scholarly journals Multivariate GWAS of Structural Dental Anomalies and Dental Caries in a Multi-Ethnic Cohort

2022 ◽  
Vol 2 ◽  
Author(s):  
Rasha N. Alotaibi ◽  
Brian J. Howe ◽  
Lina M. Moreno Uribe ◽  
Consuelo Valencia Ramirez ◽  
Claudia Restrepo ◽  
...  
Keyword(s):  
Dental Caries ◽  
Genome Wide Association Study ◽  
Tooth Development ◽  
Tooth Agenesis ◽  
Genetic Associations ◽  
Dental Anomalies ◽  
Enamel Hypoplasia ◽  
Multivariate Tests ◽  
Study Approach ◽  
Genome Wide

Odontogenesis is a complex process, where disruption can result in dental anomalies and/or increase the risk of developing dental caries. Based on previous studies, certain dental anomalies tend to co-occur in patients, suggesting that these traits may share common genetic and etiological components. The main goal of this study was to implement a multivariate genome wide association study approach to identify genetic variants shared between correlated structural dental anomalies and dental caries. Our cohort (N = 3,579) was derived from the Pittsburgh Orofacial Clefts Study, where multiple dental traits were assessed in both the unaffected relatives of orofacial cleft (OFC) cases (n = 2,187) and unaffected controls (n = 1,392). We identified four multivariate patterns of correlated traits in this data: tooth agenesis, impaction, and rotation (AIR); enamel hypoplasia, displacement, and rotation (HDR); displacement, rotation, and mamelon (DRM); and dental caries, tooth agenesis and enamel hypoplasia (CAH). We analyzed each of these four models using genome-wide multivariate tests of association. No genome-wide statistically significant results were found, but we identified multiple suggestive association signals (P ≤ 10−5) near genes with known biological roles during tooth development, including ADAMTS9 and PRICKLE2 associated with AIR; GLIS3, WDR72, and ROR2 associated with HDR and DRM; ROBO2 associated with DRM; BMP7 associated with HDR; and ROBO1, SMAD2, and MSX2 associated with CAH. This is the first study to investigative genetic associations for multivariate patterns of correlated dental anomalies and dental caries. Further studies are needed to replicate these results in independent cohorts.

Genetics of spondyloarthritis

2016 ◽  
Author(s):  
Matthew A. Brown ◽  
John Reveille
Keyword(s):  
Genome Wide Association Study ◽  
Hla B27 ◽  
Genetic Associations ◽  
Study Approach ◽  
Histocompatibility Complex ◽  
Genome Wide ◽  
Great Progress ◽  
Mediterranean Fever ◽  
Inflammatory Bowel ◽  
Shed Light

In addition to sharing clinical, histopathological, and immunological features, spondyloarthritis (SpA) encompasses a group of diseases that are genetically linked through shared associations with HLA-B27, as well as other genes of the IL-23R and aminopeptidase groups. Great progress has been made since the development of the genome-wide association study approach, with better dissection of the HLA associations of this group of diseases, as well as the discovery of multiple genetic loci found outside of the major histocompatibility complex, in ankylosing spondylitis (AS) in particular. These genetic data shed light on the related pathogenesis of AS and psoriatic arthritis (PsA), inflammatory bowel disease (IBD)-related arthritis, and reactive arthritis (ReA). Genetic associations also strengthen the suggestive data that Behçet’s disease (BD) and Familial Mediterranean Fever (FMF) are related to the more classical forms of SpA.

A Proteome-Wide Association Study Identified Candidate Human Brain Proteins Associated with Coffee Consumption

2021 ◽  
Author(s):  
Chun'e Li ◽  
Xiao Liang ◽  
Yumeng Jia ◽  
Yan Wen ◽  
Huijie Zhang ◽  
...  
Keyword(s):  
Human Brain ◽  
Association Study ◽  
Plasma Proteins ◽  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
Coffee Consumption ◽  
Genetic Associations ◽  
Brain Proteins ◽  
Genome Wide ◽  
Brain Proteome

