scholarly journals Genome-wide association study of periodontal pocketing in Finnish adults

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Paula Tegelberg ◽  
Jussi Miikkael Leppilahti ◽  
Atte Ylöstalo ◽  
Tellervo Tervonen ◽  
Johannes Kettunen ◽  
...  
Keyword(s):  
Association Study ◽  
Fixed Effects ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Fixed Effects Model ◽  
Number Of Teeth ◽  
Genome Wide ◽  
A Genome ◽  
Additive Regression

Abstract Background A genome‐wide association study is an analytical approach that investigates whether genetic variants across the whole genome contribute to disease progression. The aim of this study was to investigate genome-wide associations of periodontal condition measured as deepened periodontal pockets (≥ 4 mm) in Finnish adults. Methods This study was based on the data of the national Health 2000 Survey (BRIF8901) in Finland and the Northern Finland Birth Cohort 1966 Study totalling 3,245 individuals. The genotype data were analyzed using the SNPTEST v.2.4.1. The number of teeth with deepened periodontal pockets (≥ 4 mm deep) was employed as a continuous response variable in additive regression analyses performed separately for the two studies and the results were combined in a meta-analysis applying a fixed effects model. Results Genome-wide significant associations with the number of teeth with ≥ 4 mm deep pockets were not found at the p-level of < 5 × 10−8, while in total 17 loci reached the p-level of 5 × 10−6. Of the top hits, SNP rs4444613 in chromosome 20 showed the strongest association (p = 1.35 × 10−7). Conclusion No statistically significant genome-wide associations with deepened periodontal pockets were found in this study.

scholarly journals Genome-wide Association Study of Periodontal Pocketing in Finnish Adults

2021 ◽  
Author(s):  
Paula Tegelberg ◽  
Jussi Miikkael Leppilahti ◽  
Atte Ylöstalo ◽  
Tellervo Tervonen ◽  
Johannes Kettunen ◽  
...  
Keyword(s):  
Association Study ◽  
Fixed Effects ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Fixed Effects Model ◽  
Number Of Teeth ◽  
Genome Wide ◽  
A Genome ◽  
Additive Regression

Abstract Background: A genome‐wide association study is an analytical approach that investigates whether genetic variants across the whole genome contribute to disease progression. The aim of this study was to investigate genome-wide associations of periodontal condition measured as deepened periodontal pockets (≥ 4 mm) in Finnish adults. Methods: This study was based on the data of the national Health 2000 Survey (BRIF8901) in Finland and the Northern Finland Birth Cohort 1966 Study totalling 3,245 individuals. The genotype data were analyzed using the SNPTEST v.2.4.1. The number of teeth with deepened periodontal pockets (≥ 4 mm deep) was employed as a continuous response variable in additive regression analyses performed separately for the two studies and the results were combined in a meta-analysis applying a fixed effects model. Results: Genome-wide significant associations with the number of teeth with ≥ 4 mm deep pockets were not found at the p-level of < 5 × 10-8, while in total 27 loci reached the p-level of 5 x 10-6. Of the top hits, SNP rs4444613 in chromosome 20 showed the strongest association (p = 1.35 × 10–7).Conclusion: No statistically significant genome-wide associations with deepened periodontal pockets were found in this study.

scholarly journals A genome-wide association study meta-analysis of clinical fracture in 10,012 African American women

Bone Reports ◽  
2016 ◽  
Vol 5 ◽  
pp. 233-242 ◽  
Author(s):  
Kira C. Taylor ◽  
Daniel S. Evans ◽  
Digna R. Velez Edwards ◽  
Todd L. Edwards ◽  
Tamar Sofer ◽  
...  
Keyword(s):  
African American ◽  
Association Study ◽  
African American Women ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
American Women ◽  
Clinical Fracture ◽  
Genome Wide ◽  
A Genome

scholarly journals The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response

2015 ◽  
Vol 5 (4) ◽  
pp. e553-e553 ◽  
Author(s):  
J M Biernacka ◽  
K Sangkuhl ◽  
G Jenkins ◽  
R M Whaley ◽  
P Barman ◽  
...  
Keyword(s):  
Association Study ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Genome Wide Association Study ◽  
Transmembrane Domain ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Research Network ◽  
Genome Wide ◽  
A Genome ◽  
Increased Risk

