Peter Kraft
@peter-kraft.bsky.social
Cancer epidemiologist, statistical geneticist, biostatistician. National Cancer Institute, Harvard. Views my own.
Reposted by Peter Kraft
@ajhgnews.bsky.social sat with Julie-Alexia Dias, MSc, in the latest "Inside AJHG" to discuss her recently published paper, “Evaluating multi-ancestry genome-wide association methods: statistical power, population structure, and practical implications.”➡️ ashg.org/ajhg/inside-... #ASHG #humangenetics
October 6, 2025 at 8:31 PM
@ajhgnews.bsky.social sat with Julie-Alexia Dias, MSc, in the latest "Inside AJHG" to discuss her recently published paper, “Evaluating multi-ancestry genome-wide association methods: statistical power, population structure, and practical implications.”➡️ ashg.org/ajhg/inside-... #ASHG #humangenetics
This was neat work by @nmancuso.bsky.social et al developing and benchmarking a new multi-ancestry fine-mapping method (“SuShiE”). I learned something about the performance of pooled v stratified analyses but still have some Qs. 1/n
📢OUT TODAY @natgenet.nature.com
📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.
By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues.
⬇️
www.nature.com/articles/s41...
📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.
By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues.
⬇️
www.nature.com/articles/s41...
Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk - Nature Genetics
SuShiE is a multiancestry fine-mapping method for molecular quantitative trait loci that leverages linkage disequilibrium heterogeneity to improve resolution, infer cross-ancestry effect size correlat...
www.nature.com
September 8, 2025 at 11:37 AM
This was neat work by @nmancuso.bsky.social et al developing and benchmarking a new multi-ancestry fine-mapping method (“SuShiE”). I learned something about the performance of pooled v stratified analyses but still have some Qs. 1/n
Reposted by Peter Kraft
The observation that joint analysis can safely improve power strikes me as being a similar observation to that of @genandgenes.bsky.social et al in their Nature 2019 manuscript: www.nature.com/articles/s41...
Genetic analyses of diverse populations improves discovery for complex traits - Nature
Genetic analyses of ancestrally diverse populations show evidence of heterogeneity across ancestries and provide insights into clinical implications, highlighting the importance of including ancestral...
www.nature.com
September 2, 2025 at 4:23 PM
The observation that joint analysis can safely improve power strikes me as being a similar observation to that of @genandgenes.bsky.social et al in their Nature 2019 manuscript: www.nature.com/articles/s41...
Multi-ancestry GWAS can increase power and precision, but how should we analyze them? Pooled or stratified? We answer that question in a paper out today in AJHG, led by Julie Dias and Haoyu Zhang. 1/7 www.cell.com/ajhg/fulltex...
Evaluating multi-ancestry genome-wide association methods: Statistical power, population structure, and practical implications
Multi-ancestry GWASs enhance discovery in diverse populations, but optimal methods
remain debated. Using theory, simulations, and analyses from the UK Biobank and All
of Us, we show that pooled analys...
www.cell.com
September 2, 2025 at 3:26 PM
Multi-ancestry GWAS can increase power and precision, but how should we analyze them? Pooled or stratified? We answer that question in a paper out today in AJHG, led by Julie Dias and Haoyu Zhang. 1/7 www.cell.com/ajhg/fulltex...
Reposted by Peter Kraft
An evergreen thread: Race/Ethnicity is *not the same* as genetics, and you can't use Race/Ethnicity as a sort of stand-in for genetics. These two concepts are connected via aspects like skin colour, but the connection is alot less profound and categorical than most people think.
August 29, 2025 at 10:13 AM
An evergreen thread: Race/Ethnicity is *not the same* as genetics, and you can't use Race/Ethnicity as a sort of stand-in for genetics. These two concepts are connected via aspects like skin colour, but the connection is alot less profound and categorical than most people think.
Reposted by Peter Kraft
Nice blog and good to see this also from the twins/shared environment side. We (with my colleagues in @wittbrodtlab.bsky.social) have tried to tackle the non-additive in experimental settings (in medaka fish) which we can map to human (as the medaka fish are "wild") www.biorxiv.org/content/10.1...
Discovery and characterisation of gene by environment and epistatic genetic effects in a vertebrate model
Phenotypic variation arises from the interplay between genetic and environmental factors. However, disentangling these interactions for complex traits remains challenging in observational cohorts such...
www.biorxiv.org
August 28, 2025 at 3:10 PM
Nice blog and good to see this also from the twins/shared environment side. We (with my colleagues in @wittbrodtlab.bsky.social) have tried to tackle the non-additive in experimental settings (in medaka fish) which we can map to human (as the medaka fish are "wild") www.biorxiv.org/content/10.1...
Reposted by Peter Kraft
I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:
Beneath the surface of the sum
When genetic interactions matter and when they don't
open.substack.com
August 27, 2025 at 8:41 PM
I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:
Upvoting this response to the NIH RFI on limiting publishing fees, and highlighting two points. 1/3
I've made my personal response to The National Institutes of Health Request for Information on Maximizing Research Funds by Limiting Allowable Publishing Costs available to all to read here:
https://doi.org/10.54900/da84n-4hx26
https://doi.org/10.54900/da84n-4hx26
My Response to the NIH Request for Information on Proposed APC Caps
In my last blog post for Upstream, I noted that there were some potential issues with, and good alternatives to, the NIH plan to cap grant spending on article processing charges. One of my suggestions was that the NIH put its plan out for public comment so they could draw
upstream.force11.org
August 27, 2025 at 5:11 PM
Upvoting this response to the NIH RFI on limiting publishing fees, and highlighting two points. 1/3
Congrats to Yuxi Liu & co. for showing adherence to a Mediterranean diet lowers dementia risk—especially for those who inherited risky genes. (1/4)
Closely following the Mediterranean diet lowered the risk of dementia by at least 35% in people with two copies of the APOE4 gene, a major risk factor for Alzheimer's, according to a new study. https://cnn.it/45UbHPX
August 26, 2025 at 2:08 PM
Congrats to Yuxi Liu & co. for showing adherence to a Mediterranean diet lowers dementia risk—especially for those who inherited risky genes. (1/4)