Lili Milani
@lilimilani.bsky.social
Head of Estonian Biobank & Professor of Pharmacogenomics at the Estonian Genome Centre, University of Tartu.
Reposted by Lili Milani
New study of 800K+ genomes from gnomAD reveals most “pathogenic” variants in healthy people aren’t truly disease-tolerant. They are explained by annotation errors, mosaicism, or compensatory variants. 🧬
A big step for precision medicine!
www.nature.com/articles/s41...
A big step for precision medicine!
www.nature.com/articles/s41...
Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database - Nature Communications
Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD),…
www.nature.com
November 4, 2025 at 3:06 PM
New study of 800K+ genomes from gnomAD reveals most “pathogenic” variants in healthy people aren’t truly disease-tolerant. They are explained by annotation errors, mosaicism, or compensatory variants. 🧬
A big step for precision medicine!
www.nature.com/articles/s41...
A big step for precision medicine!
www.nature.com/articles/s41...
Reposted by Lili Milani
1/7 New BMI GWAS out! Using Estonian Biobank (n=204,747) and replication in FinnGen, we show that even in Europe you can still find region-specific biology if you zoom into population-tailored sumstats. Big thanks to co-author @kanwalbatool.bsky.social :)
October 16, 2025 at 6:54 PM
1/7 New BMI GWAS out! Using Estonian Biobank (n=204,747) and replication in FinnGen, we show that even in Europe you can still find region-specific biology if you zoom into population-tailored sumstats. Big thanks to co-author @kanwalbatool.bsky.social :)
Reposted by Lili Milani
#PacBio announces major upcoming advances for #Revio and #Vega designed to lower genome costs, expand multiomic capabilities, and support regulated research.
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
October 14, 2025 at 3:33 PM
#PacBio announces major upcoming advances for #Revio and #Vega designed to lower genome costs, expand multiomic capabilities, and support regulated research.
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
Reposted by Lili Milani
The Open Targets Platform autumn release is out! 🍂
We have ingested the full dataset of over 13 million enhancer-gene regulatory interactions in the human genome across 1,458 DNase-seq experiments covering 369 cell types and tissues from the ENCODE-rE2G model
blog.opentargets.org/open-targets...
We have ingested the full dataset of over 13 million enhancer-gene regulatory interactions in the human genome across 1,458 DNase-seq experiments covering 369 cell types and tissues from the ENCODE-rE2G model
blog.opentargets.org/open-targets...
Open Targets Platform 25.09 has been released!
The September 25 release includes enhancer-gene data predicted by ENCODE-rE2G, molQTL credible sets for targets, new options for the variant structural viewer, and a number of data updates from GWAS C...
blog.opentargets.org
September 18, 2025 at 10:39 AM
The Open Targets Platform autumn release is out! 🍂
We have ingested the full dataset of over 13 million enhancer-gene regulatory interactions in the human genome across 1,458 DNase-seq experiments covering 369 cell types and tissues from the ENCODE-rE2G model
blog.opentargets.org/open-targets...
We have ingested the full dataset of over 13 million enhancer-gene regulatory interactions in the human genome across 1,458 DNase-seq experiments covering 369 cell types and tissues from the ENCODE-rE2G model
blog.opentargets.org/open-targets...
Reposted by Lili Milani
🧵 The summer of 2025 has been AI's "cruel summer"—wrongful deaths, dangerous therapy chatbots, medical misinformation, facial recognition failures. These aren't isolated glitches but predictable harms from systems deployed without adequate oversight. www.science.org/doi/10.1126/...
An ELSI for AI: Learning from genetics to govern algorithms
In the United States, the summer of 2025 will be remembered as artificial intelligence’s (AI’s) cruel summer—a season when the unheeded risks and dangers of AI became undeniably clear. Recent months h...
www.science.org
September 11, 2025 at 8:48 PM
🧵 The summer of 2025 has been AI's "cruel summer"—wrongful deaths, dangerous therapy chatbots, medical misinformation, facial recognition failures. These aren't isolated glitches but predictable harms from systems deployed without adequate oversight. www.science.org/doi/10.1126/...