Abstract Response to treatment with selective serotonin reuptake inhibitors (SSRIs) varies considerably between patients. The International SSRI Pharmacogenomics Consortium (ISPC) was formed with the primary goal of identifying genetic variation that may contribute to response to SSRI treatment of major depressive disorder. A genome-wide association study of 4-week treatment outcomes, measured using the 17-item Hamilton Rating Scale for Depression (HRSD-17), was performed using data from 865 subjects from seven sites. The primary outcomes were percent change in HRSD-17 score and response, defined as at least 50% reduction in HRSD-17. Data from two prior studies, the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study (PGRN-AMPS) and the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, were used for replication, and a meta-analysis of the three studies was performed (N=2394). Although many top association signals in the ISPC analysis map to interesting candidate genes, none were significant at the genome-wide level and the associations were not replicated using PGRN-AMPS and STAR*D data. Top association results in the meta-analysis of response included single-nucleotide polymorphisms (SNPs) in the HPRTP4 (hypoxanthine phosphoribosyltransferase pseudogene 4)/VSTM5 (V-set and transmembrane domain containing 5) region, which approached genome-wide significance (P=5.03E−08) and SNPs 5’ upstream of the neuregulin-1 gene, NRG1 (P=1.20E−06). NRG1 is involved in many aspects of brain development, including neuronal maturation and variations in this gene have been shown to be associated with increased risk for mental disorders, particularly schizophrenia. Replication and functional studies of these findings are warranted.

scholarly journals Genome-wide association study of early-onset bipolar I disorder in the Han Taiwanese population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lawrence Shih-Hsin Wu ◽  
Ming-Chyi Huang ◽  
Cathy Shen-Jang Fann ◽  
Hsien-Yuan Lane ◽  
Chian-Jue Kuo ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Association Study ◽  
Early Onset ◽  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Chinese Descent

AbstractThe search for susceptibility genes underlying the heterogeneous bipolar disorder has been inconclusive, often with irreproducible results. There is a hope that narrowing the phenotypes will increase the power of genetic analysis. Early-onset bipolar disorder is thought to be a genetically homogeneous subtype with greater symptom severity. We conducted a genome-wide association study (GWAS) for this subtype in bipolar I (BPI) disorder. Study participants included 1779 patients of Han Chinese descent with BPI disorder recruited by the Taiwan Bipolar Consortium. We conducted phenotype assessment using the Chinese version of the Schedules for Clinical Assessment in Neuropsychiatry and prepared a life chart with graphic depiction of lifetime clinical course for each of the BPI patient recruited. The assessment of onset age was based on this life chart with early onset defined as ≤20 years of age. We performed GWAS in a discovery group of 516 early-onset and 790 non-early-onset BPI patients, followed by a replication study in an independent group of 153 early-onset and 320 non-early-onset BPI patients and a meta-analysis with these two groups. The SNP rs11127876, located in the intron of CADM2, showed association with early-onset BPI in the discovery cohort (P = 7.04 × 10−8) and in the test of replication (P = 0.0354). After meta-analysis, this SNP was demonstrated to be a new genetic locus in CADM2 gene associated with early-onset BPI disorder (P = 5.19 × 10−8).

scholarly journals Genome-wide association study reveals genetic link between diarrhea-associated Entamoeba histolytica infection and inflammatory bowel disease

2017 ◽  
Author(s):  
Genevieve L Wojcik ◽  
Chelsea Marie ◽  
Mayuresh M Abhyankar ◽  
Nobuya Yoshida ◽  
Koji Watanabe ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Association Study ◽  
Entamoeba Histolytica ◽  
Bowel Disease ◽  
Fixed Effects ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Inflammatory Bowel

