Josep Mercader
@josepmercader.bsky.social
Reposted by Josep Mercader
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 Josep Mercader
🎉 Congrats to Julie-Alexia Dias and thanks for the shout out to @prsmethods.bsky.social !
"Some of the most formative parts of my own training have come from working across groups and institutions...through my involvement in PRIMED (Polygenic Risk Methods Development)..."
"Some of the most formative parts of my own training have come from working across groups and institutions...through my involvement in PRIMED (Polygenic Risk Methods Development)..."
@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
November 7, 2025 at 12:49 AM
🎉 Congrats to Julie-Alexia Dias and thanks for the shout out to @prsmethods.bsky.social !
"Some of the most formative parts of my own training have come from working across groups and institutions...through my involvement in PRIMED (Polygenic Risk Methods Development)..."
"Some of the most formative parts of my own training have come from working across groups and institutions...through my involvement in PRIMED (Polygenic Risk Methods Development)..."
Reposted by Josep Mercader
We’ve put up summary statistics for over 3,000 traits in the All of Us resource, and a shiny new browser alongside it! Explore your favorite gene or phenotype here: allbyall.researchallofus.org #ASHG24
All by All
The All by All browser maps known and novel associations between genotypes and phenotypes using data contributed by All of Us Research Program participants as of July 1, 2022. All by All encompasses a...
allbyall.researchallofus.org
November 8, 2024 at 8:32 PM
We’ve put up summary statistics for over 3,000 traits in the All of Us resource, and a shiny new browser alongside it! Explore your favorite gene or phenotype here: allbyall.researchallofus.org #ASHG24
Reposted by Josep Mercader
A new @natgenet.nature.com study by Broad, @mgbresearch.bsky.social, and VA Boston collaborators reveals a genetic variant that helps explain the high dilated cardiomyopathy risk in people of African ancestry.
Genetic variant increases risk of heart muscle disease common in individuals of African ancestry
A single mutation in the CD36 gene, present in 17 percent of people with African ancestry, increases a person's dilated cardiomyopathy risk by 33 percent.
broad.io
October 31, 2025 at 3:28 PM
A new @natgenet.nature.com study by Broad, @mgbresearch.bsky.social, and VA Boston collaborators reveals a genetic variant that helps explain the high dilated cardiomyopathy risk in people of African ancestry.
Reposted by Josep Mercader
👀 🔖 ICYMI @prsmethods.bsky.social investigators report on incorporating social determinants of health into disease prediction in the NIH All of Us research program - www.medrxiv.org/content/10.1...
Quantifying Social Determinants of Health for Disease Prediction: A Multi-Level Approach Using Healthy People 2030 and All of Us Data
Despite the growing recognition that social determinants of health (SDoH) play a prominent role in shaping health outcomes, inconsistent measures across health systems and research studies - and the a...
www.medrxiv.org
October 29, 2025 at 10:15 PM
👀 🔖 ICYMI @prsmethods.bsky.social investigators report on incorporating social determinants of health into disease prediction in the NIH All of Us research program - www.medrxiv.org/content/10.1...
Reposted by Josep Mercader
New pre-print "Mendelian randomization in a multi-ancestry world: reflections and practical advice" led by @amymariemason.bsky.social on - arxiv.org/abs/2510.17554
Mendelian randomization in a multi-ancestry world: reflections and practical advice
Many Mendelian randomization (MR) papers have been conducted only in people of European ancestry, limiting transportability of results to the global population. Expanding MR to diverse ancestry groups...
arxiv.org
October 27, 2025 at 8:43 AM
New pre-print "Mendelian randomization in a multi-ancestry world: reflections and practical advice" led by @amymariemason.bsky.social on - arxiv.org/abs/2510.17554
Reposted by Josep Mercader
🚨 Using the GWAS Catalog “All associations” tsv download file? We recently made some changes that may affect your pipelines.
The data now includes >1m curated associations! This means the “All associations” file is extremely large!
