Biobank data for studying the genetic architecture of osteoporosis and developing genetic risk scores

Osteoporosis is a chronic systemic disease of the skeleton, characterized by a decrease in bone mass and an impairment of bone microarchitecture, which can lead to a decrease in bone strength and an increase in the risk of minor trauma fractures. Osteoporosis is diagnosed on the basis of bone mineral density (BMD). BMD is characterized by high heritability that ranges according to various sources from 50 to 85%. As in the case of other complex traits, the most common approach to searching for genetic variants that affect BMD is a genome-wide association study. The lower effect size or frequency of a variant is, the larger the sample size is required to achieve statistically significant data on associations. Therefore, the studies involving hundreds of thousands of participants based on biobank data can identify the largest number of variants associated with BMD. In addition, biobank data are used in the development of genetic risk scores for osteoporosis that can be used both in combination with existing prognosis algorithms and independently of them. The aim of this review was to present the most significant studies of osteoporosis genetics, including those based on biobank data and genome-wide association studies, as well as studies on the genetic risk scores and the contribution of rare variants.

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Interaction between Genetic Risk Scores for reduced pulmonary function and smoking, asthma and endotoxin

Thorax ◽

10.1136/thoraxjnl-2020-215624 ◽

2021 ◽

pp. thoraxjnl-2020-215624

Author(s):

Sinjini Sikdar ◽

Annah B Wyss ◽

Mi Kyeong Lee ◽

Thanh T Hoang ◽

Marie Richards ◽

...

Keyword(s):

Pulmonary Function ◽

Genetic Risk ◽

Association Studies ◽

European Ancestry ◽

Risk Scores ◽

P Value ◽

Genome Wide Association Studies ◽

Inverse Association ◽

Genetic Risk Scores ◽

Genome Wide

RationaleGenome-wide association studies (GWASs) have identified numerous loci associated with lower pulmonary function. Pulmonary function is strongly related to smoking and has also been associated with asthma and dust endotoxin. At the individual SNP level, genome-wide analyses of pulmonary function have not identified appreciable evidence for gene by environment interactions. Genetic Risk Scores (GRSs) may enhance power to identify gene–environment interactions, but studies are few.MethodsWe analysed 2844 individuals of European ancestry with 1000 Genomes imputed GWAS data from a case–control study of adult asthma nested within a US agricultural cohort. Pulmonary function traits were FEV1, FVC and FEV1/FVC. Using data from a recent large meta-analysis of GWAS, we constructed a weighted GRS for each trait by combining the top (p value<5×10−9) genetic variants, after clumping based on distance (±250 kb) and linkage disequilibrium (r2=0.5). We used linear regression, adjusting for relevant covariates, to estimate associations of each trait with its GRS and to assess interactions.ResultsEach trait was highly significantly associated with its GRS (all three p values<8.9×10−8). The inverse association of the GRS with FEV1/FVC was stronger for current smokers (pinteraction=0.017) or former smokers (pinteraction=0.064) when compared with never smokers and among asthmatics compared with non-asthmatics (pinteraction=0.053). No significant interactions were observed between any GRS and house dust endotoxin.ConclusionsEvaluation of interactions using GRSs supports a greater impact of increased genetic susceptibility on reduced pulmonary function in the presence of smoking or asthma.

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Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study

10.21203/rs.3.rs-800781/v1 ◽

2021 ◽

Author(s):

Kim Philipp Jablonski ◽

Leopold Carron ◽

Julien Mozziconacci ◽

Thierry Forné ◽

Marc-Thorsten Hütt ◽

...

Keyword(s):

Genetic Risk ◽

Genome Organization ◽

Computational Study ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Topological Domains ◽

