Linda Kachuri
@lindakachuri.bsky.social
Assistant Professor @ Stanford
Genetic & cancer epidemiology
Views my own 🇺🇦🇽🇰🇨🇦
Genetic & cancer epidemiology
Views my own 🇺🇦🇽🇰🇨🇦
Reposted by Linda Kachuri
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
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
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Linda Kachuri
Genomic superstar @chundru.bsky.social taking on fake-news genotypes in >900k individuals. He shows allele-level filtering is rarely suffifient, and makes the brave choice to properly tackle chrX!
We’ll be providing our filtered AoU WGS plink pgens for all registered users: watch this space
We’ll be providing our filtered AoU WGS plink pgens for all registered users: watch this space
New paper on everyone’s favourite topic, QC!
We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”
We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”
Genotype-level quality control substantially reduces error rates in population-scale whole-genome sequencing
Population-scale whole-genome sequencing data will contain many individual-level genotype errors, even after allele-level quality control (QC). We establish the need for genotype-level QC using UK Bio...
www.biorxiv.org
November 10, 2025 at 1:10 PM
Genomic superstar @chundru.bsky.social taking on fake-news genotypes in >900k individuals. He shows allele-level filtering is rarely suffifient, and makes the brave choice to properly tackle chrX!
We’ll be providing our filtered AoU WGS plink pgens for all registered users: watch this space
We’ll be providing our filtered AoU WGS plink pgens for all registered users: watch this space
Reposted by Linda Kachuri
A few programming notes for #ashg25 from trainees in my group @mdanderson.bsky.social + a thread of me being a proud PI. Please drop by these sessions and talk to @taylorhead.bsky.social, @seantbres.bsky.social , @ytchang11.bsky.social, and me in Boston @geneticssociety.bsky.social next week!
October 8, 2025 at 11:31 PM
A few programming notes for #ashg25 from trainees in my group @mdanderson.bsky.social + a thread of me being a proud PI. Please drop by these sessions and talk to @taylorhead.bsky.social, @seantbres.bsky.social , @ytchang11.bsky.social, and me in Boston @geneticssociety.bsky.social next week!
Reposted by Linda Kachuri
Samples of DNA collected from thousands of Ukrainians are part of a study probing the genetics of type 1 diabetes. https://scim.ag/4nabr6B
Amid war, a Ukrainian genomics research program blooms
Inaugural project for new center searches for genes involved in diabetes
www.science.org
September 21, 2025 at 1:31 AM
Samples of DNA collected from thousands of Ukrainians are part of a study probing the genetics of type 1 diabetes. https://scim.ag/4nabr6B
Can anyone recommend a good immigration lawyer?
September 20, 2025 at 7:16 PM
Can anyone recommend a good immigration lawyer?
Reposted by Linda Kachuri
Happy to see this online!
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
📣Online now!
📄 #PheWAS of male and female sex chromosome trisomies in 1.5 million participants of MVP, FinnGen, and UK Biobank
@finngen.bsky.social @ukbiobank.bsky.social
📄 #PheWAS of male and female sex chromosome trisomies in 1.5 million participants of MVP, FinnGen, and UK Biobank
@finngen.bsky.social @ukbiobank.bsky.social
Phenome-wide association study of male and female sex chromosome trisomies in 1.5 million participants of MVP, FinnGen, and UK Biobank
We examined disease associations for sex chromosome trisomies (SCTs) by performing
a phenome-wide association study in 2,769 individuals with SCT (47,XXY: 1,319; 47,XYY:
1,108; and 47,XXX: 342). Many ...
www.cell.com
August 22, 2025 at 8:59 AM
Happy to see this online!
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
Reposted by Linda Kachuri
Grateful for this terrific commentary by @tomonroe.bsky.social in @jclinical-invest.bsky.social on our paper that is out in final print format today: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
August 15, 2025 at 7:40 PM
Grateful for this terrific commentary by @tomonroe.bsky.social in @jclinical-invest.bsky.social on our paper that is out in final print format today: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
Reposted by Linda Kachuri
Our new AJHG paper is online. We develop a new TWAS tool that uses local-ancestry information to improve power of gene mapping in admixed samples. Lead author Taylor Head (now at MD Anderson) did a phenomenal job spearheading this work!
🚨New method!