So excited about this year’s Gene Forum in Tartu being kicked off now by our keynote speaker @eimearekenny.bsky.social 🤩
September 9, 2025 at 6:22 AM
So excited about this year’s Gene Forum in Tartu being kicked off now by our keynote speaker @eimearekenny.bsky.social 🤩
Huge congrats @klehto.bsky.social on this achievement!! Her work has already enriched the @estbiobank.bsky.social and will continue to do so! 💙🖤🤍
Are adult attention deficit hyperactivity disorder (ADHD) features truly the same as childhood ADHD?
Kelli Letho, a new ERC Starting Grantee at the University of Tartu will dissect the causal mechanisms of adult ADHD features
More 👉 buff.ly/nci5eve
#ERCStG #FontierResearch @klehto.bsky.social
Kelli Letho, a new ERC Starting Grantee at the University of Tartu will dissect the causal mechanisms of adult ADHD features
More 👉 buff.ly/nci5eve
#ERCStG #FontierResearch @klehto.bsky.social
September 4, 2025 at 11:44 AM
Huge congrats @klehto.bsky.social on this achievement!! Her work has already enriched the @estbiobank.bsky.social and will continue to do so! 💙🖤🤍
Reposted by Lili Milani
🚨 Our parent-of-origin study is out in Nature! 🧬
Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss.
🔗 www.nature.com/articles/s41...
Highlights below!
Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss.
🔗 www.nature.com/articles/s41...
Highlights below!
August 6, 2025 at 6:27 PM
🚨 Our parent-of-origin study is out in Nature! 🧬
Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss.
🔗 www.nature.com/articles/s41...
Highlights below!
Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss.
🔗 www.nature.com/articles/s41...
Highlights below!
📢 (on more!) New study from our team in the Journal of Translational Medicine:
Polygenic and pharmacogenomic contributions to medication dosing: a real-world longitudinal biobank study
🔗 tinyurl.com/25u3a5j7
(thread below) 👇
Polygenic and pharmacogenomic contributions to medication dosing: a real-world longitudinal biobank study
🔗 tinyurl.com/25u3a5j7
(thread below) 👇
Polygenic and pharmacogenomic contributions to medication dosing: a real-world longitudinal biobank study - Journal of Translational Medicine
Background Understanding interindividual variability in medication dosing is central to precision medicine. Despite significant pharmacogenomic (PGx) insights into key biological pathways influencing ...
translational-medicine.biomedcentral.com
July 3, 2025 at 12:40 PM
📢 (on more!) New study from our team in the Journal of Translational Medicine:
Polygenic and pharmacogenomic contributions to medication dosing: a real-world longitudinal biobank study
🔗 tinyurl.com/25u3a5j7
(thread below) 👇
Polygenic and pharmacogenomic contributions to medication dosing: a real-world longitudinal biobank study
🔗 tinyurl.com/25u3a5j7
(thread below) 👇
Reposted by Lili Milani
🎉(1/4) Excited to share that our latest paper is now published!
We investigated genetic factors linked to antidepressant side effects in 13,000 individuals from the @estbiobank.bsky.social , leveraging data from questionnaires and clinical notes using NLP.
www.nature.com/articles/s41...
We investigated genetic factors linked to antidepressant side effects in 13,000 individuals from the @estbiobank.bsky.social , leveraging data from questionnaires and clinical notes using NLP.
www.nature.com/articles/s41...
Genetic influences on antidepressant side effects: a CYP2C19 gene variation and polygenic risk study in the Estonian Biobank - European Journal of Human Genetics
European Journal of Human Genetics - Genetic influences on antidepressant side effects: a CYP2C19 gene variation and polygenic risk study in the Estonian Biobank
www.nature.com
July 2, 2025 at 8:47 AM
🎉(1/4) Excited to share that our latest paper is now published!
We investigated genetic factors linked to antidepressant side effects in 13,000 individuals from the @estbiobank.bsky.social , leveraging data from questionnaires and clinical notes using NLP.
www.nature.com/articles/s41...
We investigated genetic factors linked to antidepressant side effects in 13,000 individuals from the @estbiobank.bsky.social , leveraging data from questionnaires and clinical notes using NLP.
www.nature.com/articles/s41...