3D Genome ◽

Genome Wide ◽

A Genome

Abstract Background Genome-wide association studies have identified statistical associations between various diseases, including cancers, and a large number of single-nucleotide polymorphisms (SNPs). However, they provide no direct explanation of the mechanisms underlying the association. Based on the recent discovery that changes in 3-dimensional genome organization may have functional consequences on gene regulation favoring diseases, we investigated systematically the genome-wide distribution of disease-associated SNPs with respect to a specific feature of 3D genome organization: topologically-associating domains (TADs) and their borders. Results For each of 449 diseases, we tested whether the associated SNPs are present in TAD borders more often than observed by chance, where chance (i.e. the null model in statistical terms) corresponds to the same number of pointwise loci drawn at random either in the entire genome, or in the entire set of disease-associated SNPs listed in the GWAS catalog. Our analysis shows that a fraction of diseases displays such a preferential localization of their risk loci. Moreover, cancers are relatively more frequent among these diseases, and this predominance is generally enhanced when considering only intergenic SNPs. The structure of SNP-based diseasome networks confirms that localization of risk loci in TAD borders differ between cancers and non-cancer diseases. Furthermore, different TAD border enrichments are observed in embryonic stem cells and differentiated cells, consistent with changes in topological domains along embryogenesis and delineating their contribution to disease risk. Conclusions Our results suggest that, for certain diseases, part of the genetic risk lies in a local genetic variation affecting the genome partitioning in topologically-insulated domains. Investigating this possible contribution to genetic risk is particularly relevant in cancers. This study thus opens a way of interpreting genome-wide association studies, by distinguishing two types of disease-associated SNPs: one with a direct effect on an individual gene, the other acting in interplay with 3D genome organization.

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Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study

Human Genomics ◽

10.1186/s40246-022-00375-2 ◽

2022 ◽

Vol 16 (1) ◽

Author(s):

Kim Philipp Jablonski ◽

Leopold Carron ◽

Julien Mozziconacci ◽

Thierry Forné ◽

Marc-Thorsten Hütt ◽

...

Keyword(s):

Genetic Risk ◽

Genome Organization ◽

Computational Study ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Topological Domains ◽

3D Genome ◽

Genome Wide ◽

A Genome

Abstract Background Genome-wide association studies have identified statistical associations between various diseases, including cancers, and a large number of single-nucleotide polymorphisms (SNPs). However, they provide no direct explanation of the mechanisms underlying the association. Based on the recent discovery that changes in three-dimensional genome organization may have functional consequences on gene regulation favoring diseases, we investigated systematically the genome-wide distribution of disease-associated SNPs with respect to a specific feature of 3D genome organization: topologically associating domains (TADs) and their borders. Results For each of 449 diseases, we tested whether the associated SNPs are present in TAD borders more often than observed by chance, where chance (i.e., the null model in statistical terms) corresponds to the same number of pointwise loci drawn at random either in the entire genome, or in the entire set of disease-associated SNPs listed in the GWAS catalog. Our analysis shows that a fraction of diseases displays such a preferential localization of their risk loci. Moreover, cancers are relatively more frequent among these diseases, and this predominance is generally enhanced when considering only intergenic SNPs. The structure of SNP-based diseasome networks confirms that localization of risk loci in TAD borders differs between cancers and non-cancer diseases. Furthermore, different TAD border enrichments are observed in embryonic stem cells and differentiated cells, consistent with changes in topological domains along embryogenesis and delineating their contribution to disease risk. Conclusions Our results suggest that, for certain diseases, part of the genetic risk lies in a local genetic variation affecting the genome partitioning in topologically insulated domains. Investigating this possible contribution to genetic risk is particularly relevant in cancers. This study thus opens a way of interpreting genome-wide association studies, by distinguishing two types of disease-associated SNPs: one with an effect on an individual gene, the other acting in interplay with 3D genome organization.

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Genetic determinants of glucose levels in pregnancy: genetic risk scores analysis and GWAS in the Norwegian STORK cohort

Acta Endocrinologica ◽

10.1530/eje-18-0478 ◽

2018 ◽

Vol 179 (6) ◽

pp. 363-372 ◽

Cited By ~ 2

Author(s):

Gunn-Helen Moen ◽

Marissa LeBlanc ◽

Christine Sommer ◽

Rashmi B Prasad ◽

Tove Lekva ◽

...

Keyword(s):

