Genotyping by sequencing
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In this study, we utilize the genome-wide singlenucleotide polymorphisms (SNPs) data obtained through Multiplexed Inter Simple Sequence Repeat Genotyping by sequencing (MIG-seq) to explore the phylogenetic relationships among Quercus species in Vietnam. The results of this study reveal that all Quercus species in Vietnam belong to subgenus Cerris and the phylogenetic analysis strongly supports the recognition of two infrageneric sections: Quercus and Ilex section for the Vietnamese Quercus.
10p dianmotminh02 03-05-2024 1 1 Download
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In Vietnam, SMEDI syndrome in sows caused by PPV is nationwide and has been of concern since the early 1990s. Previous studies have investigated the prevalence of PPVs using serological testing and PCR methods. The objective of this study is to analyze the genotypic prevalence of PPVs and molecular characterization of VP gene of PPV2 from slaughtered pigs in Central Vietnam.
10p viritesh 02-04-2024 1 1 Download
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Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have only recently emerged as routine clinical diagnostic tests. To date, few systematic analyses of mosaic variants detected by diagnostic exome sequencing for diverse clinical indications have been performed.
11p vibransone 28-03-2024 2 2 Download
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The concentrations of the highly atherogenic lipoprotein(a) [Lp(a)] are mainly genetically determined by the LPA gene locus. However, up to 70% of the coding sequence is located in the complex so-called kringle IV type 2 (KIV-2) copy number variation, a region hardly accessible by common genotyping and sequencing technologies.
13p vibransone 28-03-2024 3 2 Download
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Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells.
16p vibransone 28-03-2024 2 1 Download
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Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences offers an alternative to laboratory-based drugsusceptibility testing. User-friendly and accurate resistance prediction tools are needed to enable public health and clinical practitioners to rapidly diagnose resistance and inform treatment regimens.
14p vibransone 28-03-2024 3 2 Download
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Exome sequencing (ES) is becoming more widely available in prenatal diagnosis. However, data on its clinical utility and integration into clinical management remain limited in practice. Herein, we report our experience implementing prenatal ES (pES) in a large cohort of fetuses with anomalies detected by ultrasonography using a hospital-based in-house multidisciplinary team (MDT) facilitated by a three-step genotype-driven followed by phenotype-driven analysis framework.
20p viellison 28-03-2024 5 2 Download
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This case-control study aimed to determine the association between PD-1.9 polymorphism and the risk of HCC in the cohort of chronic HBV-infected patients. Subject and method: Genotyping of PD-1.9 polymorphism was performed by direct sanger sequencing in 499 HBV-infected patients.
7p vishekhar 01-11-2023 0 0 Download
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Gout is an inflammatory type of arthritis caused by the deposition of crystals of monosodium urate monohydrate (MSU) in the joints. The arthritis is mediated by the release of proinflammatory cytokines including IL-1β, TNF-α and IL-6 by leukocytes including macrophages.
6p vicaptainmarvel 21-04-2023 5 2 Download
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Poor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice. In this study, the GP of 177 rice varieties was investigated in three locations across 2 years. By combining the genotype data of 261 simple sequence repeat (SSR) markers, association mapping was conducted to identify the marker-GP association loci.
9p vinarcissa 21-03-2023 2 1 Download
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Accurate imputation plays a major role in genomic studies of livestock industries, where the number of genotyped or sequenced animals is limited by costs. This study explored methods to create an ideal reference population for imputation to Next Generation Sequencing data in cattle.
12p vinarcissa 21-03-2023 4 1 Download
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Rare variant association analysis in case-parents studies by allowing for missing parental genotypes
The development of next-generation sequencing technologies has facilitated the identification of rare variants. Family-based design is commonly used to effectively control for population admixture and substructure, which is more prominent for rare variants.
8p vinarcissa 21-03-2023 4 1 Download
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Genotyping-by-sequencing (GBS) has emerged as a powerful and cost-effective approach for discovering and genotyping single-nucleotide polymorphisms. The GBS technique was largely used in crop species where its low sequence coverage is not a drawback for calling genotypes because inbred lines are almost homozygous.
14p vinarcissa 21-03-2023 3 1 Download
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Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations.
14p vinarcissa 21-03-2023 4 1 Download
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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 Download
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Accurate identification of crop cultivars is crucial in assessing the impact of crop improvement research outputs. Two commonly used identification approaches, elicitation of variety names from farmer interviews and morphological plant descriptors, have inherent uncertainty levels.
11p vinarcissa 21-03-2023 2 1 Download
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In recent years, with the development of high-throughput sequencing technology and the commercial availability of genotyping bead chips, more attention is being directed towards the utilization of abundant genetic markers in animal and plant breeding programs, human disease risk prediction and personal medicine.
11p vinarcissa 21-03-2023 3 1 Download
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The objective of research "Identification of SNP markers linked to Rf locus in carrot using GBS" was to identify SNP markers linked to Rf locus and develop a genetic map of Rf gene in carrot. For this purpose, a carrot F2 population segregating for male sterility was produced and segregating 10,425 SNP markers were discovered by using genotyping by sequencing (GBS).
15p lyhuyenthu 31-01-2023 7 1 Download
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Reniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States. Management of R. reniformis has been hindered by the lack of resistant G. hirsutum cultivars; however, resistance has been frequently identified in germplasm accessions from the G. arboreum collection.
11p vihagrid 30-01-2023 7 3 Download
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Increasing grain yield is a primary objective of maize breeding. Dissecting the genetic architecture of grain yield furthers genetic improvements to increase yield. Presented here is an association panel composed of 126 maize inbreds (AM126), which were genotyped by the genotyping-by-sequencing (tGBS) method.
12p vihagrid 30-01-2023 8 3 Download