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23
datasets available to search
ShareScore release 0.9.0
Dataset results
23 results for “SNP detection”
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
<p>Knowledge on the genetic composition of <em>Quercus petraea</em> in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-tag sequences to the <em>Quercus robur</em> reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of <em>Q. petraea</em> were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined <em>Q. petraea</em> populations.</p>
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>
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>
Construction of genetic linkage map based on SNP markers, QTL mapping and detection of candidate genes of growth-related traits in Pacific abalone using genotyping-by-sequencing
<p><a name="_Hlk72585736"><span>Pacific abalone (<i>Haliotis discus hannai</i>) is a commercially important high valued molluscan species. Its wild population has decreased in recent years. Pacific abalone is widely cultured in Korea. Traditional breeding programs have been implemented for hatchery production of abalone seeds. To obtain more genetic information for the molecular breeding program, a high-density linkage map and quantitative trait locus (QTL) for three growth-related traits was constructed for Pacific abalone. F1 cross population with two parents were sampled to construct the linkage map using genotyping by sequencing (GBS). A total of 664,630,534 clean reads and 56,686 SNPs were generated. In sum, 3,345 segregating SNPs were used to construct a consensus linkage map. The map spanned 1,747.023 cM with 18 linkage groups and an average interval of 0.55 cM. QTL analysis revealed two significant QTL in LG10 on the consensus linkage map in each growth-related trait. Both the QTLs are located in the telomere region of the chromosome. Moreover, four potential candidate genes for growth-related traits were identified in the QTL region. Expression analysis revealed that identified genes are involved in growth regulation of abalone. The newly constructed genetic linkage map, growth-related QTLs and potential candidate genes identified in the present study can be used as valuable genetic resources and will be useful for marker-assisted selection (MAS) of Pacific abalone in molecular breeding program.</span></a></p>
Construction of genetic linkage map based on SNP markers, QTL mapping and detection of candidate genes of growth-related traits in Pacific abalone using genotyping-by-sequencing
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Data from: A new multiplex SNP genotyping assay for detecting hybridization and introgression between the M and S molecular forms of Anopheles gambiae
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Data from: Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples
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Genome Wide SNP Array-based Approach to Detect Micro-cytogenetic Lesions and KIT Mutation to Improve Treatment Outcomes in Patients With Core-binding Factor Positive Acute Myeloid Leukemia
ClinicalTrials.gov study NCT01066286. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Evaluation of Wpa-generated amplicons for SNP typing (allele bias), locus bias, and detection of known CNVs
GEO Series GSE12751. Homo sapiens. 19 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array; Genome variation profiling by genome tiling array.
Affymetrix 6.0 SNP arrays interrogated to detect allele-specific DNA modification in the brain
GEO Series GSE71443. Homo sapiens. 230 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array; Methylation profiling by SNP array.
Segmentation-based detection of allelic imbalance and LOH in cancer cells using whole genome SNP arrays
GEO Series GSE11976. Homo sapiens. 20 samples. Type: Genome variation profiling by SNP array.
A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma
GEO Series GSE16122. Homo sapiens. 203 samples. Type: Expression profiling by array; Genome variation profiling by SNP array.
DNA copy number detection from exome sequencing - Exploiting the off-targets (SNP)
GEO Series GSE60168. Homo sapiens. 6 samples. Type: Genome variation profiling by SNP array.
Detection of chromosomal aberrations in renal tumors by virtual karyotyping with SNP microarrays
GEO Series GSE12808. Homo sapiens. 19 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Integrated genomics approach to detect allelic imbalances in multiple myeloma, SNP data
GEO Series GSE16121. Homo sapiens. 45 samples. Type: Genome variation profiling by SNP array.
SNP arrays to detect copy number changes in t(1;19) E2A-PBX1 positive leukemias
GEO Series GSE52654. Homo sapiens. 21 samples. Type: Genome variation profiling by genome tiling array.
Detection of Single Nucleotide Polymorphism (SNP) Rs2235371 of IRF6 Gene in Egyptian Patients with Non-Syndromic Cleft Lip and Palate
ClinicalTrials.gov study NCT06730880. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing (ALL_SNP)
GEO Series GSE117693. Homo sapiens. 9 samples. Type: Genome variation profiling by SNP array.
SNP genotyping of cryptic complexity in structural chromosome abnormalities previously detected by cytogenetic analysis
GEO Series GSE20623. Homo sapiens. 40 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Application of CGH-array and SNP-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause
GEO Series GSE62440. Homo sapiens. 5 samples. Type: Genome variation profiling by SNP array; Genome variation profiling by array.
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International Brain Laboratory public data
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OpenNeuro
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