyura jamaicensis), a stiff-tailed diving duck comprising three subspecies distributed from Canada to Tierra del Fuego and inhabiting wetlands from sea level to 4500 m in the Andes. We sequenced the mitochondrial DNA, four autosomal introns and three haemoglobin genes (αA, αD, βA) and used isolation-with-migration (IM) models to study gene flow between North America and South America, and between the tropical and southern Andes. Our analyses indicated that ruddy ducks dispersed first from North America to the tropical Andes, then from the tropical Andes to the southern Andes. While no nonsynonymous substitutions were found in either α globin gene, three amino acid substitutions were observed in the βA globin. Based on phylogenetic reconstruction and power analysis, the first βA substitution, found in all Andean individuals, was acquired when ruddy ducks dispersed from low altitude in North America to high altitude in the tropical Andes, whereas the two additional substitutions occurred more recently, when ruddy ducks dispersed from high altitude in the tropical Andes to low altitude in the southern Andes. This stepwise colonization pattern accompanied by polarized βA globin amino acid replacements suggest that ruddy ducks first acclimatized or adapted to the Andean highlands and then again to the lowlands. In addition, ruddy ducks colonized the Andean highlands via a less common route as compared to other waterbird species that colonized the Andes northwards from the southern cone of South America.
FIGURE 4. Piezura pardalina ssp. pardalina Rondani. A. Male genitalia external structures, posterior. B. Male mesolobus, variant form. C. Female spermatheca. D. Female genitalia, ventral. E. Male sternite 5 in A taxonomic revision of Piezura Rondani (Diptera: Fanniidae)
FIGURE 4. Piezura pardalina ssp. pardalina Rondani. A. Male genitalia external structures, posterior. B. Male mesolobus, variant form. C. Female spermatheca. D. Female genitalia, ventral. E. Male sternite 5, ventral.
Data from: Whole genome sequencing and rare variant analysis in essential tremor families
Essential tremor (ET) is one of the most common movement disorders. The etiology of ET remains largely unexplained. Whole genome sequencing (WGS) is likely to be of value in understanding a large proportion of ET with Mendelian and complex disease inheritance patterns. In ET families with Mendelian inheritance patterns, WGS may lead to gene identification where WES analysis failed to identify the causative single nucleotide variant (SNV) or indel due to incomplete coverage of the entire coding region of the genome, in addition to accurate detection of larger structural variants (SVs) and copy number variants (CNVs). Alternatively, in ET families with complex disease inheritance patterns with gene x gene and gene x environment interactions enrichment of functional rare coding and non-coding variants may explain the heritability of ET. We performed WGS in eight ET families (n=40 individuals) enrolled in the Family Study of Essential Tremor. The analysis included filtering WGS data based on allele frequency in population databases, rare SNV and indel classification and association testing using the Mixed-Model Kernel Based Adaptive Cluster (MM-KBAC) test. A separate analysis of rare SV and CNVs segregating within ET families was also performed. Prioritization of candidate genes identified within families was performed using phenolyzer. WGS analysis identified candidate genes for ET in 5/8 (62.5%) of the families analyzed. WES analysis in a subset of these families in our previously published study failed to identify candidate genes. In one family, we identified a deleterious and damaging variant (c.1367G>A, p.(Arg456Gln)) in the candidate gene, CACNA1G, which encodes the pore forming subunit of T-type Ca(2+) channels, CaV3.1, and is expressed in various motor pathways and has been previously implicated in neuronal autorhythmicity and ET. Other candidate genes identified include SLIT3 which encodes an axon guidance molecule and in three families, phenolyzer prioritized genes that are associated with hereditary neuropathies (family A, KARS, family B, KIF5A and family F, NTRK1). Functional studies of CACNA1G and SLIT3 suggest a role for these genes in ET disease pathogenesis.
