scholarly journals Using functional genomics to advance the understanding of psoriatic arthritis

Rheumatology ◽  
2020 ◽  
Vol 59 (11) ◽  
pp. 3137-3146
Author(s):  
Chenfu Shi ◽  
Magnus Rattray ◽  
Anne Barton ◽  
John Bowes ◽  
Gisela Orozco
Keyword(s):  
Psoriatic Arthritis ◽  
Functional Genomics ◽  
Complex Disease ◽  
Association Studies ◽  
Joint Damage ◽  
Underlying Disease ◽  
Genome Wide Association Studies ◽  
Disease Mechanism ◽  
Genome Wide ◽  
Functional Mechanisms

Abstract Psoriatic arthritis (PsA) is a complex disease where susceptibility is determined by genetic and environmental risk factors. Clinically, PsA involves inflammation of the joints and the skin, and, if left untreated, results in irreversible joint damage. There is currently no cure and the few treatments available to alleviate symptoms do not work in all patients. Over the past decade, genome-wide association studies (GWAS) have uncovered a large number of disease-associated loci but translating these findings into functional mechanisms and novel targets for therapeutic use is not straightforward. Most variants have been predicted to affect primarily long-range regulatory regions such as enhancers. There is now compelling evidence to support the use of chromatin conformation analysis methods to discover novel genes that can be affected by disease-associated variants. Here, we will review the studies published in the field that have given us a novel understanding of gene regulation in the context of functional genomics and how this relates to the study of PsA and its underlying disease mechanism.

scholarly journals Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Tianxiao Huan ◽  
Roby Joehanes ◽  
Ci Song ◽  
Fen Peng ◽  
Yichen Guo ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
Dna Methylation ◽  
Whole Blood ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Transcriptional Regulatory ◽  
Disease Associations ◽  
Independent Replication ◽  
Functional Mechanisms

Abstract Identifying methylation quantitative trait loci (meQTLs) and integrating them with disease-associated variants from genome-wide association studies (GWAS) may illuminate functional mechanisms underlying genetic variant-disease associations. Here, we perform GWAS of >415 thousand CpG methylation sites in whole blood from 4170 individuals and map 4.7 million cis- and 630 thousand trans-meQTL variants targeting >120 thousand CpGs. Independent replication is performed in 1347 participants from two studies. By linking cis-meQTL variants with GWAS results for cardiovascular disease (CVD) traits, we identify 92 putatively causal CpGs for CVD traits by Mendelian randomization analysis. Further integrating gene expression data reveals evidence of cis CpG-transcript pairs causally linked to CVD. In addition, we identify 22 trans-meQTL hotspots each targeting more than 30 CpGs and find that trans-meQTL hotspots appear to act in cis on expression of nearby transcriptional regulatory genes. Our findings provide a powerful meQTL resource and shed light on DNA methylation involvement in human diseases.

scholarly journals Genetics of Atrial Fibrillation in 2020

2020 ◽  
Vol 127 (1) ◽  
pp. 21-33 ◽  
Author(s):  
Carolina Roselli ◽  
Michiel Rienstra ◽  
Patrick T. Ellinor
Keyword(s):  
Atrial Fibrillation ◽  
Complex Disease ◽  
Association Studies ◽  
Heart Rhythm ◽  
Genome Wide Association Studies ◽  
Future Directions ◽  
Genetics Research ◽  
Genome Wide ◽  
Increased Risk ◽  
Rhythm Disorder

Atrial fibrillation is a common heart rhythm disorder that leads to an increased risk for stroke and heart failure. Atrial fibrillation is a complex disease with both environmental and genetic risk factors that contribute to the arrhythmia. Over the last decade, rapid progress has been made in identifying the genetic basis for this common condition. In this review, we provide an overview of the primary types of genetic analyses performed for atrial fibrillation, including linkage studies, genome-wide association studies, and studies of rare coding variation. With these results in mind, we aim to highlighting the existing knowledge gaps and future directions for atrial fibrillation genetics research.