Pregnant Women ◽

Genetic Risk ◽

Association Studies ◽

Risk Scores ◽

Oral Glucose ◽

Genome Wide Association Studies ◽

Shape Information ◽

Genetic Risk Scores ◽

Genome Wide ◽

In Pregnancy

Objective Hyperglycaemia during pregnancy increases the risk of adverse health outcomes in mother and child, but the genetic aetiology is scarcely studied. Our aims were to (1) assess the overlapping genetic aetiology between the pregnant and non-pregnant population and (2) assess the importance of genome-wide polygenic contributions to glucose traits during pregnancy, by exploring whether genetic risk scores (GRSs) for fasting glucose (FG), 2-h glucose (2hG), type 2 diabetes (T2D) and BMI in non-pregnant individuals were associated with glucose measures in pregnant women. Methods We genotyped 529 Norwegian pregnant women and constructed GRS from known genome-wide significant variants and SNPs weakly associated (p > 5 × 10−8) with FG, 2hG, BMI and T2D from external genome-wide association studies (GWAS) and examined the association between these scores and glucose measures at gestational weeks 14–16 and 30–32. We also performed GWAS of FG, 2hG and shape information from the glucose curve during an oral glucose tolerance test (OGTT). Results GRSFG explained similar variance during pregnancy as in the non-pregnant population (~5%). GRSBMI and GRST2D explained up to 1.3% of the variation in the glucose traits in pregnancy. If we included variants more weakly associated with these traits, GRS2hG and GRST2D explained up to 2.4% of the variation in the glucose traits in pregnancy, highlighting the importance of polygenic contributions. Conclusions Our results suggest overlap in the genetic aetiology of FG in pregnant and non-pregnant individuals. This was less apparent with 2hG, suggesting potential differences in postprandial glucose metabolism inside and outside of pregnancy.

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Genetic Risk of Clozapine Induced Leukopenia and Neutropenia: A Genome-Wide Association Study

SSRN Electronic Journal ◽

10.2139/ssrn.3676216 ◽

2020 ◽

Author(s):

Jianhua Chen ◽

Ping Yang ◽

Qian Zhang ◽

Ruirui Chen ◽

Peng Wang ◽

...

Keyword(s):

Association Study ◽

Genetic Risk ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

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Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses

Genes ◽

10.3390/genes10050370 ◽

2019 ◽

Vol 10 (5) ◽

pp. 370 ◽

Cited By ~ 5

Author(s):

Annik Imogen Gmel ◽

Thomas Druml ◽

Rudolf von Niederhäusern ◽

Tosso Leeb ◽

Markus Neuditschko

Keyword(s):

Joint Angle ◽

Association Studies ◽

Genome Wide Association ◽

Cranial Morphology ◽

Genome Wide Association Studies ◽

Joint Angles ◽

Mineral Density ◽

Mixed Effect ◽

Stifle Joint ◽

Genome Wide

The evaluation of conformation traits is an important part of selection for breeding stallions and mares. Some of these judged conformation traits involve joint angles that are associated with performance, health, and longevity. To improve our understanding of the genetic background of joint angles in horses, we have objectively measured the angles of the poll, elbow, carpal, fetlock (front and hind), hip, stifle, and hock joints based on one photograph of each of the 300 Franches-Montagnes (FM) and 224 Lipizzan (LIP) horses. After quality control, genome-wide association studies (GWASs) for these traits were performed on 495 horses, using 374,070 genome-wide single nucleotide polymorphisms (SNPs) in a mixed-effect model. We identified two significant quantitative trait loci (QTL) for the poll angle on ECA28 (p = 1.36 × 10−7), 50 kb downstream of the ALX1 gene, involved in cranial morphology, and for the elbow joint on ECA29 (p = 1.69 × 10−7), 49 kb downstream of the RSU1 gene, and 75 kb upstream of the PTER gene. Both genes are associated with bone mineral density in humans. Furthermore, we identified other suggestive QTL associated with the stifle joint on ECA8 (p = 3.10 × 10−7); the poll on ECA1 (p = 6.83 × 10−7); the fetlock joint of the hind limb on ECA27 (p = 5.42 × 10−7); and the carpal joint angle on ECA3 (p = 6.24 × 10−7), ECA4 (p = 6.07 × 10−7), and ECA7 (p = 8.83 × 10−7). The application of angular measurements in genetic studies may increase our understanding of the underlying genetic effects of important traits in equine breeding.

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Association analysis of juvenile idiopathic arthritis genetic susceptibility factors in Estonian patients

Clinical Rheumatology ◽

10.1007/s10067-021-05756-x ◽

2021 ◽

Author(s):

Tiit Nikopensius ◽

Priit Niibo ◽

Toomas Haller ◽

Triin Jagomägi ◽

Ülle Voog-Oras ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Juvenile Idiopathic Arthritis ◽

