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Genotyping arrays
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DNA methylation levels change along with age, but few studies have examined the variation in the rate of such changes between individuals. Methods: We performed a longitudinal analysis to quantify the variation in the rate of change of DNA methylation between individuals using whole blood DNA methylation array profiles collected at 2–4 time points (N = 2894) in 954 individuals (67–90 years).
11p
vibransone
28-03-2024
5
2
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Exon-targeted microarrays can detect small (
15p
vioraclene
31-03-2024
5
2
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We evaluated the performance of single-nucleotide polymorphism (SNP) genotyping arrays OncoScan (Thermo Fisher Scientific, San Diego, CA) and Infinium CytoSNP-850K (CytoSNP; Illumina, Waltham, MA) for assessing homologous recombination deficiency (HRD) genomic instability.
9p
vileonardodavinci
23-12-2023
4
3
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Part 1 book "Equine genomics" includes content: Defining the equine genome - The nuclear genome and the mitochondrial genome, genetic linkage maps, physical and comparative maps, the Y-chromosome, unexpected structural features of the equine major histocompatibility complex, assembly and analysis of the equine genome sequence, genomic tools and resources - Development and applications of an equine SNP genotyping array, functional genomics, coat color genomics.
167p
oursky04
14-09-2023
4
2
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The soil borne, obligate biotrophic fungus Synchytrium endobioticum causes tumor-like tissue proliferation (wart) in potato tubers and thereby considerable crop damage. Chemical control is not effective and unfriendly to the environment. S. endobioticum is therefore a quarantined pathogen. The emergence of new pathotypes of the fungus aggravate this agricultural problem.
16p
vinarcissa
21-03-2023
5
1
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Accurate genotype imputation can greatly reduce costs and increase benefits by combining whole-genome sequence data of varying read depth and array genotypes of varying densities. For large populations, an efficient strategy chooses the two haplotypes most likely to form each genotype and updates posterior allele probabilities from prior probabilities within those two haplotypes as each individual’s sequence is processed.
12p
vinarcissa
21-03-2023
6
1
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Multiple layers of genetic and epigenetic variability are being simultaneously explored in an increasing number of health studies. We summarize here different approaches applied in the Data Mining and Machine Learning group at the GAW20 to integrate genome-wide genotype and methylation array data.
8p
vihagrid
30-01-2023
3
3
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Although harness racing is of high economic importance to the global equine industry, significant genomic resources have yet to be applied to mapping harness racing success. To identify genomic regions associated with harness racing success, the current study performs genome-wide association analyses with three racing performance traits in the Norwegian-Swedish Coldblooded Trotter using the 670 K Axiom Equine Genotyping Array.
13p
vihagrid
30-01-2023
7
3
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Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes
Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array.
9p
vihagrid
30-01-2023
11
3
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Two individuals with a first-degree relationship share about 50 percent of their alleles. Parent–offspring relationships cannot be homozygous for alternative alleles (genetic exclusion). Methods: Applying the concept of genetic exclusion to HD arrays typed in animals for experimental purposes or genomic selection allows estimation of the rate of rejection of first-degree relationships as the rate at which two individuals typed for a large number of Single Nucleotide Polymorphisms (SNPs) do not share at least one allele.
12p
vihagrid
30-01-2023
8
3
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High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which gave rise to the field of “integrative genetics”. Other omics technologies, such as proteomics and
15p
vialfrednobel
29-01-2022
9
0
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Heat stress leads to an array of physiological, biochemical, and molecular changes in plants affecting its growth and development. An experiment was conducted to find out the effect of short-term heat stress on osmo-protectant and antioxidants in 37 genotypes.
8p
schindler
30-12-2021
11
1
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The detection of signatures of selection in genomic regions provides insights into the evolutionary process, enabling discoveries regarding complex phenotypic traits. In this research, we focused on identifying genomic regions affected by different selection pressures, mainly highlighting the recent positive selection, as well as understanding the candidate genes and functional pathways associated with the signatures of selection in the Mangalarga Marchador genome.
17p
vilarryellison
29-10-2021
16
0
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Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available.
16p
vibeauty
23-10-2021
9
1
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Understanding the underlying genetic structure of human populations is of fundamental interest to both biological and social sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation. The most widely used methods for collecting variant information at the DNA-level include whole genome sequencing, which remains costly, and the more economical solution of array-based techniques, as these are capable of simultaneously genotyping a pre-selected set of variable DNA sites in the human genome.
13p
vitzuyu2711
29-09-2021
14
1
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Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection.
12p
visilicon2711
20-08-2021
10
1
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The sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure and levels of autozygosity of 377 Lipizzan horses originating from five different European stud farms utilizing the SNP genotype information of the high density 700 k Affymetrix Axiom™ Equine genotyping array.
17p
visilicon2711
20-08-2021
6
1
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Genomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation by breeders.
16p
visilicon2711
20-08-2021
9
1
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Palatoschisis or cleft palate is a known anomaly in pigs resulting in their death. However, little is known about its aetiology. A detailed description of the phenotype was derived from necropsy and by computed tomography revealing that all 20 cases also exhibited hypodontia and renal cysts.
11p
visilicon2711
20-08-2021
9
1
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China has the richest local chicken breeding resources in the world and is the world’s second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas.
12p
visilicon2711
20-08-2021
7
2
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