scholarly journals Association between a variation inLRCH1 and knee osteoarthritis: A genome-wide single-nucleotide polymorphism association study using DNA pooling

2006 ◽  
Vol 54 (2) ◽  
pp. 524-532 ◽  
Author(s):  
Tim D. Spector ◽  
Richard H. Reneland ◽  
Steven Mah ◽  
Ana M. Valdes ◽  
Deborah J. Hart ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Knee Osteoarthritis ◽  
Association Study ◽  
Nucleotide Polymorphism ◽  
Dna Pooling ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Single Nucleotide Polymorphism Association

scholarly journals Genome-Wide Association Study Meta-Analysis of Stroke in 22 000 Individuals of African Descent Identifies Novel Associations With Stroke

Stroke ◽  
2020 ◽  
Vol 51 (8) ◽  
pp. 2454-2463
Author(s):  
Keith L. Keene ◽  
Hyacinth I. Hyacinth ◽  
Joshua C. Bis ◽  
Steven J. Kittner ◽  
Braxton D. Mitchell ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Meta Analysis ◽  
African Descent ◽  
Genome Wide Association ◽  
Minority Population ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome

Background and Purpose: Stroke is a complex disease with multiple genetic and environmental risk factors. Blacks endure a nearly 2-fold greater risk of stroke and are 2× to 3× more likely to die from stroke than European Americans. Methods: The COMPASS (Consortium of Minority Population Genome-Wide Association Studies of Stroke) has conducted a genome-wide association meta-analysis of stroke in >22 000 individuals of African ancestry (3734 cases, 18 317 controls) from 13 cohorts. Results: In meta-analyses, we identified one single nucleotide polymorphism (rs55931441) near the HNF1A gene that reached genome-wide significance ( P =4.62×10 −8 ) and an additional 29 variants with suggestive evidence of association ( P <1×10 −6 ), representing 24 unique loci. For validation, a look-up analysis for a 100 kb region flanking the COMPASS single nucleotide polymorphism was performed in SiGN (Stroke Genetics Network) Europeans, SiGN Hispanics, and METASTROKE (Europeans). Using a stringent Bonferroni correction P value of 2.08×10 −3 (0.05/24 unique loci), we were able to validate associations at the HNF1A locus in both SiGN ( P =8.18×10 −4 ) and METASTROKE ( P =1.72×10 −3 ) European populations. Overall, 16 of 24 loci showed evidence for validation across multiple populations. Previous studies have reported associations between variants in the HNF1A gene and lipids, C-reactive protein, and risk of coronary artery disease and stroke. Suggestive associations with variants in the SFXN4 and TMEM108 genes represent potential novel ischemic stroke loci. Conclusions: These findings represent the most thorough investigation of genetic determinants of stroke in individuals of African descent, to date.

scholarly journals Integrative analysis of genome-wide DNA methylation and single-nucleotide polymorphism identified ACSM5 as a suppressor of lumbar ligamentum flavum hypertrophy

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Yanlin Cao ◽  
Yenan Zhan ◽  
Sujun Qiu ◽  
Zhong Chen ◽  
Kaiqin Gong ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Nucleotide Polymorphism ◽  
Ligamentum Flavum ◽  
Global Analysis ◽  
Integrated Analysis ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome

Abstract Background Hypertrophy of ligamentum flavum (HLF) is a common lumbar degeneration disease (LDD) with typical symptoms of low back pain and limb numbness owing to an abnormal pressure on spinal nerves. Previous studies revealed HLF might be caused by fibrosis, inflammatory, and other bio-pathways. However, a global analysis of HLF is needed severely. Methods A genome-wide DNA methylation and single-nucleotide polymorphism analysis were performed from five LDD patients with HLF and five LDD patients without HLF. Comprehensive integrated analysis was performed using bioinformatics analysis and the validated experiments including Sanger sequencing, methylation-specific PCR, qPCR and ROC analysis. Furthermore, the function of novel genes in ligamentum flavum cells (LFCs) was detected to explore the molecular mechanism in HLF through knock down experiment, overexpression experiment, CCK8 assay, apoptosis assay, and so on. Results We identified 69 SNP genes and 735 661 differentially methylated sites that were enriched in extracellular matrix, inflammatory, and cell proliferation. A comprehensive analysis demonstrated key genes in regulating the development of HLF including ACSM5. Furthermore, the hypermethylation of ACSM5 that was mediated by DNMT1 led to downregulation of ACSM5 expression, promoted the proliferation and fibrosis, and inhibited the apoptosis of LFCs. Conclusion This study revealed that DNMT1/ACSM5 signaling could enhance HLF properties in vitro as a potential therapeutic strategy for HLF.

scholarly journals A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Nedenia Bonvino Stafuzza ◽  
Rafael Medeiros de Oliveira Silva ◽  
Breno de Oliveira Fragomeni ◽  
Yutaka Masuda ◽  
Yijian Huang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number Variation ◽  
Copy Number ◽  
Variation Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Copy Number Variation Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Number Variation
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