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1,019 results for “SNP”
Fine-scale subpopulation detection via SNP-based unsupervised method: A case study on the 1000 Genomes Project Resources
<p>Here are the supplementary files to the paper "Fine-scale subpopulation detection via SNP-based unsupervised method:<br> A case study on the 1000 Genomes Project Resources".<br> <br> The repository is organized as:</p> <ol> <li><strong>Supplementary information</strong>: the additional detailed information for the experiments in the paper <ul> <li>Supplementary_information_IPCAPS_Chaichoompu_v1.pdf</li> </ul> </li> <li><strong>Real-life dataset</strong>: the 1000 genome dataset, which is referred to in the paper and is filtered with the parameters explained in the paper. Reference: https://www.internationalgenome.org/ <ul> <li>1000genomes_with_filtering.zip</li> </ul> </li> </ol>
Data from high throughput SNP-chip as cost effective new monitoring tool for assessing invasion dynamics in the comb jelly Mnemiopsis leidyi
<p class="MsoNormal"><span>High throughput low-density SNP arrays provide a cost-effective solution for population genetic studies and monitoring of genetic diversity as well as population structure commonly implemented in real time stock assessment of fish species. However, the application of high throughput SNP arrays for monitoring of invasive species has so far not been implemented. We developed a species-specific SNP array for the invasive comb jelly <em>Mnemiopsis leidyi</em> based on whole genome resequencing data. Initially, </span><span>a total of</span><span> </span><span>1,</span><span>395</span><span> </span><span>high quality </span><span>SNPs</span><span> were identified</span><span> </span><span>u</span><span>sing stri</span><span>ngent</span><span> filtering criteria</span><span>. From those, 192 assays were designed and validated, resulting in the final panel of 116 SNPs. Markers were diagnostic between the northern and southern <em>M. leidyi</em> lineages and highly polymorphic to distinguish populations. Despite using a reduced representation of the genome, our SNP panel yielded comparable results to using a whole genome resequencing approach (832,323 SNPs), recovering similar values of genetic differentiation between samples and detecting the same clustering groups when performing Structure analyses. The resource presented here provides a cost-effective, high throughput solution for population genetic studies, allowing to routinely genotype large number of individuals. Monitoring of genetic diversity and effective population size estimations in this highly invasive species will allow for the early detection of new introductions from distant source regions or hybridization events. Thereby, this SNP chip represents an important management tool in order to understand invasion dynamics and </span><span>opens the door for implementing such methods for a wider range of alien invasive species.</span></p> <div></div>
A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population
<p><strong>Background</strong>: Allegheny woodrats (<em>Neotoma magister</em>) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, Allegheny woodrat populations have experienced population declines throughout their range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016, and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. </p> <p><strong>Results</strong>: We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 16 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated throughout the following years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated the genetic rescue of the New Jersey population.</p> <p><strong>Conclusions</strong>: Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the risks of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.</p>
SNP amplicons results of 50 hybrid Chinook-Coho salmon
<p>These SNP panel results confirm the hybrid origin in 50 Chinook-Coho Salmon individuals. The SNP panel is composed of two amplicons and five diagnostic SNPs. DNA amplicons OkiOts_120255 and Oki_RAD41030 have SNP sites fixed for alternate base pairs in Chinook and Coho salmon (Beacham and Wallace 2019). The panel examined genotypes at one diagnostic position in OkiOts_120255 SNP: 113 (Reference=A, Variant=C) and four positions in Oki_RAD41030: 45 (TC), 51(CG), 195 (GA), and 198 (TG) called via Proton software Variant Caller®. The hybrid salmon were heterozygous for a Chinook and Coho haplotype at both SNP loci, confirming these as the parental species involved in the hybridization and consistent with all being F1 or higher order (F2 or back-cross) hybrid individuals. </p> <p>Beacham, T. D. & Wallace, C. G. (2019). Salmon species identification via direct DNA sequencing of single amplicons. <i>Conservation Genetics Resources,</i> 1-7<i>. </i><a href="https://doi.org/10.1007/s12686-o19-01102-1">https://doi.org/10.1007/s12686-o19-01102-1</a>.</p>
Determining haploblocks and haplotypes in the MAGIC winter wheat population WM-800 based on the wheat 15k Infinium and the 135k Affymetrix SNP arrays
<p><span>Haplotypes are derived from single nucleotide polymorphisms (SNPs). They are beneficial (i) to remove redundant sequence information in genetic populations and, more important, (ii) to distinguish more than two variants/alleles at a genomic locus. A haploblock locus, made of multiple haplotypes, is very useful in multiparent-advanced-generation-intercross (MAGIC) populations, where, ideally, multiple founder alleles need to be distinguished at each locus to subsequently carry out efficient genome-wide association analysis studies (GWAS). </span></p> <p><span>In this regard, the dataset contains genotype matrices (made of SNP, haploblock and haplotype data) for 800 lines of the MAGIC WHEAT population WM-800 (Sannemann et al. 2018). The datasets are based on genotyping the lines with both the already published wheat 15k Infinium SNP array (Sannemann et al. 2018) and the new wheat 135k Affymetrix SNP array.</span></p>
Genotypes of Aedes aegypti mosquitoes derived from SNP chip and low-coverage whole genome sequencing for platform cross-validation
