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Genome measures used for quality control are dependent on gene function and ancestry
2014
Computer applications in the biosciences : CABIOS
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Thus, when performing QC assessment using these two measures, care must be taken to apply the correct thresholds based on ancestry and genome region. ...
An additional two datasets (N = 581 and N = 6) were used to validate our findings from the 1000G dataset. We compared the two ratios among continental ancestry, genome regions and gene functionality. ...
ACKNOWLEDGEMENTS We like to thank Margot Bjoring for editorial support. Funding: This study was supported by P30 CA68485. ...
doi:10.1093/bioinformatics/btu668
pmid:25297068
pmcid:PMC4308666
fatcat:43cwxfgoynh7veh2p7itc5uy5q
Replication of Genome Wide Association Studies of Alcohol Dependence: Support for Association with Variation in ADH1C
2013
PLoS ONE
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Further studies should investigate the association of other polymorphisms in this gene with alcohol dependence and related alcohol-use phenotypes. ...
Our analysis of 808 alcoholdependent cases and 1,248 controls provided evidence of association of alcohol dependence with SNP rs1614972 in the ADH1C gene (unadjusted p = 0.0017). ...
Genotyping and Quality Control Controls were previously genotyped at the Center for Inherited Disease Research using the Illumina (San Diego, CA) 660 genome-wide SNP array. ...
doi:10.1371/journal.pone.0058798
pmid:23516558
pmcid:PMC3596339
fatcat:5nf7qynoozfhlp3wx5njcnszp4
Admixture Mapping Identifies a Quantitative Trait Locus Associated with FEV1/FVC in the COPDGene Study
2014
Genetic Epidemiology
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We analyzed estimated local ancestry and SNP genotype information to identify regions associated with FEV 1 /FVC, the ratio of forced expiratory volume in one second to forced vital capacity, measured ...
African Americans are admixed with genetic contributions from European and African ancestral populations. ...
Genome-wide permutation testing was performed by Ingo Ruczinski of the Johns Hopkins Bloomberg School of Public Health. ...
doi:10.1002/gepi.21847
pmid:25112515
pmcid:PMC4190160
fatcat:ygecqrmafbdcdc5ods3k7srn3a
Ancestry adjustment improves genome-wide estimates of regional intolerance
[article]
2020
bioRxiv
pre-print
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As the expected distributions depend on demography, if not properly controlled for, ancestral population source may obfuscate signals of selection. ...
Methods for identifying such regions can roughly be divided into those using cross species conservation and those using intolerance to standing genetic variation within a species. ...
Orion was run using a different quality control criteria and, as a result, used a significantly different set of variants. ...
doi:10.1101/2020.03.05.979203
fatcat:opsf5py5xbb3da56xtkhpjm24i
Genome-Wide Association Study of Behavioral Disinhibition in a Selected Adolescent Sample
2015
Behavior Genetics
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We conducted a GWAS of BD using a sample of 1,901 adolescents over-selected for characteristics that define high BD, such as substance and antisocial behavior problems, finding no individual locus that ...
Behavioral disinhibition (BD) is a quantitative measure designed to capture the heritable variation encompassing risky and impulsive behaviors. ...
Details of the quality control procedures and ancestry principal components estimation in the MCTFR are described in Miller et al. (2012) .
Study of Addiction: Genes and Environment (SAGE) Sample. ...
doi:10.1007/s10519-015-9705-y
pmid:25637581
pmcid:PMC4459903
fatcat:fhqdngame5bezpd7ucyr56tone
Genome-wide association studies of smooth pursuit and antisaccade eye movements in psychotic disorders: findings from the B-SNIP study
2017
Translational Psychiatry
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bipolar disorder N = 206 and healthy controls N = 258) as quantitative phenotypes in relation to genetic data, while controlling for genetically derived ancestry measures, age and sex. ...
A mixed-modeling genome-wide association studies approach was used including~4.4 million genotypes (PsychChip and 1000 Genomes imputation). ...
SNPs passing quality control procedures were used for imputation using HAPI-UR for pre-phasing 51 and IMPUTE2 for imputation 52 using the 1000 Genomes phase 1 data as a reference panel. 53 Poorly imputed ...
doi:10.1038/tp.2017.210
pmid:29064472
pmcid:PMC5682604
fatcat:vpqeqiou4fa2nap6pej4clgm2i
Trans-ancestry meta-analysis of genome wide association studies of inhibitory control
[article]
2022
medRxiv
pre-print
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Deficits in effective executive function, including inhibitory control are associated with risk for a number of psychiatric disorders and significantly impact everyday functioning. ...
sites and four ancestries (N=14,877) using behavioural traits derived from the stop-signal task, namely - go reaction time (GoRT), go reaction time variability (GoRT SD) and stop signal reaction time ( ...