📄CADET: Enhanced transcriptome-wide association analyses in admixed samples using eQTL summary data
🧑🤝🧑 @epsteinstatgen.bsky.social @yjingj.bsky.social & co
📄CADET: Enhanced transcriptome-wide association analyses in admixed samples using eQTL summary data
🧑🤝🧑 @epsteinstatgen.bsky.social @yjingj.bsky.social & co
CADET: Enhanced transcriptome-wide association analyses in admixed samples using eQTL summary data
CADET is a transcriptome-wide association test for admixed cohorts that leverages
local ancestry information to improve detection of trait-influencing genes. CADET
outperformed existing methods using ...
www.cell.com
June 23, 2025 at 12:33 PM
Our new AJHG paper is online. We develop a new TWAS tool that uses local-ancestry information to improve power of gene mapping in admixed samples. Lead author Taylor Head (now at MD Anderson) did a phenomenal job spearheading this work!
Reposted by Linda Kachuri
A final point about trust. Herasight has apparently partnered with Heliospect Genomics, founded by self-described eugenicist Jonathan Anomaly (a member of both companies). Anomaly and Heliospect were profiled last year by Hope Not Hate:
investigations.hopenothate.org.uk/superbaby-fa...
investigations.hopenothate.org.uk/superbaby-fa...
August 2, 2025 at 2:38 PM
A final point about trust. Herasight has apparently partnered with Heliospect Genomics, founded by self-described eugenicist Jonathan Anomaly (a member of both companies). Anomaly and Heliospect were profiled last year by Hope Not Hate:
investigations.hopenothate.org.uk/superbaby-fa...
investigations.hopenothate.org.uk/superbaby-fa...
Reposted by Linda Kachuri
We have 2-3 group leader positions opening @fimm-uh.bsky.social !!
We are looking for outstanding candidates in human genetics and precision medicine.
This time we have a focus on population health data science. E.g. AI for EHR/health data
Generous starting package 💰
shorturl.at/FAk6n
We are looking for outstanding candidates in human genetics and precision medicine.
This time we have a focus on population health data science. E.g. AI for EHR/health data
Generous starting package 💰
shorturl.at/FAk6n
FIMM-EMBL Group Leaders in Molecular Medicine
FIMM-EMBL Group Leaders in Molecular Medicine
jobs.helsinki.fi
June 1, 2025 at 3:38 PM
We have 2-3 group leader positions opening @fimm-uh.bsky.social !!
We are looking for outstanding candidates in human genetics and precision medicine.
This time we have a focus on population health data science. E.g. AI for EHR/health data
Generous starting package 💰
shorturl.at/FAk6n
We are looking for outstanding candidates in human genetics and precision medicine.
This time we have a focus on population health data science. E.g. AI for EHR/health data
Generous starting package 💰
shorturl.at/FAk6n
Reposted by Linda Kachuri
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
These things can take time and patience is key!
📢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
July 21, 2025 at 6:54 PM
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
These things can take time and patience is key!
IDH mutations are some of the most informative prognostic markers for #glioma. Our small, proof-of-concept study shows that #multimodal classifiers that include #polygenic risk scores can improve pre-operative molecular subtyping: www.nature.com/articles/s41... 🧠🧬
@stanford-cancer.bsky.social
@stanford-cancer.bsky.social
Integration of MRI radiomics and germline genetics to predict the IDH mutation status of gliomas - npj Precision Oncology
npj Precision Oncology - Integration of MRI radiomics and germline genetics to predict the IDH mutation status of gliomas
www.nature.com
June 21, 2025 at 6:42 PM
IDH mutations are some of the most informative prognostic markers for #glioma. Our small, proof-of-concept study shows that #multimodal classifiers that include #polygenic risk scores can improve pre-operative molecular subtyping: www.nature.com/articles/s41... 🧠🧬
@stanford-cancer.bsky.social
@stanford-cancer.bsky.social
Reposted by Linda Kachuri
New online! Making sense of the polygenicity of complex traits
Making sense of the polygenicity of complex traits
Nature Reviews Genetics, Published online: 16 June 2025; doi:10.1038/s41576-025-00866-7Hakhamanesh Mostafavi recalls a landmark paper by Boyle et al. on the omnigenic model, which proposed that complex traits are influenced by thousands of genes across the genome, including many that are only indirectly related to a trait through regulatory networks.
www.nature.com
June 16, 2025 at 12:30 PM
New online! Making sense of the polygenicity of complex traits
Reposted by Linda Kachuri
Our paper on the theoretical properties of SNP heritability in admixed populations is out in Genetics:
academic.oup.com/genetics/adv...
with @jinguohuang.bsky.social, @nicole-kleman.bsky.social , Saonli Basu, and Mark Shriver
academic.oup.com/genetics/adv...
with @jinguohuang.bsky.social, @nicole-kleman.bsky.social , Saonli Basu, and Mark Shriver
May 25, 2025 at 2:03 AM
Our paper on the theoretical properties of SNP heritability in admixed populations is out in Genetics:
academic.oup.com/genetics/adv...
with @jinguohuang.bsky.social, @nicole-kleman.bsky.social , Saonli Basu, and Mark Shriver
academic.oup.com/genetics/adv...
with @jinguohuang.bsky.social, @nicole-kleman.bsky.social , Saonli Basu, and Mark Shriver
Reposted by Linda Kachuri
It's that time of the year again: ASHG Abstracts!
