scholarly journals Private rare deletions in SEC16A and MAMDC4 may represent novel pathogenic variants in familial axial spondyloarthritis

2015 ◽  
Vol 75 (4) ◽  
pp. 772-779 ◽  
Author(s):  
Darren D O'Rielly ◽  
Mohammed Uddin ◽  
Dianne Codner ◽  
Michael Hayley ◽  
Jiayi Zhou ◽  
...  
Keyword(s):  
Axial Spondyloarthritis ◽  
Association Studies ◽  
Family Members ◽  
Genome Wide Association Studies ◽  
Intrinsically Disordered ◽  
Pathogenic Variants ◽  
Genome Wide ◽  
Multigenerational Family ◽  
Variant Frequency ◽  
The Impact

ObjectiveAxial spondyloarthritis (AxSpA) represents a group of inflammatory axial diseases that share common clinical and histopathological manifestations. Ankylosing spondylitis (AS) is the best characterised subset of AxSpA, and its genetic basis has been extensively investigated. Given that genome-wide association studies account for only 25% of AS heritability, the objective of this study was to discover rare, highly penetrant genetic variants in AxSpA pathogenesis using a well-characterised, multigenerational family.MethodsHLA-B*27 genotyping and exome sequencing was performed on DNA collected from available family members. Variant frequency was assessed by mining publically available datasets and using fragment analysis of unrelated AxSpA cases and unaffected controls. Gene expression was performed by qPCR, and protein expression was assessed by western blot analysis and immunofluorescence microscopy using patient-derived B-cell lines. Circular dichroism spectroscopy was performed to assess the impact of discovered variants on secondary structure.ResultsThis is the first report identifying two rare private familial variants in a multigenerational AxSpA family, an in-frame SEC16A deletion and an out-of-frame MAMDC4 deletion. Evidence suggests the causative mechanism for SEC16A appears to be a conformational change induced by deletion of three highly conserved amino acids from the intrinsically disordered Sec16A N-terminus and RNA-mediated decay for MAMDC4.ConclusionsThe results suggest that it is the presence of rare syntenic SEC16A and MAMDC4 deletions that increases susceptibility to AxSpA in family members who carry the HLA-B*27 allele.

The genetics of axial spondyloarthritis

2016 ◽  
Author(s):  
Stefan Siebert ◽  
Sengupta Raj ◽  
Alexander Tsoukas
Keyword(s):  
Axial Spondyloarthritis ◽  
Association Studies ◽  
Single Gene ◽  
Twin Studies ◽  
Genome Wide Association Studies ◽  
Functional Importance ◽  
Unfolded Protein ◽  
Genome Wide ◽  
Arthritogenic Peptide ◽  
Protein Response

Family and twin studies have long suggested a large genetic component in ankylosing spondylitis (AS). The genetic association with HLA-B27 remains one of the strongest single gene variant associations reported in any complex polygenic disease. The exact mechanism by which HLA-B27 contributes to AS remains unknown, with three main theories proposed: the arthritogenic peptide, endoplasmic reticulum stress with unfolded protein response, and homodimerization theories. Genome-wide association studies have identified a number of other important susceptibility genes for AS, several of which overlap with other spondyloarthritis conditions. Of these, ERAP1 and IL-23R, are covered in more detail, highlighting their functional importance.

scholarly journals The Impact of Improved Microarray Coverage and Larger Sample Sizes on Future Genome-Wide Association Studies

2013 ◽  
Vol 37 (4) ◽  
pp. 383-392 ◽  
Author(s):  
Karla J. Lindquist ◽  
Eric Jorgenson ◽  
Thomas J. Hoffmann ◽  
John S. Witte
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Sample Sizes ◽  
Genome Wide ◽  
The Impact ◽  
Larger Sample

scholarly journals Anaerobic conditions unmask antimicrobial resistance

2021 ◽  
Author(s):  
Ashton Creasy-Marrazzo ◽  
Morteza M. Saber ◽  
Manasi Kamat ◽  
Laura S. Bailey ◽  
Firdausi Qadri ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Association Studies ◽  
Anaerobic Respiration ◽  
Anaerobic Growth ◽  
Genome Wide Association Studies ◽  
Anaerobic Conditions ◽  
Aerobic Conditions ◽  
Minimal Inhibitory Concentrations ◽  
Genome Wide ◽  
The Impact