Current Challenges in the Genetics of Psoriatic Arthritis: A Report from the GRAPPA 2009 Annual Meeting

2011 ◽  
Vol 38 (3) ◽  
pp. 564-566 ◽  
Author(s):  
PROTON RAHMAN
Keyword(s):  
Psoriatic Arthritis ◽  
Annual Meeting ◽  
Association Studies ◽  
Environment Interaction ◽  
Genome Wide Association Studies ◽  
Novel Genes ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
Genome Wide

Psoriasis and psoriatic arthritis (PsA) are heterogeneous diseases. While both have a strong genetic basis, it is strongest for PsA, where fewer investigators are studying its genetics. Over the last year the number of independent genetic loci associated with psoriasis has substantially increased, mostly due to completion of multiple genome-wide association studies (GWAS) in psoriasis. At least 2 GWAS efforts are now under way in PsA to identify novel genes in this disease; a metaanalysis of genome-wide scans and further studies must follow to examine the genetics of disease expression, epistatic interaction, and gene-environment interaction. In the long term, it is anticipated that genome-wide sequencing is likely to generate another wave of novel genes in PsA. At the annual meeting of the Group for Research and Assessment of Psoriasis and Psoriatic Arthritis (GRAPPA) in Stockholm, Sweden, in 2009, members discussed issues and challenges regarding the advancement of the genetics of PsA; results of those discussions are summarized here.

Biomarkers for Comorbidities in Psoriasis: A Report from the Grappa 2011 Annual Meeting

2012 ◽  
Vol 39 (11) ◽  
pp. 2193-2195 ◽  
Author(s):  
DAFNA D. GLADMAN
Keyword(s):  
Psoriatic Arthritis ◽  
Annual Meeting ◽  
Research Team ◽  
Association Studies ◽  
Differentially Expressed ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Current Database ◽  
And Cartilage

Biomarkers are being recognized that will help identify patients with psoriasis who may be destined to develop psoriatic arthritis (PsA). Recent genome-wide association studies have identified genes that are common to both psoriasis and PsA, as well as differentially expressed in the 2 conditions. Further, biomarkers of inflammation and cartilage can differentiate between patients with PsA and those with psoriasis without arthritis. An overview of these biomarkers was presented at the 2011 annual meeting of the Group for Research and Assessment of Psoriasis and Psoriatic Arthritis. Additionally, a report was presented from the current database of the International Psoriasis and Psoriatic Arthritis Research Team, a group of dermatologists and rheumatologists with the objective to improve the lives of patients with psoriasis and PsA.

scholarly journals Current Insights in Genetics of Sarcoidosis: Functional and Clinical Impacts

2020 ◽  
Vol 9 (8) ◽  
pp. 2633 ◽  
Author(s):  
Alain Calender ◽  
Thomas Weichhart ◽  
Dominique Valeyre ◽  
Yves Pacheco
Keyword(s):  
Complex Disease ◽  
Current Knowledge ◽  
Association Studies ◽  
Genetic Research ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Whole Exome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Future Management

Sarcoidosis is a complex disease that belongs to the vast group of autoinflammatory disorders, but the etiological mechanisms of which are not known. At the crosstalk of environmental, infectious, and genetic factors, sarcoidosis is a multifactorial disease that requires a multidisciplinary approach for which genetic research, in particular, next generation sequencing (NGS) tools, has made it possible to identify new pathways and propose mechanistic hypotheses. Codified treatments for the disease cannot always respond to the most progressive forms and the identification of new genetic and metabolic tracks is a challenge for the future management of the most severe patients. Here, we review the current knowledge regarding the genes identified by both genome wide association studies (GWAS) and whole exome sequencing (WES), as well the connection of these pathways with the current research on sarcoidosis immune-related disorders.

scholarly journals Deep genotype imputation captures virtually all heritability of autoimmune vitiligo