ASHG has always provided an excellent avenue to present novel methods in StatGen and GenEpi, get early feedback, and meet your colleagues! Deadline is June 9th, so still plenty of time :D
Link below 👇
www.ashg.org/meetings/202...
ASHG has always provided an excellent avenue to present novel methods in StatGen and GenEpi, get early feedback, and meet your colleagues! Deadline is June 9th, so still plenty of time :D
Link below 👇
www.ashg.org/meetings/202...
Abstracts
Abstract submission for ASHG 2025. We encourage you to submit your latest research on human genetics and genomics for programming at the ASHG 2025 Annual Meeting.
urldefense.com
May 15, 2025 at 3:36 PM
It's that time of the year again: ASHG Abstracts!
ASHG has always provided an excellent avenue to present novel methods in StatGen and GenEpi, get early feedback, and meet your colleagues! Deadline is June 9th, so still plenty of time :D
Link below 👇
www.ashg.org/meetings/202...
ASHG has always provided an excellent avenue to present novel methods in StatGen and GenEpi, get early feedback, and meet your colleagues! Deadline is June 9th, so still plenty of time :D
Link below 👇
www.ashg.org/meetings/202...
Reposted by Linda Kachuri
Check out our scPrediXcan paper
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework
Zhou et al. introduce scPrediXcan, a novel transcriptome-wide association study framework
that integrates the deep learning-based model ctPred for cell-type-specific expression
prediction. Applied to ...
www.cell.com
May 14, 2025 at 10:41 PM
Check out our scPrediXcan paper
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
Reposted by Linda Kachuri
I'm excited to share our latest work, now out in #PLOSGenetics! If you feel limited by linear models in TWAS or PWAS but don't think you can switch to nonlinear methods due to a lack of individual-level phenotype data, this paper is for you.
🔗 journals.plos.org/plosgenetics...
Thread below 👇 (1/6)
🔗 journals.plos.org/plosgenetics...
Thread below 👇 (1/6)
May 7, 2025 at 6:12 PM
I'm excited to share our latest work, now out in #PLOSGenetics! If you feel limited by linear models in TWAS or PWAS but don't think you can switch to nonlinear methods due to a lack of individual-level phenotype data, this paper is for you.
🔗 journals.plos.org/plosgenetics...
Thread below 👇 (1/6)
🔗 journals.plos.org/plosgenetics...
Thread below 👇 (1/6)
Reposted by Linda Kachuri
Hating on “Big Pharma”? Cool, it’s a $1.6 trillion regulated industry. But hang on…the $6.3 trillion wellness industry sells you mushroom tea, dewormers, crash diets, and alkaline water—no regulations, no oversight. But hey, it’s ‘natural,’ right?
April 30, 2025 at 1:36 AM
Hating on “Big Pharma”? Cool, it’s a $1.6 trillion regulated industry. But hang on…the $6.3 trillion wellness industry sells you mushroom tea, dewormers, crash diets, and alkaline water—no regulations, no oversight. But hey, it’s ‘natural,’ right?
Reposted by Linda Kachuri
3/n
Genetic correlation is straightforward but remember HLA - largely impacting T1D & other AIDs - is excluded by LDSC.
If genetic correlation is a genome-wide non-HLA measurement, how can we get HLA back into the game?
We built a within-sample HLA PGS with weighted ridge classifiers in FinnGen.
Genetic correlation is straightforward but remember HLA - largely impacting T1D & other AIDs - is excluded by LDSC.
If genetic correlation is a genome-wide non-HLA measurement, how can we get HLA back into the game?
We built a within-sample HLA PGS with weighted ridge classifiers in FinnGen.
April 28, 2025 at 3:15 AM
3/n
Genetic correlation is straightforward but remember HLA - largely impacting T1D & other AIDs - is excluded by LDSC.
If genetic correlation is a genome-wide non-HLA measurement, how can we get HLA back into the game?
We built a within-sample HLA PGS with weighted ridge classifiers in FinnGen.
Genetic correlation is straightforward but remember HLA - largely impacting T1D & other AIDs - is excluded by LDSC.
If genetic correlation is a genome-wide non-HLA measurement, how can we get HLA back into the game?
We built a within-sample HLA PGS with weighted ridge classifiers in FinnGen.
Reposted by Linda Kachuri
🚨 New paper 🚨
Do known genetic factors for obesity and type 2 diabetes affect weight loss from GLP1-RA (Ozempic) or bariatric surgery?