Reposted by Lili Milani
New preprint! My (now former) postdoc @kvastad.bsky.social led this integration of GWAS and spatial transcriptomics (ST) data to identify tissue structures with enrichment of disease-implicated genes = likely causal drivers of disease biology.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Spatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traits
Spatially resolved transcriptomics is transforming our understanding of cellular and molecular diversity of tissues. Here, to identify tissue structures that are enriched for putatively causal disease...
www.biorxiv.org
May 5, 2025 at 3:40 PM
New preprint! My (now former) postdoc @kvastad.bsky.social led this integration of GWAS and spatial transcriptomics (ST) data to identify tissue structures with enrichment of disease-implicated genes = likely causal drivers of disease biology.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Lili Milani
Our ability to predict a person's risk of heart disease keeps getting better, even among those previously considered at low risk by traditional clinical criteria
@naturemedicine.bsky.social by my team @scripps.edu
www.nature.com/articles/s41...
@naturemedicine.bsky.social by my team @scripps.edu
www.nature.com/articles/s41...
Meta-prediction of coronary artery disease risk - Nature Medicine
A meta-prediction framework integrating polygenic risk scores spanning multiple conditions and nongenetic factors, such as laboratory tests and baseline diagnoses, had superior performance in predicti...
www.nature.com
April 16, 2025 at 2:31 PM
Our ability to predict a person's risk of heart disease keeps getting better, even among those previously considered at low risk by traditional clinical criteria
@naturemedicine.bsky.social by my team @scripps.edu
www.nature.com/articles/s41...
@naturemedicine.bsky.social by my team @scripps.edu
www.nature.com/articles/s41...
Reposted by Lili Milani
This study is a big deal. Is it going to be the one that kicks down the PRS door? Maybe. And that’s saying something.
Assessment of a Polygenic Risk Score in Screening for Prostate Cancer www.nejm.org/doi/full/10....
Assessment of a Polygenic Risk Score in Screening for Prostate Cancer www.nejm.org/doi/full/10....
April 9, 2025 at 9:09 PM
This study is a big deal. Is it going to be the one that kicks down the PRS door? Maybe. And that’s saying something.
Assessment of a Polygenic Risk Score in Screening for Prostate Cancer www.nejm.org/doi/full/10....
Assessment of a Polygenic Risk Score in Screening for Prostate Cancer www.nejm.org/doi/full/10....
Excited to share our recently published overview of the @estbiobank.bsky.social 🧬
We highlight the unique features of the biobank and the conducted scientific research it has enabled, including the many recall studies that have been carried out over the years!
www.nature.com/articles/s41...
We highlight the unique features of the biobank and the conducted scientific research it has enabled, including the many recall studies that have been carried out over the years!
www.nature.com/articles/s41...
The Estonian Biobank’s journey from biobanking to personalized medicine - Nature Communications
Large-scale biobanks have become a font of data that have led to discoveries across many fields of research. Here, the authors provide an overview of the Estonian Biobank, highlighting its value for r...
www.nature.com
April 7, 2025 at 9:13 AM
Excited to share our recently published overview of the @estbiobank.bsky.social 🧬
We highlight the unique features of the biobank and the conducted scientific research it has enabled, including the many recall studies that have been carried out over the years!
www.nature.com/articles/s41...
We highlight the unique features of the biobank and the conducted scientific research it has enabled, including the many recall studies that have been carried out over the years!
www.nature.com/articles/s41...
💡Can we use real world drug purchase data to study the genetics of medication dosing?
We explored this by analyzing 20 years of digital drug dispensing data linked to the @ESTbiobank which hosts 212,000 genotyped participants. 🧵
📄 doi.org/10.1101/2025...
We explored this by analyzing 20 years of digital drug dispensing data linked to the @ESTbiobank which hosts 212,000 genotyped participants. 🧵
📄 doi.org/10.1101/2025...
Investigating the genetic factors of medication dosing using biobank-linked drug purchase data
Despite significant pharmacogenomic (PGx) insights into key biological pathways influencing drug response, the polygenic contribution to dose variability and the potential of electronic health records...
doi.org
April 4, 2025 at 11:50 AM
💡Can we use real world drug purchase data to study the genetics of medication dosing?