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the Chocolate Tree
<p>Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet, the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao – an outcrossing, long-lived tree species that is the source of chocolate – to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160 thousand SVs, which together cover eight times more of the genome than SNPs and short indels (125 Mb vs. 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination.<br> Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs on this important local adaptation trait. Beyond revealing new empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T. cacao. </p>
Codes and dataset used in the manuscript entitled "Quantifying time-variant travel time distribution by multi-fidelity model in hillslope under nonstationary hydrologic conditions"
<p>This contains the codes and dataset for the manuscript entitled "Quantifying time-variant travel time distribution by multi-fidelity model in hillslope under nonstationary hydrologic conditions". Detailed information about the dataset is described in the Readme.txt file.</p>
Rare missense functional variants at COL4A1 and COL4A2 in sporadic intracerebral hemorrhage
<p><b>Objective</b><br> To test the genetic contribution of rare missense variants in <i>COL4A1</i> and <i>COL4A2</i> in which common variants are genetically associated with sporadic intracerebral hemorrhage (ICH), we performed rare variant analysis in multiple sequencing data for the risk for sporadic ICH.</p> <p><b>Methods</b><br> We performed sequencing across 559Kbp at 13q34 including <i>COL4A1</i> and <i>COL4A2</i> among 2,133 individuals (1,055 ICH cases; 1,078 controls) in US-based and 1,492 individuals (192 ICH cases; 1,300 controls) from Scotland-based cohorts, followed by sequence annotation, functional impact prediction, genetic association testing, and <i>in silico</i> thermodynamic modeling.</p> <p><b>Results</b><br> We identified 107 rare nonsynonymous variants in sporadic ICH, of which 2 two missense variants, rs138269346 (COL4A1<sup>I110T</sup>) and rs201716258 (COL4A2<sup>H203L</sup>), were predicted to be highly functional and occurred in multiple ICH cases but not in controls from the US-based cohort. The minor allele of rs201716258 was also present in Scottish ICH patients, and rs138269346 was observed in two ICH-free controls with a history of hypertension and myocardial infarction. Rs138269346 was nominally associated with non-lobar ICH risk (P=0.05), but not with lobar ICH (P=0.08), while associations between rs201716258 and ICH subtypes were non-significant (P>0.12). Both variants were considered pathogenic based on minor allele frequency (<0.00035 in EUR), predicted functional impact (<i>deleterious</i> or <i>probably</i> <i>damaging</i>), and <i>in silico</i> modeling studies (substantially altered physical length and thermal stability of collagen).</p> <p><b>Conclusions</b><br> We identified rare missense variants in <i>COL4A1</i>/<i>A2</i> in association with sporadic ICH. Our annotation and simulation studies suggest that these variants are highly functional and may represent targets for translational follow-up.</p>
FIGURE 3 in Sexual morphs and colour variants of Aphis (formerly Toxoptera) odinae (Hemiptera, Aphididae) in Japan
FIGURE 3. Plot of the mean scores on the first two canonical variates (CVs) of 23 samples of A. odinae: a, labelled according to the host plants on which they were collected; b, labelled according to their countries of origin and colour.
FIGURE 2 in Sexual morphs and colour variants of Aphis (formerly Toxoptera) odinae (Hemiptera, Aphididae) in Japan
FIGURE 2. Colour photographs of living A. odinae: a, fundatrix with bluish black progeny; b, fundatrix with brown progeny; c, oviparae and male; d, apterous viviparae of brown form (photograph by courtesy of Dr Poorani Janakiraman); e, apterous vivipara of green form; f, colony with mixture of the two colour forms.