Antimicrobial resistance (AMR) in Gram negative enteropathogens is an urgent threat to the antibiotic formulary. These taxa undergo anaerobic respiration within the host, yet little is known about how anaerobic conditions influence antimicrobial resistance (AMR). The facultative enteropathogen Vibrio cholerae was chosen as a model to determine the impact of anaerobic growth on AMR because cholera is one of the few non-invasive diarrhoeal diseases for which antibiotics are indicated, albeit conditionally. V. cholerae isolates from a single outbreak were tested for resistance by minimal inhibitory concentrations (MIC) under aerobic and anaerobic conditions against clinically relevant antibiotics. Here we show that the odds of classifying isolates as resistant under anaerobic compared to aerobic conditions increased over 20 times for ciprofloxacin and 50 times for azithromycin, yet for doxycycline, all isolates remained below the breakpoint for resistance. Genome-wide association studies (GWAS) found significant associations between known and unknown genetic elements and AMR phenotypes that varied by oxygen exposure and antibiotic concentrations. In most cases, AMR phenotypes were more heritable, and more genes significantly associated with AMR were discovered, under anaerobic conditions compared to aerobic conditions. These findings challenge the paradigm of testing facultative enteropathogens for AMR under aerobic conditions alone. This experimental approach establishes a new, more sensitive framework to track and investigate mechanisms of AMR.

scholarly journals Proportion of idiopathic pulmonary fibrosis risk explained by known genetic loci

2020 ◽  
Author(s):  
Olivia C Leavy ◽  
Shwu-Fan Ma ◽  
Philip L Molyneaux ◽  
Toby M Maher ◽  
Justin M Oldham ◽  
...  
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Genetic Architecture ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Genetic Loci ◽  
Risk Variants ◽  
Genome Wide ◽  
The Impact ◽  
Insight Into

Genome-wide association studies have identified 14 genetic loci associated with susceptibility to idiopathic pulmonary fibrosis (IPF), a devastating lung disease with poor prognosis. Of these, the variant with the strongest association, rs35705950, is located in the promoter region of the MUC5B gene and has a risk allele (T) frequency of 30-35% in IPF cases. Here we present estimates of the proportion of disease liability explained by each of the 14 IPF risk variants as well as estimates of the proportion of cases that can be attributed to each variant. We estimate that rs35705950 explains 5.9-9.4% of disease liability, which is much lower than previously reported estimates. Of every 100,000 individuals with the rs35705950_GG genotype we estimate 30 will have IPF, whereas for every 100,000 individuals with the rs35705950_GT genotype 152 will have IPF. Quantifying the impact of genetic risk factors on disease liability improves our understanding of the underlying genetic architecture of IPF and provides insight into the impact of genetic factors in risk prediction modelling.

scholarly journals Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies

2021 ◽  
Vol 12 ◽  
Author(s):  
Michal Marczyk ◽  
Agnieszka Macioszek ◽  
Joanna Tobiasz ◽  
Joanna Polanska ◽  
Joanna Zyla
Keyword(s):  
Association Studies ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Gene Set Analysis ◽  
Genome Wide Association Studies ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Genome Wide ◽  
The Impact

A typical genome-wide association study (GWAS) analyzes millions of single-nucleotide polymorphisms (SNPs), several of which are in a region of the same gene. To conduct gene set analysis (GSA), information from SNPs needs to be unified at the gene level. A widely used practice is to use only the most relevant SNP per gene; however, there are other methods of integration that could be applied here. Also, the problem of nonrandom association of alleles at two or more loci is often neglected. Here, we tested the impact of incorporation of different integrations and linkage disequilibrium (LD) correction on the performance of several GSA methods. Matched normal and breast cancer samples from The Cancer Genome Atlas database were used to evaluate the performance of six GSA algorithms: Coincident Extreme Ranks in Numerical Observations (CERNO), Gene Set Enrichment Analysis (GSEA), GSEA-SNP, improved GSEA for GWAS (i-GSEA4GWAS), Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA), and Over-Representation Analysis (ORA). Association of SNPs to phenotype was calculated using modified McNemar’s test. Results for SNPs mapped to the same gene were integrated using Fisher and Stouffer methods and compared with the minimum p-value method. Four common measures were used to quantify the performance of all combinations of methods. Results of GSA analysis on GWAS were compared to the one performed on gene expression data. Comparing all evaluation metrics across different GSA algorithms, integrations, and LD correction, we highlighted CERNO, and MAGENTA with Stouffer as the most efficient. Applying LD correction increased prioritization and specificity of enrichment outcomes for all tested algorithms. When Fisher or Stouffer were used with LD, sensitivity and reproducibility were also better. Using any integration method was beneficial in comparison with a minimum p-value method in specific combinations. The correlation between GSA results from genomic and transcriptomic level was the highest when Stouffer integration was combined with LD correction. We thoroughly evaluated different approaches to GSA in GWAS in terms of performance to guide others to select the most effective combinations. We showed that LD correction and Stouffer integration could increase the performance of enrichment analysis and encourage the usage of these techniques.

scholarly journals Genetic Insights into the Impact of Complement in Alzheimer’s Disease

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1990
Author(s):  
Megan Torvell ◽  
Sarah M. Carpanini ◽  
Nikoleta Daskoulidou ◽  
Robert A. J. Byrne ◽  
Rebecca Sims ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Complement Activation ◽  
Association Studies ◽  
Screening Tests ◽  
Diagnostic Tools ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Activation Products ◽  
The Impact