We explored this by analyzing 20 years of digital drug dispensing data linked to the @ESTbiobank which hosts 212,000 genotyped participants. 🧵
📄 doi.org/10.1101/2025...
We explored this by analyzing 20 years of digital drug dispensing data linked to the @ESTbiobank which hosts 212,000 genotyped participants. 🧵
📄 doi.org/10.1101/2025...
Reposted by Lili Milani
📢 Excited to share our study in @natmedicine.bsky.social
👉 www.nature.com/articles/s41...
We mapped & characterized genetic risk factors for 42 female reproductive health diagnoses. What we found & why it matters? 👇🧵
👉 www.nature.com/articles/s41...
We mapped & characterized genetic risk factors for 42 female reproductive health diagnoses. What we found & why it matters? 👇🧵
Atlas of genetic and phenotypic associations across 42 female reproductive health diagnoses - Nature Medicine
This study provides a cross-trait atlas of genetic and phenotypic associations across 42 female reproductive health diagnoses.
www.nature.com
March 17, 2025 at 9:27 AM
📢 Excited to share our study in @natmedicine.bsky.social
👉 www.nature.com/articles/s41...
We mapped & characterized genetic risk factors for 42 female reproductive health diagnoses. What we found & why it matters? 👇🧵
👉 www.nature.com/articles/s41...
We mapped & characterized genetic risk factors for 42 female reproductive health diagnoses. What we found & why it matters? 👇🧵
Reposted by Lili Milani
February 27, 2025 at 5:28 PM
Reposted by Lili Milani
Really excited to share our next population-scale WGS work preprint. Here, we analyse three anthropometric traits in nearly 700,000 individuals (discovery UKB ~450K, replication AoU). We show, for these traits, that common and rare variant heritability is convergent
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...
www.biorxiv.org
February 26, 2025 at 4:11 PM
Really excited to share our next population-scale WGS work preprint. Here, we analyse three anthropometric traits in nearly 700,000 individuals (discovery UKB ~450K, replication AoU). We show, for these traits, that common and rare variant heritability is convergent
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Lili Milani
We're delighted to share our work on scrambling the human genome using prime editing, repetitive elements, and recombinases in @science.org , led by @jonaskoeppel.bsky.social , @f-raphael.bsky.social , with @proftomellis.bsky.social and George Church.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Randomizing the human genome by engineering recombination between repeat elements
We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into re...
www.science.org
January 31, 2025 at 1:49 PM
We're delighted to share our work on scrambling the human genome using prime editing, repetitive elements, and recombinases in @science.org , led by @jonaskoeppel.bsky.social , @f-raphael.bsky.social , with @proftomellis.bsky.social and George Church.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Lili Milani
🌟 Exciting news: The Leena Peltonen School of Human Genetics returns in 2025!
This prestigious summer school brings together leaders in human genetics with PhD students
📅 July 27-31, 2025
📍 Wellcome Genome Campus, UK
📝 Apply by March 7 at www.lpshg.com
This prestigious summer school brings together leaders in human genetics with PhD students
📅 July 27-31, 2025
📍 Wellcome Genome Campus, UK
📝 Apply by March 7 at www.lpshg.com
LPSHG – Leena Peltonen Shool Of Human Genomics
www.lpshg.com
December 19, 2024 at 4:01 PM
🌟 Exciting news: The Leena Peltonen School of Human Genetics returns in 2025!
This prestigious summer school brings together leaders in human genetics with PhD students
📅 July 27-31, 2025
📍 Wellcome Genome Campus, UK
📝 Apply by March 7 at www.lpshg.com
This prestigious summer school brings together leaders in human genetics with PhD students
📅 July 27-31, 2025
📍 Wellcome Genome Campus, UK
📝 Apply by March 7 at www.lpshg.com
This is what happens when you return research results to biobank participants:
✅ The 2nd most googled “How to…?” question in Estonia 2024: “How to become a biobank participant?”
✅ "Estonian Biobank" among Top 10 search terms.
