Questions tagged [gwas]

A genome-wide association study (GWA study), also known as whole genome association study (WGA study or WGAS), is an examination of many common genetic variants in different individuals to see whether any variant is associated with a trait. [Wikipedia]

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71 views

How to represent the effect of one covariate on regression results?

I was running association analysis using --glm genotypic from: https://www.cog-genomics.org/plink/2.0/assoc with these covariates: sex,age,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,TD,array,HBA1C. The ...
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16 views

Genetic risk score

I performed a GWAS study finding some significant SNPs.Then, through the validation with an external cohort I did not confirm my results (the SNPs found in the previous cohort were not significant in ...
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23 views

How to construct a linear mixed model for GWAS with SSR markers?

I would like to construct a linear mixed model using SSR markers. I have the phenotype vector, SSR marker matrix, and the covariance matrix for the random effect (used to control the population ...
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124 views

Calculate Beta and se from GWAS summary

I have some metaGWAS data which has only odds ratio and P values. Can I estimate standard error and effect size from these data? (EX) rsID Allele1 Allele2 odds P rs12878 A T ...
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43 views

How should I interpret a weighted genetic risk score?

I created a weighted Genetic Risk Score (GRS) by summing the product of the SNP-dosages times their regression coefficients from the GWAS in which I found them. So: ...
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103 views

Why don't my GWAS QQPlots look the same?

I am trying to create a QQPlot of 100 log-transformed p values from a GWAS study. The idea is that taking the -log(p) will magnify the smallest p values to make them easier to see. (reference) I was ...
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273 views

How do children manage to pull their parents together in a PCA projection of a GWAS data set?

Take 20 random points in a 10,000-dimensional space with each coordinate iid from $\mathcal N(0,1)$. Split them into 10 pairs ("couples") and add the average of each pair ("a child") to the dataset. ...
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1answer
614 views

Principal components as covariates in a linear model

I'm working with some genetics data, performing linear regressions, and have been advised to control for population structure by performing principal components analysis. My model at the moment is of ...
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179 views

multivariate cox regression - combining genotypes for each SNP

For 53 SNP I have coded genotypes as 0 for aa, 1 for ab, and 2 for bb for 29 samples and I have outcome and time to outcome. Here outcome is called "BCR" below. I am using the survival package in R ...
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45 views

How to analyse GWAS data of co-morbid disorders?

Lets say I am running a GWAS for a disease condition O , where all my cases has one or more of the following diseases: A, B, and C, in addition to my outcome of interest O. So I include individuals ...
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110 views

Small values are sorted incorrectly, subset() gives wrong data in R [closed]

I have a (gwas-)data where one column is p-value. P-values vary from $1*10^{-8}$ to $1$. I would want to have a subset where I have only values where p-value is $5*10^{-5}$ or lower. I have the ...
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78 views

R or spss? For a conditional regression with 2 dependent variables?

Maybe you find my question a bit simple but I'm really confused as I'm not statistician. I have 2 SNPs (can be proposed 2 genes instead) that are related to a primary disease (like major depression), ...
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328 views

software for genome wide associations studies (GWAS) [closed]

I have just started learning about genome wide associations studies (GWAS) as I will have to run some of them in the near future, and I am pretty confused about which are the best computational tools ...
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42 views

Replication after Meta-Analysis in a multiple testing situation?

I was recently in an introductory seminar about Genome Wide Association Studies (GWAS). These studies aim to examine if any genetic markers are associate with a certain trait. It is not uncommon to ...
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52 views

Adjusting for population substructure in heterozygosity values using regression with principal components

I'm working on some sample level QC for a large genome wide association study and while reading through the QC documentation for the UK Biobank project, I came across this part, discussing a technique ...
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1answer
294 views

Ordered Logistic Regression GWAS

I am attempting to do an ordered logistic regression in R on SNP matrixes (presence absence matrix 1 or 0) with three outcomes (1,2,3). I am having an issue of 0 p-values when low numbers (<5%) ...
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1answer
2k views

Deflated QQ plots in genome-wide association studies

I am working on a GWAS dataset containing 920 individuals with genotype information on ~1.5M SNPs (genotyped on Illumina 2.5omni chip; no imputed SNPs). I am testing several different phenotypes in ...
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791 views

Including covariates makes QQ plot worse

I know this is similar to this question, but that one didn't seem to get a satisfactory answer. I'm using plink to run a GWAS. My phenotype data are binary, so it's performing a logistic regression ...
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79 views

Meta-analys of GWAS and interpretation of estimated p-values

I'm a bit confused about a meta-analysis performed with PLINK on two studies. The statistics look like this for a specific SNP in each study: Study_1: OR = 3.657, SE = 0.336, p= 0.0001137 Study_2: ...
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93 views

Fisher's method for P-value more conservative than OLS?

I am currently observing an interesting phenomenon in my analysis. I have a simple logistic regression model for independent Inds. The model is as follows: $$\operatorname{logit}(Y) = \beta_0+\...
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1answer
7k views

Interpretation of P values in Genome Wide Association Studies

Genome wide associate studies (GWAS) are a common method used in associating single nucleotide polymorphisms (SNPs) to a disease or trait under study. I don't work in this field and I'm always ...
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125 views

Elastic net is being used in genome wide analysis. Similar approach would work for survey analysis?

I'm approaching the elastic net procedure for genome wide analysis (GWAS) because it allows for feature selection, groups detection and improved validity. It's a powerful technique when you have many ...
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4k views

Case-control study and Logistic regression

Suppose we have case-control data, where cases have some disease ($Y$) and controls don't and we are interested in the association of some other variable(s) ($X$). I know that in this scenario we ...
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1answer
2k views

Inflated p-value after adjusting for covariates, in GWAS

I am working on some GWAS (Genome-Wide Association Studies) now. A genome scan was done for all the SNPs, with first 3 principal components adjusted (PCs are used for adjusting ethnicity effect) and ...
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197 views

Expected effect of each single-nucleotide polymorphism (SNP) in a genome-wide association study (GWAS) [closed]

It was mentioned in a genetics class that in a genetic association analyses of a trait with all SNPs, it is possible to compute the expected effect of each SNP with the trait using the correlation ...
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21k views

In genome-wide association studies, what are principal components?

In genome-wide association studies (GWAS): What are the principal components? Why are they used? How are they calculated? Can a genome-wide association study be done without using PCA?