Cerebrovascular disease progression in patients with ACTA2 Arg179 pathogenic variants supplementary materials
<p><span><span><span><span><span><span><span><span><span><span><span>Our study entitled "Cerebrovascular disease progression in patients with ACTA2 Arg179 Pathogenic Variants" examines progression of imaging biomarkers of stroke, arterial steno-occlusive disease and white matter injury in patients with smooth muscle dysfunction syndrome caused by mutations in the ACTA2 gene (ACTA2 Arg179 pathogenic variants). We found characteristic patterns of acute white matter ischemic injury and progressive internal carotid artery stenosis on MRI. Longitudinal analysis showed both stable and progressive lesion entities. The data was collected on various scanner setups. To eliminate potential bias related to improving imaging technology we re-analyzed imaging markers for those patients with available longitudinal imaging on an identical scanner setups and present the data in supplementary table e-1. Supplementary table e-2 shows results of a comparison of imaging markers between male and female sex.</span></span></span></span></span></span></span></span></span></span></span></p>
KTU: K-mer Taxonomic Units improve the biological relevance of amplicon sequence variant microbiota data
<p>Testing datasets and files for the KTU algorithm</p>
FIGURE. Canonical variate analysis of Corybas hypogaeus, C. obscurus ("darkie"), C. wallii ("triwhite") and two variants of the C. trilobus aggregate ("Rimutaka", "Trotters") in Five new species of Corybas (Diurideae, Orchidaceae) endemic to New Zealand and phylogeny of the Nematoceras clade
FIGURE. Canonical variate analysis of Corybas hypogaeus, C. obscurus ("darkie"), C. wallii ("triwhite") and two variants of the C. trilobus aggregate ("Rimutaka", "Trotters")
Historical review of terminology applied to cambial variants in Nyctaginaceae
<p><i>Premise of research. </i>The alternative patterns of secondary growth (vascular cambial variants) in stems of Nyctaginaceae are outstanding and has been widely investigated since late 19<sup>th</sup> century. However, there are controversial interpretations in the literature regarding the existence of one or two types of cambial variants (successive cambia vs. interxylary phloem). Thus, this study aims to explore the morphological diversity of stems in Nyctaginaceae, to unravel the real nature of the cambial variant present in most species of the family.</p> <p><i>Methodology. </i>Altogether we analyzed 60 species, focusing on 18 from 12 genera, which were used for the developmental studies. Anatomical and ontogenetic features were characterized from images produced by standardized plant techniques for macro and microscope analyses.</p> <p><i>Pivotal results. </i>Our analyses reveal that most species of Nyctaginaceae present stems with polycyclic eustele, which later develop a single cambium that produces secondary xylem and secondary phloem at unequal rates along the stem circumference. This unusual activity results in the absence of a regular cylinder and in the formation of secondary phloem strands (surrounded by conjunctive tissue) which are embedded within the secondary xylem. In cross-section, adult stems can be characterized by having different arrangements (i.e., phloem islands, patches, concentric bands), which results from difference in rates of phloem and conjunctive tissue forming the strands. The cambial variant in these stems are described as interxylary phloem, as similarly observed in other eudicot lineages.</p> <p><i>Conclusions. </i>Our examination of the stem development of Nyctaginaceae confirms the presence of interxylary phloem, which has been overlooked in the family since most studies reiterates the descriptions of successive cambia as the common pattern of cambial variant within the family. These findings emphasize the importance of developmental studies to further our understand of stem macromorphologies and highlight the complexity and diversity of stem architectures in Nyctaginaceae.</p>
Raw data for Association of ACE2 gene functional variants with gestational diabetes mellitus risk in a southern Chinese population
<p class="MsoNormal"><span>These data were generated to investigate the association and functional analysis of angiotensin-converting enzyme 2 genetic variants with the pathogenesis of Gestational diabetes mellitus (GDM). This study conducted a case-control study involving 569 GDM patients and 735 healthy pregnant women to explore the associations between candidate variants in the ACE2 gene variants and the pathogenesis of GDM. 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 GDM were evaluated using odds ratios (ORs) and corresponding 95% confidence intervals (CIs). </span><span>Finally, ACE2 gene variants are significantly associated with the risk of GDM via gene-gene and gene-environment combination. The rs2074192 C > T affects the splicing of ACE2 gene, which may be a potential mechanism leading to the altered susceptibility of individual female during pregnancy in Guilin to GDM</span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.