scholarly journals Fertility-Associated Polymorphism within Bovine ITGβ5 and Its Significant Correlations with Ovarian and Luteal Traits

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1579
Author(s):  
Jianing Zhao ◽  
Jie Li ◽  
Fugui Jiang ◽  
Enliang Song ◽  
Xianyong Lan ◽  
...  
Keyword(s):  
Corpus Luteum ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Cellular Processes ◽  
Indel Mutation ◽  
Genome Wide ◽  
Low Degree ◽  
Indel Polymorphisms ◽  
Hardy Weinberg Equilibrium ◽  
Bovine Fertility

There is an urgent need to improve bovine fertility, and molecular marker-assisted selection (MAS) can accelerate this process. Genome-wide association studies suggest that Integrin β5 (ITGβ5) might affect fertility in bovines. As a member of the integrins family, ITGβ5 can bind to the extracellular matrix and mediate various cellular processes. In our study, primers spanning six potential insertion/deletion (indel) polymorphisms within the ITGβ5 gene were designed and 696 ovary samples from different individuals, the vast majority not in oestrum were collected for genetic variation detection. A deletion locus, rs522759246, namely P1-D13-bp, was found to be polymorphic. The allele D frequency was 0.152 and the polymorphism information content (PIC) value was 0.224, indicating a low-degree PIC. This locus did not follow the Hardy–Weinberg equilibrium (p = 1.200E-23). Importantly, associations between P1-D13-bp and ovarian morphological traits were established. Polymorphisms of this locus had significant correlations with ovarian width (p = 0.015). The corpus luteum is also linked to fertility and P1-D13-bp was significantly correlated with corpus luteum diameter (p = 0.005). In conclusion, an indel mutation within the bovine ITGβ5 gene was identified, which was significantly associated with several ovarian and luteal traits.

scholarly journals INFERNO - INFERring the molecular mechanisms of NOncoding genetic variants

2017 ◽  
Author(s):  
Alexandre Amlie-Wolf ◽  
Mitchell Tang ◽  
Elisabeth E. Mlynarski ◽  
Pavel P. Kuksa ◽  
Otto Valladares ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Association Studies ◽  
Regulatory Elements ◽  
Genome Wide Association Studies ◽  
Cellular Processes ◽  
Genome Wide ◽  
Causal Variants ◽  
Novel Method

AbstractThe majority of variants identified by genome-wide association studies (GWAS) reside in the noncoding genome, where they affect regulatory elements including transcriptional enhancers. We propose INFERNO (INFERring the molecular mechanisms of NOncoding genetic variants), a novel method which integrates hundreds of diverse functional genomics data sources with GWAS summary statistics to identify putatively causal noncoding variants underlying association signals. INFERNO comprehensively infers the relevant tissue contexts, target genes, and downstream biological processes affected by causal variants. We apply INFERNO to schizophrenia GWAS data, recapitulating known schizophrenia-associated genes including CACNA1C and discovering novel signals related to transmembrane cellular processes.

scholarly journals Screening of Deletion Variants within the Goat PRDM6 Gene and Its Effects on Growth Traits

Animals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 208 ◽  
Author(s):  
Zhen Wang ◽  
Congliang Wang ◽  
Yongni Guo ◽  
Shuaishuai She ◽  
Baojing Wang ◽  
...  
Keyword(s):  
Growth Traits ◽  
Early Stage ◽  
Association Studies ◽  
Body Height ◽  
Shaanxi Province ◽  
Genome Wide Association Studies ◽  
Deletion Variant ◽  
Genome Wide ◽  
Hardy Weinberg Equilibrium ◽  
Pleiotropic Gene

By genome-wide association studies, the PRDM6 gene has been shown to affect multiple, apparently unrelated inherited traits, including bone density and body mass index. Therefore, it is considered a potentially pleiotropic gene. In this study, we identified a 12 bp deletion variant (NC_030814.1:rs651603667, g: 79985625-79985636delTTGACTGATCCA) within the PRDM6 gene in a large sample (SBWC goats; n = 1044). All goat samples were collected in Shaanxi province in July 2018. The frequency of the wt allele was higher than the frequency of the del allele, and this mutation polymorphism confirmed to be consistent with the Hardy–Weinberg equilibrium (p > 0.05). Further results showed that in a group of goats in the yearling period (18 months old, n = 567), this deletion variant of the PRDM6 gene was associated with heart girth (p = 0.027), cannon circumference (p = 0.008), chest depth (p = 2.10 × 10−5), chest width (p = 0.004), body height (p = 0.032), body length (p = 0.044) and hip-width (p = 0.014). For adult SBWC goats (36 months old, n = 477), the effects of the 12 bp variation on growth-related traits were found to make no difference. These findings show that the 12 bp deletion within the goat PRDM6 gene plays an important role in the early growth and development of goats. Using the 12 bp mutation, breeders can quickly and effectively select excellent individual goats at an early stage.

