Notes

GWAS catalog traits

Identify GWAS catalog traits to import to OpenGWAS
Aug 25, 2023
Gibran Hemani

Logistic regression residuals

Using REML to…
Aug 7, 2023
Gibran Hemani

Summary stat storage

Summary statistics typically have a lot of redundant information due to LD. Can we improve storage space by converting to a sparse format using an external LD reference panel?
Jul 24, 2023
Gibran Hemani

IV confounding with changing variances

When instruments arise…
Jul 20, 2023
Gibran Hemani

MR and imperfect clumping

4000 instruments for educational attainment using clumping r2 = 0.1, and se doubles when using r2 = 0.001.
Jul 13, 2023
Gibran Hemani

Meta regression using exposure effect size

Jul 9, 2023
Gibran Hemani

Confounder instruments via networks

confounding
mr
In a previous post looked at the rate of bias as GWAS sample size increases. It was predicated on smaller effects more likely acting via confounders.
Jul 7, 2023
Gibran Hemani

Standard error in two-stage least squares

statistics
How to calculate the 2sls SE that is returned by e.g. ivreg
Jul 6, 2023
Gibran Hemani

Interactions and scale

Absolute and relative risks will change across populations if the baseline risks are different.
Jul 5, 2023
Gibran Hemani

Differential susceptibility explained by interactors and mediators with different distributions

interactions
multi-ancestry
What…
Jun 9, 2023
Gibran Hemani

Cross group effect comparison

GWAS being performed on multiple ancestries, then meta-analysing to mitigate problems of LD tagging.…
Jun 7, 2023
Gibran Hemani

Checking PCA projection

Statistics
Need to be able to calculate genetic principal components in unrelateds and then project into relateds.
Jun 6, 2023
Gibran Hemani

Genetic confounding as a function of sample size

MR
genetic confounding
This is the expected effect estimate of X on Y using an instrument that arises via U:
May 13, 2023
Gibran Hemani

LDL and drug adjustment

Get a rough distribution of LDL cholesterol (e.g. like this)
Mar 24, 2023
Gibran Hemani

Gene-environment equivalence

Latest PRS for height explains ~40% of the variance. Heritability ~0.7. Height has a negative…
Mar 15, 2023
Gibran Hemani

Boosting MZ vQTL power

The MZ…
Mar 11, 2023
Gibran Hemani

Variance QTL using MZs

interactions
genetics
statistics
Data generating model
Feb 28, 2023
Gibran Hemani

Spurious vQTL simulation

genetics
interactions
statistics
How sensitive is DRM to incomplete LD in more realistic scenarios? Take a region of 1000 genomes data and choose a SNP at random to have an additive effect of some…
Feb 28, 2023
Gibran Hemani

Overlapping genes

genomics
For a list of positions, identify all genes that overlap +/- 200kb.
Feb 18, 2023
Gibran Hemani

Sandwich variance estimators to control LD leakage

See https://explodecomputer.github.io/lab-book/posts/2022-12-16-vqtl/ for inflation issues with vQTLs.
Feb 10, 2023
Gibran Hemani

Cell-specific effects for mQTLs from bulk tissue

DNA methylation
statistics
Generally seems to work but expect some shrinkage of large effects
Feb 7, 2023
Gibran Hemani

Can winner's curse generate a high conditional F statistic
statistics
winner's curse
multivariable mr
Multivariable MR requires that exposure…
Jan 30, 2023
Gibran Hemani

Metabolite power calculation

power calculation
Sample of individuals who have had heart surgery, followed up and…
Jan 26, 2023
Gibran Hemani and Nic Timpson

Convert Bayes factors to beta and standard error

statistics
fine mapping
Is it possible to convert BF to beta and standard error? According to Giambartolomei et al 2014 -
Jan 26, 2023
Gibran Hemani

BMI instrument replication

statistics
genetics
Liza’s analysis of BMI instruments clusters them by PheWAS and finds that cluster 4…
Dec 18, 2022
Gibran Hemani

Inflation of vQTLs

statistics
genetics
interactions
This paper describes how incomplete linkage disequilibrium can lead to inflated test statistics for interactions -…
Dec 16, 2022
Gibran Hemani

Sibling replication of Backman rare variants

rare variants
genetics
family studies
Backman et al 2022…
Dec 14, 2022
Gibran Hemani

Probability of a random variable being larger than all other random variables in a multivariate normal vector

statistics
I have 1k SNPs in a region. I know the causal variant and the LD matrix. The effect size at each SNP will be related to the allele frequency and the LD at all other…
Nov 1, 2022
Gibran Hemani

Regression with non i.i.d. samples

statistics
If the individuals in my dataset are correlated with known correlation structure, how can I perform regression whilst accounting for that correlation structure?
Oct 25, 2022
Gibran Hemani

Correlated SNPs

One instrument for X and X has no influence on Y
Aug 12, 2022
Gibran Hemani

Power of GWAS in ascertained case control datasets

Case control studies ascertain a fixed number of cases and controls. This changes the distribution of genetic liability in the selected sample - e.g. if the prevalence is…
Jul 24, 2022
Gibran Hemani

PRS vs IVW

statistics
Mendelian randomization
How does PRS compare to IVW fixed effects analysis
May 8, 2022
Gibran Hemani

Difference in difference models in observational data are still potentially confounded

Motivated by discussion with Tim Cadman relating to this Renzi et al (2019).…
Jan 9, 2022
Gibran Hemani
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