Huge thanks to the entire UniTartu & EstBB teams! ✨
✅ The 2nd most googled “How to…?” question in Estonia 2024: “How to become a biobank participant?”
✅ "Estonian Biobank" among Top 10 search terms.
Huge thanks to the entire UniTartu & EstBB teams! ✨
December 13, 2024 at 10:28 AM
This is what happens when you return research results to biobank participants:
✅ The 2nd most googled “How to…?” question in Estonia 2024: “How to become a biobank participant?”
✅ "Estonian Biobank" among Top 10 search terms.
Huge thanks to the entire UniTartu & EstBB teams! ✨
✅ The 2nd most googled “How to…?” question in Estonia 2024: “How to become a biobank participant?”
✅ "Estonian Biobank" among Top 10 search terms.
Huge thanks to the entire UniTartu & EstBB teams! ✨
Reposted by Lili Milani
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
December 11, 2024 at 4:29 PM
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
I'm very impressed by the thorough work @holtjma.bsky.social, @meberle.bsky.social and team have done in building #StarPhase - it really checks all the boxes for reliable calling of #pharmacogenomic star alleles, even for #CYP2D6! 🙌
“StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data” is now on biorxiv! In this work, we explore the use of long-read sequencing (#PacBio #HiFi) for #pharmacogenomics #PGx. 1/N
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets
A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase
github.com
December 11, 2024 at 3:55 PM
I'm very impressed by the thorough work @holtjma.bsky.social, @meberle.bsky.social and team have done in building #StarPhase - it really checks all the boxes for reliable calling of #pharmacogenomic star alleles, even for #CYP2D6! 🙌
Reposted by Lili Milani
🚨 Our preprint on parent-of-origin effects (POEs) is out!
With our novel method, we inferred the parental origin of alleles for >220,000 individuals, uncovering novel insights into genetics, evolution, and health.
👉 Read here: www.medrxiv.org/content/10.1...
👇 Highlights below!
With our novel method, we inferred the parental origin of alleles for >220,000 individuals, uncovering novel insights into genetics, evolution, and health.
👉 Read here: www.medrxiv.org/content/10.1...
👇 Highlights below!
Parent-of-Origin inference and its role in the genetic architecture of complex traits: evidence from ~220,000 individuals
Parent-of-origin effects (POEs) occur when the impact of a genetic variant depends on its parental origin. Traditionally linked to genomic imprinting, these effects are believed to have evolved from p...
www.medrxiv.org
December 6, 2024 at 12:12 PM
🚨 Our preprint on parent-of-origin effects (POEs) is out!
With our novel method, we inferred the parental origin of alleles for >220,000 individuals, uncovering novel insights into genetics, evolution, and health.
👉 Read here: www.medrxiv.org/content/10.1...
👇 Highlights below!
With our novel method, we inferred the parental origin of alleles for >220,000 individuals, uncovering novel insights into genetics, evolution, and health.
👉 Read here: www.medrxiv.org/content/10.1...
👇 Highlights below!
Reposted by Lili Milani
Worth stressing that computers from across the world access EMBL-EBI 100 million times a day - sometimes for a tiny lookup, sometimes to download large amounts of public domain information about the world we live in.
I am very proud to be part of the @ebi.embl.org community delivering on this
I am very proud to be part of the @ebi.embl.org community delivering on this
Our data resources underpin life science research and scientists worldwide use them on a regular basis:
🌍 101 million requests to our data resource websites on an average day
💻 36 million unique IP addresses annually
Which of our resources have you used recently? 👀
www.ebi.ac.uk/about/our-im...
🌍 101 million requests to our data resource websites on an average day
💻 36 million unique IP addresses annually
Which of our resources have you used recently? 👀
www.ebi.ac.uk/about/our-im...
November 25, 2024 at 2:12 PM
Worth stressing that computers from across the world access EMBL-EBI 100 million times a day - sometimes for a tiny lookup, sometimes to download large amounts of public domain information about the world we live in.
I am very proud to be part of the @ebi.embl.org community delivering on this
I am very proud to be part of the @ebi.embl.org community delivering on this