scholarly journals Assessment of possible association between rs378854 and prostate cancer risk in the Serbian population

2013 ◽  
Vol 65 (2) ◽  
pp. 475-486
Author(s):  
G. Brajuskovic ◽  
Zorana Nikolic ◽  
A. Kojic ◽  
Dusanka Savic-Pavicevic ◽  
Snezana Cerovic ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Association Studies ◽  
Prostate Cancer Risk ◽  
Quality Analysis ◽  
Control Group ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Study Population ◽  
Hardy Weinberg Equilibrium

Prostate cancer (PCa) is the second most commonly diagnosed cancer among men worldwide. Despite its high incidence rate, the molecular basis of PCa onset and its progression remains little understood. Genome-wide association studies (GWAS) have greatly contributed to the identification of single nucleotide polymorphisms (SNP) associated with PCa risk. Several GWAS identified 8q24 as one of the most significant PCa-associated regions. The aim of this study was to evaluate the association of SNP rs378854 at 8q24 with PCa risk in the Serbian population. The study population included 261 individuals diagnosed with PCa, 257 individuals diagnosed with benign prostatic hyperplasia (BPH) and 106 healthy controls. Data quality analysis yielded results showing deviations from Hardy-Weinberg equilibrium in groups of PCa patients and BPH patients as well as in the control group. There was no significant association between alleles and genotypes of the genetic variant rs378854 and PCa risk in the Serbian population.

Colorectal cancer inherited susceptibility: The first replication study in the Brazilian population.

2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 361-361
Author(s):  
Israel Gomy ◽  
Erika Maria Monteiro Santos ◽  
Graziela Machado Gruner Turco Spilborghs ◽  
Sandra Regina de Araujo da Silva Viola ◽  
Samuel Aguiar ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Association Studies ◽  
Twin Studies ◽  
Brazilian Population ◽  
European Ancestry ◽  
Genome Wide Association Studies ◽  
Replication Studies ◽  
Inherited Susceptibility ◽  
Genome Wide ◽  
Hardy Weinberg Equilibrium

361 Background: Inherited susceptibility to colorectal cancer (CRC) is known since twin studies have revealed 35% of heritability. Genome-wide association studies (GWAS) have uncovered less than a half of this proportion through genotyping tagSNPs of individuals with European ancestry. To date only 20 common SNPs have achieved genome-wide significance and replication studies from non-European populations are scarce. Here we show preliminary data of the first study of CRC inherited susceptibility in the Brazilian population and aimed to replicate European studies. Methods: We genotyped 1,395 individuals (675 cases and 720 controls) for 10 tagSNPs (rs6983267, rs4939827, rs4779584, rs16892766, rs10795668, rs4444235, rs9929218, rs10411210, rs961253, rs3802842) using TaqMan SNP Genotyping Assays and SDS2.3 software (Applied Biosystems). We exclude from the analysis SNPs with significant deviation from Hardy-Weinberg equilibrium. Results: Significant association was found between six out of ten SNPs and CRC risk for most genetic models. One SNP (rs10411210) was associated with a low risk of CRC. Conclusions: Despite we did not analyze population stratification, this study partially replicate European GWAS in an admixed population. Therefore, it is worth to explore other ethnic backgrounds that would ultimately help to uncover the missing heritability of CRC and narrow the boundaries of the genetic architecture of CRC susceptibility. [Table: see text]

scholarly journals Genoppi: a web application for interactive integration of experimental proteomics results with genetic datasets

2017 ◽  
Author(s):  
April Kim ◽  
Edyta Malolepsza ◽  
Justin Lim ◽  
Kasper Lage
Keyword(s):  
Web Application ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Proteomics Data ◽  
Protein Protein Interaction ◽  
Cellular Processes ◽  
Genome Wide ◽  
Interaction Proteomics ◽  
User Friendly ◽  
Insight Into

AbstractSummaryIntegrating protein-protein interaction experiments and genetic datasets can lead to new insight into the cellular processes implicated in diseases, but this integration is technically challenging. Here, we present Genoppi, a web application that integrates quantitative interaction proteomics data and results from genome-wide association studies or exome sequencing projects, to highlight biological relationships that might otherwise be difficult to discern. Written in R, Python and Bash script, Genoppi is a user-friendly framework easily deployed across Mac OS and Linux distributions.AvailabilityGenoppi is open source and available at https://github.com/lagelab/[email protected] and [email protected]

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