The presence of complement activation products at sites of pathology in post-mortem Alzheimer’s disease (AD) brains is well known. Recent evidence from genome-wide association studies (GWAS), combined with the demonstration that complement activation is pivotal in synapse loss in AD, strongly implicates complement in disease aetiology. Genetic variations in complement genes are widespread. While most variants individually have only minor effects on complement homeostasis, the combined effects of variants in multiple complement genes, referred to as the “complotype”, can have major effects. In some diseases, the complotype highlights specific parts of the complement pathway involved in disease, thereby pointing towards a mechanism; however, this is not the case with AD. Here we review the complement GWAS hits; CR1 encoding complement receptor 1 (CR1), CLU encoding clusterin, and a suggestive association of C1S encoding the enzyme C1s, and discuss difficulties in attributing the AD association in these genes to complement function. A better understanding of complement genetics in AD might facilitate predictive genetic screening tests and enable the development of simple diagnostic tools and guide the future use of anti-complement drugs, of which several are currently in development for central nervous system disorders.

scholarly journals Smallness for gestational age interacts with high mobility group A2 gene genetic variation to modulate height

2009 ◽  
Vol 160 (4) ◽  
pp. 557-560 ◽  
Author(s):  
Nabila Bouatia-Naji ◽  
Marion Marchand ◽  
Christine Cavalcanti-Proença ◽  
Samia Daghmoun ◽  
Emmanuelle Durand ◽  
...  
Keyword(s):  
Gestational Age ◽  
Association Studies ◽  
High Mobility ◽  
Insulin Resistance Syndrome ◽  
High Mobility Group ◽  
Genome Wide Association Studies ◽  
Normal Birth ◽  
Genome Wide ◽  
Catch Up ◽  
The Impact

ObjectiveHeight variability is largely under genetic control, although identifying the genetic variants involved has been until recently challenging. Smallness for gestational age (SGA) is a risk factor for adult short stature. Genome-wide association studies have identified a single nucleotide polymorphism (SNP) (rs1042725) in the high mobility group A2 gene (HMGA2) that consistently associates with height variability but its interaction with SGA is unknown.DesignWe assess the contribution of rs1042725 SNP and height variability in a French population and the impact of rs1042725 on SGA status at birth and height at adulthood in SGA individuals.MethodsWe genotyped rs1042725 in 4710 healthy participants from the Data from an Epidemiological Study on the Insulin Resistance syndrome (DESIR) cohort, 743 normal birth weight and 660 SGA individuals from the Haguenau study.Resultsrs1042725 is associated with increased height in the cohort participants (0.36 cm 95% CI (0.12–0.61) per C allele, P=0.004) but not with the SGA status or birth length. Interestingly, rs1042725 had a stronger effect on height in SGA participants (0.94 cm 95% CI (0.24–1.64) per C allele, P=0.009), especially in men (1.45 cm 95% CI (0.44–2.46) per C allele, P=0.005) in whom rs1042725 may explain 3% of height variability. SGA men carrying at least one C allele copy experienced more frequent catch-up in height (Padd=0.07; Pdom=0.03).ConclusionsOur study supports further the contribution of HMGA2 rs1042725 to height variability in European populations and shows an increased effect on height in SGA individuals where this variant favors height catch-up.

scholarly journals Fine-scale population structure in the UK Biobank: implications for genome-wide association studies

2020 ◽  
Vol 29 (16) ◽  
pp. 2803-2811
Author(s):  
James P Cook ◽  
Anubha Mahajan ◽  
Andrew P Morris
Keyword(s):  
Population Structure ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Fine Scale ◽  
Uk Biobank ◽  
Genome Wide ◽  
Scale Population ◽  
The Uk ◽  
The Impact

Abstract The UK Biobank is a prospective study of more than 500 000 participants, which has aggregated data from questionnaires, physical measures, biomarkers, imaging and follow-up for a wide range of health-related outcomes, together with genome-wide genotyping supplemented with high-density imputation. Previous studies have highlighted fine-scale population structure in the UK on a North-West to South-East cline, but the impact of unmeasured geographical confounding on genome-wide association studies (GWAS) of complex human traits in the UK Biobank has not been investigated. We considered 368 325 white British individuals from the UK Biobank and performed GWAS of their birth location. We demonstrate that widely used approaches to adjust for population structure, including principal component analysis and mixed modelling with a random effect for a genetic relationship matrix, cannot fully account for the fine-scale geographical confounding in the UK Biobank. We observe significant genetic correlation of birth location with a range of lifestyle-related traits, including body-mass index and fat mass, hypertension and lung function, even after adjustment for population structure. Variants driving associations with birth location are also strongly associated with many of these lifestyle-related traits after correction for population structure, indicating that there could be environmental factors that are confounded with geography that have not been adequately accounted for. Our findings highlight the need for caution in the interpretation of lifestyle-related trait GWAS in UK Biobank, particularly in loci demonstrating strong residual association with birth location.

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