<p>The mosquito <em>Aedes aegypti </em>is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people world-wide. Population genetics studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse <em>Ae. aegypti </em>populations to facilitate genomic studies on this species. Here we evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shot-gun sequencing approach using mosquitoes from the species' native (Africa) and invasive range (outside Africa). These analyses indicate that the results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low coverage whole genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases, opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole genome sequencing for population genetic studies of <em>Ae. aegypti</em> that do not rely on full allelic frequency spectra. Whole genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches. </p>
SNP data (DArTseq) for population genomics of Araucaria bidwillii
<p><span>We took Araucaria bidwillii leaf DNA samples from a total of 31 sites and 171 samples, representing 3 sites from a northern population in the Australian Wet Tropics and 28 sites from a southern population in Southeast Queensland, Australia. </span>SNP data was obtained from genotyping-by-sequencing platform Divesity Arrays Technology (DArTseq) and the resultant dataset has not been processed for quality control.</p>
Autosomal SNP-genotype data of brown bears (Ursus arctos) in Finland
<p>Harmonising methodology between countries is crucial in transborder population monitoring. However, immediate application of alleged, established DNA-based methods across the extended area can entail drawbacks and may lead to biases. Therefore, genetic methods need to be tested across the whole area before being deployed. Around 4,500 brown bears (<em>Ursus arctos</em>) live in Norway, Sweden, and Finland and they are divided into the western (Scandinavian) and eastern (Karelian) population. Both populations have recovered and are connected via asymmetric migration. DNA-based population monitoring in Norway and Sweden uses the same set of genetic markers. With Finland aiming to implement monitoring, we tested the available SNP-panel developed to assess brown bears in Norway and Sweden, on tissue samples from a representative set of 93 legally harvested individuals from Finland. The aim was to test for ascertainment bias and evaluate its suitability for DNA-based transnational-monitoring covering all three countries. We compared results to the performance of microsatellite genotypes of the same individuals in Finland and against SNP-genotypes from individuals sampled in Sweden (<em>N</em>=95) and Norway (<em>N</em>=27). In Finland, a higher resolution for individual identification was obtained for SNPs (PI=1.18E-27) compared to microsatellites (PI=4.2E-11). Compared to Norway and Sweden, probability of identity of the SNP-panel was slightly higher and expected heterozygosity lower in Finland indicating ascertainment bias. Yet, our evaluation show that the available SNP-panel outperforms the microsatellite panel currently applied in Norway and Sweden. The SNP-panel represents a powerful tool that could aid improving transnational DNA-based monitoring of brown bears across these three countries.</p>
SNP genotyping of indigenous goats of Uganda based on the Goat_IGGC_65K_v2 illumina chip
<p>Uganda's indigenous goats are characterised based on ethnic communities that raise them, average mature weight, and hair coat characteristics. Uganda's indigenous goats have been genotyped based on the Goat_IGGC_65K_v2 illumina chip to study their population structure and genetic characteristics. Information generated from this data is vital for the sustainable utilisation, development, and conservation of Uganda's goat genetic resources.</p>
SNP data set of Peruvian highland maize races
<p>Peruvian maize exhibits significant morphological diversity, with landraces cultivated from sea level up to 3,500 meters above sea level. Previous research based on morphological descriptors identified at least 52 Peruvian maize races, but their genetic diversity and population structure remain largely unknown. In this study, we used genotyping-by-sequencing (GBS) to infer the genetic structure and diversity of 423 maize accessions from the Genebank of La Molina National Agrarian University (UNALM). These accessions represent nine races and one sub-race, along with 15 open-pollinated lines (purple corn) and two yellow maize hybrids. We obtained 14,235 high-quality SNPs distributed along the 10 maize chromosomes. Gene diversity ranged from 0.33 (Pachia) to 0.362 (Ancashino), with Cusco showing the lowest inbreeding coefficient (0.205) and Ancashino the highest (0.274) among the landraces. Population divergence (FST) was very low (mean = 0.017), indicating extensive interbreeding among Peruvian maize varieties. Population structure analysis revealed that these 423 distinct genotypes could be grouped into 10 clusters, with some maize races clustering together. Peruvian maize races did not form monophyletic groups; instead, our phylogenetic tree identified two clades corresponding to the chronological classification of Peruvian maize races: <em>Anciently Derived or Primary Races</em> (ADPR) and <em>Lately Derived or Secondary Races</em> (LDSR). These clades also align with the geographic origins of the maize races, reflecting their mixed evolutionary backgrounds. Further investigation of Peruvian maize germplasm using modern technologies is essential to enhance their use in breeding programs, particularly in the Andean region of Peru.</p>
SNP genotype dataset from brown and anadromous trout
<p>Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed the high-confidence assignment of known-origin individuals to the region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.</p>
Simulation dataset for "Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters"
<p>Simulated Illumina reads for SNP distance method evaluation and comparison used in the article "Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters".</p> <p>Details for simulation can be found at https://gitlab.com/rki_bioinformatics/panpasco/tree/master/simulation_dataset.</p>
Concatenated SNP data: Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data
<p>Concatenated unliked SNP data in phylip format used in 'Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data' study.</p>
Crab Eating Macaque SNP Calls VCF
<p>Bgzipped vcf and tabix index files of crab eating macaque SNP calls of 26 individuals on the macFas5 assembly.</p>
Rhesus Macaque SNP Calls VCF
<p>Bgzipped vcf and tabix index files of rhesus macaque SNP calls of 526 individuals on the rheMac8 assembly.</p>
CT-FM-SNP cancer bed files
Open the record for dataset details and reuse information.