Abstract Background Increasing evidence suggests the association between caffeine and the brain and nervous system. However, there is limited research on the genetic associations between coffee consumption subtypes and brain proteome, plasma proteomes, and peripheral metabolites. Methods First, proteome-wide association study (PWAS) of coffee consumption subtypes was performed by integrating two independent genome-wide association study (GWAS) datasets (91,462–502,650 subjects) with two reference human brain proteomes (ROS/MAP and Banner), by using the FUSION pipeline. Second, transcriptome-wide association study (TWAS) analysis of coffee consumption subtypes was conducted by integrating the two gene expression weight references (RNAseq and splicing) of brain RNA-seq and the two GWAS datasets (91,462–502,650 subjects) of coffee consumption subtypes. Finally, we used the LD Score Regression (LDSC) analysis to evaluate the genetic correlations of coffee consumption subtypes with plasma proteomes and peripheral metabolites. Results For the traits related to coffee consumption, we identified 3 common PWAS proteins, such as MADD (P PWAS−Banner−dis=0.0114, P PWAS−ROS/MAP−rep =0.0489). In addition, 11 common TWAS genes were found in two cohorts, such as ARPC2 (P TWAS−splicing−dis =2063×10− 12, P TWAS−splicing−dis =1.25×10− 10, P TWAS−splicing−dis =1.24e-08, P TWAS−splicing−rep =3.25×10− 9 and P TWAS−splicing−rep =3.42×10− 13). Importantly, we have identified 8 common genes between PWAS and TWAS, such as ALDH2 (P PWAS−banner−rep =1.22×10− 22, PTWAS− splicing−dis = 4.54×10− 92). For the LDSC analysis of human plasma proteome, we identified 11 plasma proteins, such as CHL1 (P dis = 0.0151, P rep =0.0438). For the LDSC analysis of blood metabolites, 5 metabolites have been found, such as myo-inositol (P dis = 0.0073, P dis = 0.0152, P dis =0.0414, P rep =0.0216). Conclusions We identified several brain proteins and genes associated with coffee consumption subtypes. In addition, we also detected several candidate plasma proteins and metabolites related to these subtypes.

scholarly journals Kleine-Levin syndrome is associated with birth difficulties and genetic variants in the TRANK1 gene loci

2021 ◽  
Vol 118 (12) ◽  
pp. e2005753118
Author(s):  
Aditya Ambati ◽  
Ryan Hillary ◽  
Smaranda Leu-Semenescu ◽  
Hanna M. Ollila ◽  
Ling Lin ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Genome Wide Association Study ◽  
Perinatal Outcomes ◽  
Case Control ◽  
Risk Scores ◽  
Circadian Regulation ◽  
Genetic Associations ◽  
Imaging Studies ◽  
Genome Wide

Kleine-Levin syndrome (KLS) is a rare disorder characterized by severe episodic hypersomnia, with cognitive impairment accompanied by apathy or disinhibition. Pathophysiology is unknown, although imaging studies indicate decreased activity in hypothalamic/thalamic areas during episodes. Familial occurrence is increased, and risk is associated with reports of a difficult birth. We conducted a worldwide case−control genome-wide association study in 673 KLS cases collected over 14 y, and ethnically matched 15,341 control individuals. We found a strong genome-wide significant association (rs71947865, Odds Ratio [OR] = 1.48, P = 8.6 × 10−9) within the 3′region of TRANK1 gene locus, previously associated with bipolar disorder and schizophrenia. Strikingly, KLS cases with rs71947865 variant had significantly increased reports of a difficult birth. As perinatal outcomes have dramatically improved over the last 40 y, we further stratified our sample by birth years and found that recent cases had a significantly reduced rs71947865 association. While the rs71947865 association did not replicate in the entire follow-up sample of 171 KLS cases, rs71947865 was significantly associated with KLS in the subset follow-up sample of 59 KLS cases who reported birth difficulties (OR = 1.54, P = 0.01). Genetic liability of KLS as explained by polygenic risk scores was increased (pseudo R2 = 0.15; P < 2.0 × 10−22 at P = 0.5 threshold) in the follow-up sample. Pathway analysis of genetic associations identified enrichment of circadian regulation pathway genes in KLS cases. Our results suggest links between KLS, circadian regulation, and bipolar disorder, and indicate that the TRANK1 polymorphisms in conjunction with reported birth difficulties may predispose to KLS.

scholarly journals Genetic Determinants of Telomere Length in African American Youth

2018 ◽  
Author(s):  
Andrew M. Zeiger ◽  
Marquitta J. White ◽  
Sam S. Oh ◽  
Jonathan Witonsky ◽  
Maria G. Contreras ◽  
...  
Keyword(s):  
African American ◽  
Telomere Length ◽  
Genome Wide Association Study ◽  
African Ancestry ◽  
African American Youth ◽  
Genetic Associations ◽  
Disease States ◽  
Genome Wide ◽  
Pediatric Populations ◽  
Genetic And Environmental Factors