2020 ◽  
Vol 29 (5) ◽  
pp. 859-863 ◽  
Author(s):  
Genevieve H L Roberts ◽  
Stephanie A Santorico ◽  
Richard A Spritz
Keyword(s):  
Complex Disease ◽  
Rare Variants ◽  
Association Studies ◽  
Genotype Imputation ◽  
Genome Wide Association Studies ◽  
Common Variants ◽  
Genome Wide ◽  
Autoimmune Vitiligo ◽  
Family Based ◽  
Project Data

Abstract Autoimmune vitiligo is a complex disease involving polygenic risk from at least 50 loci previously identified by genome-wide association studies. The objectives of this study were to estimate and compare vitiligo heritability in European-derived patients using both family-based and ‘deep imputation’ genotype-based approaches. We estimated family-based heritability (h2FAM) by vitiligo recurrence among a total 8034 first-degree relatives (3776 siblings, 4258 parents or offspring) of 2122 unrelated vitiligo probands. We estimated genotype-based heritability (h2SNP) by deep imputation to Haplotype Reference Consortium and the 1000 Genomes Project data in unrelated 2812 vitiligo cases and 37 079 controls genotyped genome wide, achieving high-quality imputation from markers with minor allele frequency (MAF) as low as 0.0001. Heritability estimated by both approaches was exceedingly high; h2FAM = 0.75–0.83 and h2SNP = 0.78. These estimates are statistically identical, indicating there is essentially no remaining ‘missing heritability’ for vitiligo. Overall, ~70% of h2SNP is represented by common variants (MAF > 0.01) and 30% by rare variants. These results demonstrate that essentially all vitiligo heritable risk is captured by array-based genotyping and deep imputation. These findings suggest that vitiligo may provide a particularly tractable model for investigation of complex disease genetic architecture and predictive aspects of personalized medicine.

Identifying Novel Psoriatic Disease Drug Targets Using a Genetics-Based Priority Index Pipeline

2021 ◽  
pp. 247553032110260
Author(s):  
Audrey Bui ◽  
Jared Liu ◽  
Julie Hong ◽  
Edward Hadeler ◽  
Megan Mosca ◽  
...  
Keyword(s):  
Psoriatic Arthritis ◽  
Drug Targets ◽  
Association Studies ◽  
Therapeutic Targets ◽  
Genome Wide Association Studies ◽  
Priority Index ◽  
Psoriatic Disease ◽  
Genome Wide ◽  
Pathway Crosstalk ◽  
Potential Drug Targets

Background: Despite numerous genome-wide association studies conducted in psoriasis and psoriatic arthritis, only a small fraction of the identified genes has been therapeutically targeted. Objective: We sought to identify and analyze potential therapeutic targets for psoriasis and psoriatic arthritis (PsA) using the priority index (Pi), a genetics-dependent drug target prioritization approach. Methods: Significant genetic variants from GWAS for psoriasis, PsA, and combined psoriatic disease were annotated and run through the Pi pipeline. Potential drug targets were identified based on genomic predictors, annotation predictors, pathway enrichment, and pathway crosstalk. Results: Several gene targets were identified for psoriasis and PsA that demonstrated biological associations to their respective diseases. Some are currently being explored as potential therapeutic targets (i.e. ICAM1, NF-kB, REV3 L, ADRA1B for psoriasis; CCL11 for PsA); others have not yet been investigated (i.e. LNPEP, LCE3 for psoriasis; UBLCP1 for PsA). Additionally, many nodal points of potential intervention were identified as promising therapeutic targets. Of these, some are currently being studied such as TYK2 for psoriasis, and others have yet to be explored (i.e. PPP2CA, YAP1, PI3 K, AKT, FOXO1, RELA, CSF2, IFNGR1, IFNGR2 for psoriasis; GNAQ, PLCB1, GNAI2 for PsA). Conclusion: Through Pi, we identified data-driven candidate therapeutic gene targets and pathways for psoriasis and PsA. Given the sparse PsA specific genetic studies and PsA specific drug targets, this analysis could prove to be particularly valuable in the pipeline for novel psoriatic therapies.

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