To minimise variation in the genomic data all study sites used the same reference panel for imputation and imputation quality filter (r 2 >0.8). ...
doi:10.1101/2022.10.13.22281074
fatcat:52ixgotwsfazboraj4kkn4tnnq
Antithrombin, protein C and protein S: Genome and transcriptome wide association studies identify 7 novel loci regulating plasma levels
[article]
2022
medRxiv
pre-print
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Functional experiments provided evidence for the involvement of GCKR, SNX17, and HP genes in antithrombin regulation. ...
In the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, we meta-analyzed across ancestries the results from 10 genome-wide association studies (GWAS) of plasma levels ...
Population-Specific and Cross-Ancestry Meta-Analysis Quality control across studies was conducted using EasyQC 33 . Details of meta-analysis quality control can be found in Supplementary Materials. ...
doi:10.1101/2022.11.01.22281689
fatcat:42oyyx57ffh6fnvw4tci2cqnki
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
[article]
2021
bioRxiv
pre-print
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to control conditions and, on average, each treatment revealed expression quantitative trait loci (eQTL) at 11% of genes. ...
In total, 22% of all eQTL were context-dependent, and this group was enriched for trait- and disease-associated loci. ...
We also thank Andrea Graham and members of the Graham lab for thoughtful input and discussion. We thank Aaron Wolf, ...
doi:10.1101/2021.11.04.467311
fatcat:ucvsw5wgrvdzvfzhhcp4wwvqzi
Genome-wide association study of cognitive function in diverse Hispanics/Latinos: results from the Hispanic Community Health Study/Study of Latinos
2020
Translational Psychiatry
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In addition, we derived a measure of general cognitive function based on these cognitive tests and generated genome-wide association summary results, providing a resource to the research community for ...
Four novel loci were identified: one for B-SEVLT at 4p14, two for WFT at 3p14.1 and 6p21.32, and one for DSST at 10p13. ...
The authors thank the staff and participants of the HCHS/SOL for their important contributions. ...
doi:10.1038/s41398-020-00930-2
pmid:32699239
pmcid:PMC7376098
fatcat:hgrmscgnovhdxlezy2rlemngc4
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
2022
Genome Research
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relative to control conditions, and on average, each treatment revealed new expression quantitative trait loci (eQTLs) at 11% of genes. ...
Across our experiments, 22% of all identified eQTLs were context-dependent, and this group was enriched for trait- and disease-associated loci. ...
We also thank Andrea Graham and members of the Graham laboratory for thoughtful input and discussion. ...
doi:10.1101/gr.276430.121
pmid:36229124
pmcid:PMC9712631
fatcat:kltuojnwu5f47fhapdcvw46mcm
Genome-wide association study of heart rate and its variability in Hispanic/Latino cohorts
2017
Heart Rhythm
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Results-Two genome-wide significant SNPs replicated in a European ancestry cohort, one for RMSSD (rs4963772; chromosome 12) and another for SDNN (rs12982903; chromosome 19). ...
Background-Although time-domain measures of heart rate variability (HRV) are used to estimate cardiac autonomic tone and disease risk in multi-ethnic populations, the genetic epidemiology of HRV in Hispanics ...
Values of r 2 with respect to rs4963772 are displayed using color. Nearby genes are displayed under the horizontal axis. ...
doi:10.1016/j.hrthm.2017.06.018
pmid:28610988
pmcid:PMC5671896
fatcat:audffhm5kncbpigqajfgsucrqq
Genome-Wide Association Study of Cardiac Structure and Systolic Function in African Americans: The Candidate Gene Association Resource (CARe) Study
2012
Circulation: Cardiovascular Genetics
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(LV) structure and function. ...
Replication results suggest that these loci may be unique to individuals of African ancestry. Additional large-scale studies are warranted for these complex phenotypes. ...
Each of the 5 participating cohorts in the CARe Study has implemented several quality control measures for echocardiography and MRI. ...
doi:10.1161/circgenetics.111.962365
pmid:23275298
pmcid:PMC3591479
fatcat:7boamucrqfgm7i33frtyld3bs4
A catalog of genetic loci associated with kidney function from analyses of a million individuals
2019
Nature Genetics
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Of these, 147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). ...
Through trans-ancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 ...
Johnson (GlaxoSmithKline) for sharing his code and discussion on credible set fine-mapping and colocalization analysis. ...
doi:10.1038/s41588-019-0407-x
pmid:31152163
pmcid:PMC6698888
fatcat:k6wxxblrqzchzjwz635cgf2qfm
Genome-wide association studies
2021
Nature Reviews Methods Primers
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, concluding with an overview of the current and future applications for GWAS results. ...
In this Primer, we provide the reader with an introduction to GWAS, explaining their statistical basis and how they are conducted, describe state-of-the art approaches and discuss limitations and challenges ...
Cases and controls should be matched by ancestry to avoid confounding; for example, a GWAS for chopstick use where cases are defined as 'using chopsticks regularly' and controls as 'not using chopsticks ...
doi:10.1038/s43586-021-00056-9
fatcat:beq6cklwojaobfqum75kbn5she
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