Jeff Spence
@jeffspence.github.io
assistant professor at ucsf interested in genetics, statistics, etc…
jeffspence.github.io
jeffspence.github.io
Interference within haplotypes is super interesting and something that people are looking into in humans (e.g., www.medrxiv.org/content/10.1...).
For both GWAS and standard burden methods, these effects should attenuate the amount of signal, but it would be interesting to think about more!
For both GWAS and standard burden methods, these effects should attenuate the amount of signal, but it would be interesting to think about more!
November 7, 2025 at 6:52 PM
Interference within haplotypes is super interesting and something that people are looking into in humans (e.g., www.medrxiv.org/content/10.1...).
For both GWAS and standard burden methods, these effects should attenuate the amount of signal, but it would be interesting to think about more!
For both GWAS and standard burden methods, these effects should attenuate the amount of signal, but it would be interesting to think about more!
It was an absolute pleasure to work on this with amazing collaborators: @hakha.bsky.social, @minetoota.bsky.social, @nikhilmilind.dev, @tamigj.bsky.social, @courtsmithrun.bsky.social, @yuvalsim.bsky.social, @gs2747.bsky.social, and @jkpritch.bsky.social.
20/20
www.nature.com/articles/s41...
20/20
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
It was an absolute pleasure to work on this with amazing collaborators: @hakha.bsky.social, @minetoota.bsky.social, @nikhilmilind.dev, @tamigj.bsky.social, @courtsmithrun.bsky.social, @yuvalsim.bsky.social, @gs2747.bsky.social, and @jkpritch.bsky.social.
20/20
www.nature.com/articles/s41...
20/20
www.nature.com/articles/s41...
There’s a lot more in the paper! We started by saying that it would be nice to rank genes by importance or specificity, and showed that standard methods rank genes in part by specificity, not importance. Read the paper for suggestions on how to rank genes by importance.
19/n
19/n
November 7, 2025 at 12:05 AM
There’s a lot more in the paper! We started by saying that it would be nice to rank genes by importance or specificity, and showed that standard methods rank genes in part by specificity, not importance. Read the paper for suggestions on how to rank genes by importance.
19/n
19/n
Basically, when a variant gets lucky and drifts to high frequency, it is more likely to be a hit for every trait that it affects. This makes top hits APPEAR more pleiotropic, when in fact they’re actually LESS pleiotropic on average.
18/n
18/n
November 7, 2025 at 12:05 AM
Basically, when a variant gets lucky and drifts to high frequency, it is more likely to be a hit for every trait that it affects. This makes top hits APPEAR more pleiotropic, when in fact they’re actually LESS pleiotropic on average.
18/n
18/n