Autoimmune Diseases ◽

Genetic Risk ◽

Association Studies ◽

Control Sample ◽

Case Control ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide

Abstract Background Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic condition of childhood. Genetic association studies have revealed several JIA susceptibility loci with the strongest effect size observed in the human leukocyte antigen (HLA) region. Genome-wide association studies have augmented the number of JIA-associated loci, particularly for non-HLA genes. The aim of this study was to identify new associations at non-HLA loci predisposing to the risk of JIA development in Estonian patients. Methods We performed genome-wide association analyses in an entire JIA case–control sample (All-JIA) and in a case–control sample for oligoarticular JIA, the most prevalent JIA subtype. The entire cohort was genotyped using the Illumina HumanOmniExpress BeadChip arrays. After imputation, 16,583,468 variants were analyzed in 263 cases and 6956 controls. Results We demonstrated nominal evidence of association for 12 novel non-HLA loci not previously implicated in JIA predisposition. We replicated known JIA associations in CLEC16A and VCTN1 regions in the oligoarticular JIA sample. The strongest associations in the All-JIA analysis were identified at PRKG1 (P = 2,54 × 10−6), LTBP1 (P = 9,45 × 10−6), and ELMO1 (P = 1,05 × 10−5). In the oligoarticular JIA analysis, the strongest associations were identified at NFIA (P = 5,05 × 10−6), LTBP1 (P = 9,95 × 10−6), MX1 (P = 1,65 × 10−5), and CD200R1 (P = 2,59 × 10−5). Conclusion This study increases the number of known JIA risk loci and provides additional evidence for the existence of overlapping genetic risk loci between JIA and other autoimmune diseases, particularly rheumatoid arthritis. The reported loci are involved in molecular pathways of immunological relevance and likely represent genomic regions that confer susceptibility to JIA in Estonian patients. Key Points• Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease with heterogeneous presentation and genetic predisposition.• Present genome-wide association study for Estonian JIA patients is first of its kind in Northern and Northeastern Europe.• The results of the present study increase the knowledge about JIA risk loci replicating some previously described associations, so adding weight to their relevance and describing novel loci.• The study provides additional evidence for the existence of overlapping genetic risk loci between JIA and other autoimmune diseases, particularly rheumatoid arthritis.

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Genome-wide association study of psychiatric and substance use comorbidity in Mexican individuals

Scientific Reports ◽

10.1038/s41598-021-85881-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

José Jaime Martínez-Magaña ◽

Alma Delia Genis-Mendoza ◽

Jorge Ameth Villatoro Velázquez ◽

Marycarmen Bustos-Gamiño ◽

Isela Esther Juárez-Rojop ◽

...

Keyword(s):

Substance Use ◽

Association Study ◽

Genome Wide Association Study ◽

Logistic Models ◽

Genome Wide Association ◽

Risk Scores ◽

Multinomial Models ◽

Gamma Receptor ◽

Genome Wide ◽

A Genome

AbstractThe combination of substance use and psychiatric disorders is one of the most common comorbidities. The objective of this study was to perform a genome-wide association study of this comorbidity (Com), substance use alone (Subs), and psychiatric symptomatology alone (Psych) in the Mexican population. The study included 3914 individuals of Mexican descent. Genotyping was carried out using the PsychArray microarray and genome-wide correlations were calculated. Genome-wide associations were analyzed using multiple logistic models, polygenic risk scores (PRSs) were evaluated using multinomial models, and vertical pleiotropy was evaluated by generalized summary-data-based Mendelian randomization. Brain DNA methylation quantitative loci (brain meQTL) were also evaluated in the prefrontal cortex. Genome-wide correlation and vertical pleiotropy were found between all traits. No genome-wide association signals were found, but 64 single-nucleotide polymorphism (SNPs) reached nominal associations (p < 5.00e−05). The SNPs associated with each trait were independent, and the individuals with high PRSs had a higher prevalence of tobacco and alcohol use. In the multinomial models all of the PRSs (Subs-PRS, Com-PRS, and Psych-PRS) were associated with all of the traits. Brain meQTL of the Subs-associated SNPs had an effect on the genes enriched in insulin signaling pathway, and that of the Psych-associated SNPs had an effect on the Fc gamma receptor phagocytosis pathway.

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Genetic components of human pain sensitivity: a protocol for a genome-wide association study of experimental pain in healthy volunteers

BMJ Open ◽

10.1136/bmjopen-2018-025530 ◽

2019 ◽

Vol 9 (4) ◽

pp. e025530 ◽

Cited By ~ 2

Author(s):

Annina B Schmid ◽

Kaustubh Adhikari ◽

Luis Miguel Ramirez-Aristeguieta ◽

Juan-Camilo Chacón-Duque ◽

Giovanni Poletti ◽

...