AbstractDiarrhea is the second leading cause of death for children globally, causing 760,000 deaths each year in children under the age of 5. Amoebic dysentery contributes significantly to this burden, especially in developing countries. We hypothesize that genetic variation contributes to susceptibility to diarrhea-associated Entamoeba histolytica infection in Bangladeshi infants; thus, we conducted a genome-wide association study (GWAS) in two independent birth cohorts of diarrhea-associated E. histolytica infection. Cases were defined as children with at least one diarrheal episode positive for E. histolytica through either PCR or ELISA within the first year of life. Controls were children without any episodes positive for E. histolytica in the same time frame. Meta-analyses under a fixed-effects inverse variance weighting model identified variants in two neighboring genes on chromosome 10: CUL2 (cullin 2) and CREM (cAMP responsive element modulator) associated with E. histolytica infection, with SNP rs58000832 achieving genome-wide significance (Pmeta=4.2x10−10). Each additional risk allele (an intergenic insertion between CREM and CCNY) of rs58000832 conferred 2.5 increased odds of a diarrhea-associated E. histolytica infection. The most associated SNP within a gene was in an intron of CREM (rs58468685, Pmeta=2.3x10−9), which with CUL2, has been implicated as a susceptibility locus for Inflammatory Bowel Disease (IBD) and Crohn’s Disease. Gene expression resources suggest these loci are related to the higher expression of CREM, but not CUL2. Increased CREM expression is also observed in early E. histolytica infection. Further, CREM-/- mice were more susceptible to E. histolytica amebic colitis. These genetic associations reinforce the pathological similarities observed in gut inflammation between E. histolytica infection and IBD.

scholarly journals A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study

PLoS ONE ◽  
2018 ◽  
Vol 13 (7) ◽  
pp. e0199461 ◽  
Author(s):  
Cherif Ben Hamda ◽  
Raphael Sangeda ◽  
Liberata Mwita ◽  
Ayton Meintjes ◽  
Siana Nkya ◽  
...  
Keyword(s):  
Sickle Cell Disease ◽  
Association Study ◽  
Sickle Cell ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Molecular Signature ◽  
Cell Disease ◽  
Genome Wide ◽  
A Genome

Abstract 15402: A Multi-ethnic Genome Wide Association Study of Aortic Stenosis in the Million Veteran Program Identifies Several Novel Loci

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Aeron M Small ◽  
Gina Peloso ◽  
Jayashri Aragam ◽  
JASON LINEFSKY ◽  
Ashley Galloway ◽  
...  
Keyword(s):  
Aortic Stenosis ◽  
Association Study ◽  
Fixed Effects ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
European Ancestry ◽  
High Morbidity ◽  
Genetic Loci ◽  
Genome Wide

Introduction: Valvular aortic stenosis (AS) is common with high morbidity and mortality in the absence of surgical intervention, but no current medical therapies are known to prevent or slow disease progression. Previous genetic studies have identified several genetic loci associated with prevalent AS, including LPA and PALMD , although most evidence is limited to populations of European ancestry. Methods: We performed a trans-ethnic genome-wide association study (GWAS) of prevalent AS in the Veterans Administration Million Veteran Program (MVP). Cases were identified by a combination of diagnostic billing and surgical codes and validated by association to the known LPA variant (rs10455872). GWAS was run separately for White, Black, and Hispanic individuals, controlling for age, sex, and six principal components, and combined using fixed effects meta-analysis. Results were limited to variants with a minor allele frequency greater than 1% in the trans-ancestry analysis. Lead independent genome wide significant loci were annotated by nearest gene. Results: 300,182 White, 80,744 Black, and 32,069 Hispanic participants were available for analysis. Of these, there were 12,385 (4.1%) White, 1,444 (1.8%) Black, and 611 (1.9%) Hispanic AS cases. Trans-ethnic analyses identified 10 independent genome wide significant (GWS, p≤5x10 -8 ) loci, replicating 6 known AS genetic loci ( ALPL, PALMD, TEX41, LPA, IL6, FADS1 ), and identifying 4 novel genetic loci ( CEP85L, CELSR2, NCK1, SLMAP ), of which 2 were present at nominal significance in Hispanic ( CELS2R ) or Black ( SLMAP ) individuals. Ethnicity-specific analyses additionally identified 9 novel GWS loci in White individuals, and 3 novel GWS loci in Hispanic individuals. Newly identified loci supported known biological pathways in AS including lipid/metabolic, inflammatory, and calcification, but also implicated new pathways such as those pertaining to QT interval ( SLC35F1 ) and the Brugada Syndrome ( SLMAP ). Conclusions: In this large trans-ethnic GWAS for AS we replicate previously identified genetic loci for AS, and identified several novel loci both in trans-ethnic and in ethnic-specific analyses. These loci implicate known and novel biological mechanisms for future prevention and treatment of AS.

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