🔍 10,960 people, 9 biobanks, 6 countries
🧬 Minimal genetic impact on GLP1-RA response
📉 Modest effect after surgery
www.nature.com/articles/s41...
Do known genetic factors for obesity and type 2 diabetes affect weight loss from GLP1-RA (Ozempic) or bariatric surgery?
🔍 10,960 people, 9 biobanks, 6 countries
🧬 Minimal genetic impact on GLP1-RA response
📉 Modest effect after surgery
www.nature.com/articles/s41...
Association between plausible genetic factors and weight loss from GLP1-RA and bariatric surgery - Nature Medicine
The authors found, after analyzing 10,960 individuals from 9 multiancestry biobanks across 6 countries, that genetic factors previously associated with BMI have limited impact on GLP-1 receptor agonis...
www.nature.com
April 18, 2025 at 1:32 PM
🚨 New paper 🚨
Do known genetic factors for obesity and type 2 diabetes affect weight loss from GLP1-RA (Ozempic) or bariatric surgery?
🔍 10,960 people, 9 biobanks, 6 countries
🧬 Minimal genetic impact on GLP1-RA response
📉 Modest effect after surgery
www.nature.com/articles/s41...
Do known genetic factors for obesity and type 2 diabetes affect weight loss from GLP1-RA (Ozempic) or bariatric surgery?
🔍 10,960 people, 9 biobanks, 6 countries
🧬 Minimal genetic impact on GLP1-RA response
📉 Modest effect after surgery
www.nature.com/articles/s41...
Reposted by Linda Kachuri
I started a newsletter.
My first post is going to be a deeper dive into insider trading on Wednesday.
I’ll be writing about tech, San Francisco, politics, and AI. With kindness.
I’d be grateful for any boosts as I’m excited and nervous for this.
data-and-politics.ghost.io
My first post is going to be a deeper dive into insider trading on Wednesday.
I’ll be writing about tech, San Francisco, politics, and AI. With kindness.
I’d be grateful for any boosts as I’m excited and nervous for this.
data-and-politics.ghost.io
Data and Politics
Data + Politics. San Francisco, Tech, Politics. With Kindness.
data-and-politics.ghost.io
April 12, 2025 at 2:31 AM
I started a newsletter.
My first post is going to be a deeper dive into insider trading on Wednesday.
I’ll be writing about tech, San Francisco, politics, and AI. With kindness.
I’d be grateful for any boosts as I’m excited and nervous for this.
data-and-politics.ghost.io
My first post is going to be a deeper dive into insider trading on Wednesday.
I’ll be writing about tech, San Francisco, politics, and AI. With kindness.
I’d be grateful for any boosts as I’m excited and nervous for this.
data-and-politics.ghost.io
Reposted by Linda Kachuri
Accurately describes the phenomenon of Bureaucratic Capture, where a bureaucracy is set up to serve an organization, but everyone ends up serving the bureaucracy instead (not confined to universities, of course)
"We are losing sight of the academic mission: to think, to enquire, to design & perform new research, to innovate, to teach & communicate our findings for the purpose of societal improvement"
A painfully accurate read. That lays out the folly of the modern uni!
academic.oup.com/brain/articl...
A painfully accurate read. That lays out the folly of the modern uni!
academic.oup.com/brain/articl...
On the responsibilities of intellectuals and the rise of bullshit jobs in universities
You may never have considered yourself to be one. Why would you? But if you’re reading this, there is more than a likelihood that you are one. If you’re a
academic.oup.com
March 25, 2025 at 3:12 PM
Accurately describes the phenomenon of Bureaucratic Capture, where a bureaucracy is set up to serve an organization, but everyone ends up serving the bureaucracy instead (not confined to universities, of course)
Reposted by Linda Kachuri
1/ Hey y'all, I'm excited to share my latest paper, which is out now in PNAS! We introduce FAVA, a statistical framework to measure compositional variability across microbiome samples. If you want to measure variability across a stacked bar plot, FAVA is for you! Paper: doi.org/10.1073/pnas...
March 14, 2025 at 8:46 PM
1/ Hey y'all, I'm excited to share my latest paper, which is out now in PNAS! We introduce FAVA, a statistical framework to measure compositional variability across microbiome samples. If you want to measure variability across a stacked bar plot, FAVA is for you! Paper: doi.org/10.1073/pnas...
Reposted by Linda Kachuri
Wishing a joyous St. Patrick's Day to everyone celebrating
☘️☘️☘️
☘️☘️☘️
March 17, 2025 at 6:18 PM
Wishing a joyous St. Patrick's Day to everyone celebrating
☘️☘️☘️
☘️☘️☘️