Keyword(s):

Latin American ◽

Pain Sensitivity ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Healthy Individuals ◽

Genetic Components ◽

Genome Wide ◽

A Genome ◽

The University ◽

Genetic Contributions

IntroductionPain constitutes a major component of the global burden of diseases. Recent studies suggest a strong genetic contribution to pain susceptibility and severity. Whereas most of the available evidence relies on candidate gene association or linkage studies, research on the genetic basis of pain sensitivity using genome-wide association studies (GWAS) is still in its infancy. This protocol describes a proposed GWAS on genetic contributions to baseline pain sensitivity and nociceptive sensitisation in a sample of unrelated healthy individuals of mixed Latin American ancestry.Methods and analysisA GWAS on genetic contributions to pain sensitivity in the naïve state and following nociceptive sensitisation will be conducted in unrelated healthy individuals of mixed ancestry. Mechanical and thermal pain sensitivity will be evaluated with a battery of quantitative sensory tests evaluating pain thresholds. In addition, variation in mechanical and thermal sensitisation following topical application of mustard oil to the skin will be evaluated.Ethics and disseminationThis study received ethical approval from the University College London research ethics committee (3352/001) and from the bioethics committee of the Odontology Faculty at the University of Antioquia (CONCEPTO 01–2013). Findings will be disseminated to commissioners, clinicians and service users via papers and presentations at international conferences.

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Abstract P359: A Sickle Cell Variant Associates With Urine Albumin Excretion in Genome Wide Association Study of Hispanics: The HCHS/SOL Study

Circulation ◽

10.1161/circ.131.suppl_1.p359 ◽

2015 ◽

Vol 131 (suppl_1) ◽

Author(s):

Nora Franceschini ◽

Adrienne Stilp ◽

Christina L Wassel ◽

Holly J Mattix-Kramer ◽

Michael F Flessner ◽

...

Keyword(s):

Allele Frequency ◽

Sickle Cell ◽

Missense Variant ◽

Genome Wide Association ◽

European Ancestry ◽

Minority Population ◽

Genome Wide Association Studies ◽

Urine Albumin ◽

Genome Wide ◽

A Genome

Introduction: Genome wide association studies have identified genetic variants in the Cubillin gene ( CUBN ) that explain inter-individual variation in urine albumin-to-creatinine excretion (UACR) in populations. These studies have not included Hispanics/Latinos, the fast growing minority population in the U.S., who has also high prevalence of chronic kidney disease and its risk factors. Hypothesis: By leveraging on population admixture of Hispanics and using a genome wide association approach, we hypothesized that novel loci associated with UACR would be identified. Methods: We used data from 12,212 self-identified Hispanic individuals recruited in a community-based study, aged 18-74 years at screening (2008-2011), and randomly selected from households in four U.S. field centers (Chicago, IL; Miami, FL; Bronx, NY; San Diego, CA). Urine albumin (mg/dl) and creatinine (g/dl) were measured at the baseline exam. UACR was log-transformed for analysis. Individuals were excluded if reporting to have end-stage renal disease. Genotyping was performed using a custom Illumina Omni2.5M array. Imputation of variants was performed using 1000 Genome Project data from cosmopolitan HapMap samples. After quality control of imputed data, we performed mixed linear regression analyses that accounted for the sampling strategy and family relatedness, for variants with minor allele frequency (MAF) > 0.01 and imputation quality > 0.3. We used additive genetic models and adjusted for age, sex, and principal components which were estimated from the data. In a secondary analysis, we also examine the association of significant variants with kidney function using estimated glomerular filtration rate (eGFR) equations. Results: Among 12,212 participants, 41% were men, and mean age was 46 (SD =13). There was little evidence for genome wide inflation (lambda =1.024). We identified significant associations of single nucleotide polymorphisms (SNPs) with UACR at two loci: CUBN and HBB . The CUBN SNP (chr10:16966414, p=2.1x10-8) is an indel variant with MAF of 0.14, which was not in linkage disequilibrium with previously reported SNP rs1801239 (rsq=0.38, p=1.3x10-4) identified in individuals of European ancestry. The HBB SNP is a missense variant which results in an E [Glu] ⇒ A [Ala] substitution in the beta-globin chain of hemoglobin and a cause of the Mendelian disorder sickle cell anemia (rs334, T allele frequency =0.01, beta=0.44, SE=0.06, p=7.6x10-12). rs344 was not associated with eGFR in our data (p>0.05). Conclusion: This study identified a novel association of a sickle cell missense variant with UACR in Hispanics, and provided evidence for allelic heterogeneity at the CUBN locus. Our findings suggest a role for Mendelian gene variants in increased albuminuria in Hispanic populations with admixture.

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