List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)
<p>The profiling of epigenetic marks like DNA methylation has become a central aspect of studies in evolution and ecology. Bisulfite sequencing is commonly used for assessing genome-wide DNA methylation at single nucleotide resolution but these data can also provide information on genetic variants like single nucleotide polymorphisms (SNPs). However, bisulfite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment and subsequent SNP calling. Several tools have been developed to overcome this challenge, but there is no independent evaluation of such tools for non-model species, which often lack genomic references. Here, we used whole-genome bisulfite sequencing (WGBS) data from four female great tits (<i>Parus major</i>) to evaluate the performance of seven tools for SNP calling from bisulfite sequencing data. We used SNPs from whole-genome resequencing data of the same samples as baseline SNPs to assess common performance metrics like sensitivity, precision, and the number of true positive, false positive, and false negative SNPs for the full range of variant and genotype quality values. We found clear differences between the tools in either optimizing precision (Bis-SNP), sensitivity (biscuit), or a compromise between both (all other tools). Overall, the choice of SNP caller strongly depends on which performance parameter should be maximized and whether ascertainment bias should be minimized to optimize downstream analysis, highlighting the need for studies that assess such differences.</p>
Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation
<p>Of two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular setting. As a single flowering cherry occurring on Ulleung Island in East Sea, <i>Prunus takesimensis</i> Nakai has been presumed as derived through anagenetic speciation on the Island. Based on morphological similarities, <i>P. sargentii </i>distributed in adjacent continental areas and islands has been suggested as its purported continental progenitor.<i> </i>However, the overall genetic complexity and resultant non-monophylies of closely related flowering cherries have hindered determining their phylogenetic relationships as well as establishing concrete continental progenitor and insular derivative relationship. Based on extensive sampling of wild flowering cherries including <i>P. takesimensis</i> and<i> P. sargentii</i> from Ulleung Island and its adjacent areas, this study inferred the origin and evolution of <i>P. takesimensis</i> using multiple different molecular markers. As the result of phylogeny and population genetic structure analyses based on SNPs detected by MIG-Seq and complementary cpDNA haplotypes, we could provide the extensive and convincing evidence for (1) the monophyly of<i> P. takesimensis</i>,<i> </i>(2) clear genetic differentiation between <i>P. takesimensis</i> (insular derivative) and <i>P. sargentii</i> (continental progenitor), (3) the geographic origin of <i>P. takesimensis</i> via single introduction from source population of <i>P. sargentii</i> in Korean Peninsula, (4) no significant genetic reduction in anagenetically derived insular species <i>P. takesimsnsis</i> compared to continental progenitor <i>P. sargentii</i>, (5) no strong population genetic structuring or geographical patters in the insular derived species, and (6) Mig-seq method as an effective tool to unravel complex evolutionary history of plant groups.</p>
An intron SNP rs2069837 in IL-6 is associated with osteonecrosis of the femoral head development
<p>Two variants (rs2069837, and rs13306435) in the IL-6 gene were identified and genotyped from 566 patients with ONFH and 566 healthy controls. The associations between IL-6 polymorphisms and ONFH susceptibility were assessed using odds ratio (OR) and 95% confidence interval (95% CI) via logistic regression. The results of the overall analysis revealed that IL-6 rs2069837 is correlated with decreased risk of ONFH among the Chinese Han population (<em>p</em> < 0.05). In stratified analysis, rs2069837 also reduced the susceptibility to ONFH in older people (> 51 years), males, nonsmokers, and nondrinkers (<em>p</em> < 0.05).</p>
Malus species SNP calls VCF
<p>Bgzipped vcf and tabix index files of Malus species SNP calls of 168 individuals on the GDDH13 v1.1 assembly.</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)
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DANDI Archive for NWB datasets
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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.