ABSTRACTTelomere length (TL) is associated with numerous disease states and is affected by genetic and environmental factors. However, TL has been mostly studied in adult populations of European or Asian ancestry. These studies have identified 34 TL-associated genetic variants recently used as genetic proxies for TL. The generalizability of these associations to pediatric populations and racially diverse populations, specifically of African ancestry, remains unclear. Furthermore, six novel variants associated with TL in a population of European children have been identified but not validated. We measured TL from whole blood samples of 492 healthy African American youth (children and adolescents between 8 and 20 years old) and performed the first genome-wide association study of TL in this population. We were unable to replicate neither the 34 reported genetic associations found in adults nor the six genetic associations found in European children. However, we discovered a novel genome-wide significant association between TL and rs1483898 on chromosome 14. Our results underscore the importance of examining these genetic associations with TL in diverse pediatric populations such as African Americans.

scholarly journals Genetic Associations with Subjective Well-Being Also Implicate Depression and Neuroticism

2015 ◽  
Author(s):  
Aysu Okbay ◽  
Bart M. L. Baselmans ◽  
Jan-Emmanuel De Neve ◽  
Patrick Turley ◽  
Michel G. Nivard ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Genome Wide Association Study ◽  
Well Being ◽  
Genome Wide Association ◽  
Subjective Well Being ◽  
Genetic Associations ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Significance

We conducted a genome-wide association study of subjective well-being (SWB) in 298,420 individuals. We also performed auxiliary analyses of depressive symptoms ("DS";N= 161,460) and neuroticism (N= 170,910), both of which have a substantial genetic correlation with SWB (ρ≈-0.8). We identify three SNPs associated with SWB at genome-wide significance. Two of them are significantly associated with DS in an independent sample. In our auxiliary analyses, we identify 13 additional genome-wide-significant associations: two with DS and eleven with neuroticism, including two inversion polymorphisms. Across our phenotypes, loci regulating expression in central nervous system and adrenal/pancreas tissues are enriched. The discovery of genetic loci associated with the three phenotypes we study has proven elusive; our findings illustrate the payoffs from studying them jointly.

Genetic associations with taxane-induced neuropathy by a genome-wide association study (GWAS) in E5103.

2011 ◽  
Vol 29 (15_suppl) ◽  
pp. 1000-1000 ◽  
Author(s):  
B. P. Schneider ◽  
L. Li ◽  
K. Miller ◽  
D. Flockhart ◽  
M. Radovich ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genetic Associations ◽  
Genome Wide ◽  
A Genome

297 Genetic associations of ICD in parkinson’s disease

2018 ◽  
Vol 89 (10) ◽  
pp. A47.2-A47
Author(s):  
Rees Richard ◽  
Hubbard Leon ◽  
Ben-Shlomo Yoav ◽  
Grosset Donald ◽  
Williams Nigel ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Genome Wide Association Study ◽  
Early Stage ◽  
Age At Onset ◽  
Genetic Associations ◽  
Longitudinal Assessment ◽  
Genetic Determinants ◽  
Genome Wide ◽  
A Genome

IntroductionImpuse Control Disorders (ICD) are a potentially devastating side-effect of dopaminergic therapy in Parkinson’s disease (PD). We explore the genetic factors associated with ICD in Tracking Parkinson’s/PRoBaND – a UK-wide cohort of early-stage PD.MethodsParticipants were diagnosed with PD within 3 years and had longitudinal assessment including the Questionnaire for ICD in Parkinson’s (QUIP) for up to 5 years. We defined cases as having any positive response to the QUIP (lax criteria) or 2 positive responses in any domain (strict criteria). We performed a candidate-gene analysis based on systematic review, followed by a genome-wide association study. We used age at onset, gender, and three significant principle components as covariates.ResultsAfter clinical and genetic quality control steps, we analysed 1602 participants. Prevalence was significantly affected by classification criteria (strict/lax): ICD – 26.8%/11.1%, IRB 29.3%/27.2%, any 31.7%/41.9%. Six SNPs in dopamine, glutamate and adreno- receptor genes achieved nominal significance (p<0.05) in the candidate study. We have identified several SNPs in the GWAS that approach genome wide significance (p<5 × 10–7).ConclusionsThis work is the first genome-wide study of genetic determinants of ICD. Our findings support the hypothesis of genetic determinants of ICD in Parkinson’s and further work will allow understanding of the biology of ICD.

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