In the latest release, you now have a choice of two formats 👇
The data now includes >1m curated associations! This means the “All associations” file is extremely large!
In the latest release, you now have a choice of two formats 👇
October 23, 2025 at 4:26 PM
🚨 Using the GWAS Catalog “All associations” tsv download file? We recently made some changes that may affect your pipelines.
The data now includes >1m curated associations! This means the “All associations” file is extremely large!
In the latest release, you now have a choice of two formats 👇
The data now includes >1m curated associations! This means the “All associations” file is extremely large!
In the latest release, you now have a choice of two formats 👇
Very proud of four posters presented by our team right now (2.30) from: @aliciahuerta.bsky.social, Katie Taylor, Maheak Vora, Harsh Wadhwa , and Thinley Wangden.
October 15, 2025 at 6:51 PM
Very proud of four posters presented by our team right now (2.30) from: @aliciahuerta.bsky.social, Katie Taylor, Maheak Vora, Harsh Wadhwa , and Thinley Wangden.
Reposted by Josep Mercader
Reposted by Josep Mercader
Welcome to #ASHG25! As our President Sarah Tishkoff just noted, next year for the first time the ASHG exec cmte will be all women. Glad to have anyone and everyone participating in this society now and in the future.
October 14, 2025 at 8:25 PM
Welcome to #ASHG25! As our President Sarah Tishkoff just noted, next year for the first time the ASHG exec cmte will be all women. Glad to have anyone and everyone participating in this society now and in the future.
Reposted by Josep Mercader
Attending #ASHG25? Learn how @prsmethods.bsky.social investigators are improving polygenic risk prediction in diverse populations by visiting these talks and posters docs.google.com/spreadsheets...
ASHG 2025 PRIMED Abstracts
docs.google.com
October 14, 2025 at 4:14 PM
Attending #ASHG25? Learn how @prsmethods.bsky.social investigators are improving polygenic risk prediction in diverse populations by visiting these talks and posters docs.google.com/spreadsheets...
Reposted by Josep Mercader
After yrs of disappointment scientists have made a genuine advance in treating Huntington's. The new gene therapy slowed disease progression by 75%. But it's still experimental and will likely be $$, @parshallison.bsky.social reports for @sciam.bsky.social: www.scientificamerican.com/article/firs...
How Scientists Finally Found a Treatment that Slows Huntington’s Disease
After years of heartbreak, researchers have found an experimental treatment that can slow the progression of Huntington’s disease, according to early results from a small clinical trial
www.scientificamerican.com
October 1, 2025 at 5:35 PM
After yrs of disappointment scientists have made a genuine advance in treating Huntington's. The new gene therapy slowed disease progression by 75%. But it's still experimental and will likely be $$, @parshallison.bsky.social reports for @sciam.bsky.social: www.scientificamerican.com/article/firs...
Reposted by Josep Mercader
We’re getting ready for an exciting week at #ASHG2025 in Boston! Come meet the FinnGen team at booth 147 - we’ll be sharing updates and showcasing new public resources and tools. Plus, don’t miss the various presentations featuring FinnGen results across the program!
www.finngen.fi/en/meet-finn...
www.finngen.fi/en/meet-finn...
Meet FinnGen at the ASHG 2025! | FinnGen
Results based on the FinnGen data are presented in almost 40 talks or posters during the 2025 Annual Meeting of the American Society of Human Genetics (ASHG) in Boston, October 14-18. We also have a b...
www.finngen.fi
October 10, 2025 at 11:59 AM
We’re getting ready for an exciting week at #ASHG2025 in Boston! Come meet the FinnGen team at booth 147 - we’ll be sharing updates and showcasing new public resources and tools. Plus, don’t miss the various presentations featuring FinnGen results across the program!
www.finngen.fi/en/meet-finn...
www.finngen.fi/en/meet-finn...
