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Genotypic data
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Part 2 book "Quantitative genetics, genomics and plant breeding" includes content: Genotype–environment interaction - Progress and prospects; analysing QTL–environment interaction by factorial regression, with an application to the cimmy drought and low nitrogen STR; elements of genotype–environment interaction - genetic components of the photoperiod response in maize; mechanisms of improved nitrogen use efficiency in cereals; biplot analysis of multi environment trial data,... and other contents.
182p
dianmotminh04
12-07-2024
0
0
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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
2
1
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Here, we present the Northeast Asian Reference Database (NARD), including whole-genome sequencing data of 1779 individuals from Korea, Mongolia, Japan, China, and Hong Kong. NARD provides the genetic diversity of Korean (n = 850) and Mongolian (n = 384) ancestries that were not present in the 1000 Genomes Project Phase 3 (1KGP3).
10p
vibransone
28-03-2024
2
2
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A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret wholegenome sequencing data for genotypic drug susceptibility testing (DST).
8p
vibransone
28-03-2024
3
2
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Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic review. Recent work has shown that systematic integration of clinical phenotype data with genotype information can improve diagnostic workflows and prioritization of filtered rare variants.
17p
vioraclene
31-03-2024
1
1
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Identifying breast cancer patients with DNA repair pathway-related germline pathogenic variants (GPVs) is important for effectively employing systemic treatment strategies and risk-reducing interventions.
15p
viellison
28-03-2024
4
2
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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
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Genotypes are strongly associated with disease phenotypes, particularly in brain disorders. However, the molecular and cellular mechanisms behind this association remain elusive. With emerging multimodal data for these mechanisms, machine learning methods can be applied for phenotype prediction at different scales, but due to the black-box nature of machine learning, integrating these modalities and interpreting biological mechanisms can be challenging.
19p
vicwell
29-02-2024
4
2
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The aim of the study was to comprehensively explore the genetic susceptibility correlations among diseases and traits from large-scale individual genotype data. The study suggests that common genetic background exists between diseases and traits with epidemiologic associations. The GRS correlation approach provides a rich source of candidate associations among diseases and traits from the genetic perspective, warranting further epidemiologic studies.
6p
visteverogers
24-06-2023
4
2
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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
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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
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Accurate genotype calling for high throughput Illumina data is an important step to extract more genetic information for a large scale genome wide association studies. Many popular calling algorithms use mixture models to infer genotypes of a large number of single nucleotide polymorphisms in a fast and efficient way.
9p
vinarcissa
21-03-2023
3
1
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The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources.
13p
vinarcissa
21-03-2023
4
1
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The use of multiple genetic backgrounds across years is appealing for genomic prediction (GP) because past years’ data provide valuable information on marker effects. Nonetheless, single-year GP models are less complex and computationally less demanding than multi-year GP models.
17p
vinarcissa
21-03-2023
7
1
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Bipolar affective disorder (BP) is a common, highly heritable psychiatric disorder characterized by periods of depression and mania. Using dense SNP genotype data, we characterized CNVs in 388 members of an Old Order Amish Pedigree with bipolar disorder.
16p
vinarcissa
21-03-2023
3
1
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Population-wide genotypic and phenotypic data is frequently used to predict the disease risk or genetic/phenotypic values, or to localize genetic variations responsible for complex traits. GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures.
6p
vinarcissa
21-03-2023
2
1
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Genotype imputation is an important tool for whole-genome prediction as it allows cost reduction of individual genotyping. However, benefits of genotype imputation have been evaluated mostly for linear additive genetic models.
10p
vinarcissa
21-03-2023
5
1
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Genomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait loci (QTL). Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor that may be overcome by combining data from multiple breeds or using crossbred information.
9p
vinarcissa
21-03-2023
2
1
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Imputation of partially missing or unobserved genotypes is an indispensable tool for SNP data analyses. However, research and understanding of the impact of initial SNP-data quality control on imputation results is still limited. In this paper, we aim to evaluate the effect of different strategies of pre-imputation quality filtering on the performance of the widely used imputation algorithms MaCH and IMPUTE.
11p
vinarcissa
21-03-2023
2
1
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Accurate classification of patients with a complex disease into subtypes has important implications for medicine and healthcare. Using more homogeneous disease subtypes in genetic association analysis will facilitate the detection of new genetic variants that are not detectible using the non-differentiated disease phenotype.
12p
vinarcissa
21-03-2023
4
1
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