Reposted by Josep Mercader
📃 We’re excited to share our latest work, now published in Nature Communications — a major update to the Genome Aggregation Database (gnomAD) that improves allele frequency resolution for two gnomAD-defined genetic ancestry groups using local ancestry inference (LAI).
Improved allele frequencies in gnomAD through local ancestry inference - Nature Communications
This study incorporates local ancestry into the Genome Aggregation Database (gnomAD) to improve allele frequency estimates for admixed populations, enhancing variant interpretation and enabling more accurate and equitable genomic research and clinical care.
www.nature.com
October 6, 2025 at 6:31 PM
📃 We’re excited to share our latest work, now published in Nature Communications — a major update to the Genome Aggregation Database (gnomAD) that improves allele frequency resolution for two gnomAD-defined genetic ancestry groups using local ancestry inference (LAI).
Reposted by Josep Mercader
GWAS finds millions of variants — but what are the Predicted Effector Genes (PEGs)? Our Nature Genetics Perspective rdcu.be/eoqVk showed big inconsistencies.
At ASHG 2025, we’ll introduce a new standard to make PEG data FAIR.
🗓️ Ancillary Session: Oct 17 | 11:45 | Room 259A
📌Poster: Oct 16 | 2:30
At ASHG 2025, we’ll introduce a new standard to make PEG data FAIR.
🗓️ Ancillary Session: Oct 17 | 11:45 | Room 259A
📌Poster: Oct 16 | 2:30
Realizing the promise of genome-wide association studies for effector gene prediction
Nature Genetics - This Perspective argues that predicting effector genes for complex diseases is a key outcome of genetic association studies where standards are urgently needed to maximize...
rdcu.be
September 30, 2025 at 8:51 PM
GWAS finds millions of variants — but what are the Predicted Effector Genes (PEGs)? Our Nature Genetics Perspective rdcu.be/eoqVk showed big inconsistencies.
At ASHG 2025, we’ll introduce a new standard to make PEG data FAIR.
🗓️ Ancillary Session: Oct 17 | 11:45 | Room 259A
📌Poster: Oct 16 | 2:30
At ASHG 2025, we’ll introduce a new standard to make PEG data FAIR.
🗓️ Ancillary Session: Oct 17 | 11:45 | Room 259A
📌Poster: Oct 16 | 2:30
Reposted by Josep Mercader
Exome-wide association study in 54,698 south Asians identifies novel type 2 diabetes associations with RNF19A, HNF4A, and dissects role of coding variants in GP2 and CDKAL1 https://www.medrxiv.org/content/10.1101/2025.09.24.25336527v1
September 26, 2025 at 10:40 PM
Exome-wide association study in 54,698 south Asians identifies novel type 2 diabetes associations with RNF19A, HNF4A, and dissects role of coding variants in GP2 and CDKAL1 https://www.medrxiv.org/content/10.1101/2025.09.24.25336527v1
Reposted by Josep Mercader
Massive sibling regression study finds that human traits are largely environmentally driven (average heritability = 0.3)
Within-family heritability estimates for behavioural and disease phenotypes from 500,000 sibling pairs of diverse ancestries
Quantification of the direct effect of genetic variation on human behavioural traits is important for understanding between-individual variation in socio-economic and health outcomes but estimates of ...
www.medrxiv.org
September 20, 2025 at 6:19 PM
Massive sibling regression study finds that human traits are largely environmentally driven (average heritability = 0.3)
Reposted by Josep Mercader
A project many years in the process, we’re pleased to present our work on multi-ancestry meta-analysis across a boatload of traits in the UK Biobank: www.nature.com/articles/s41...
Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects - Nature Genetics
Genome-wide analyses for 7,266 traits leveraging data from several genetic ancestry groups in UK Biobank identify new associations and enhance resources for interpreting risk variants across diverse p...
www.nature.com
September 18, 2025 at 5:25 PM
A project many years in the process, we’re pleased to present our work on multi-ancestry meta-analysis across a boatload of traits in the UK Biobank: www.nature.com/articles/s41...
Reposted by Josep Mercader
I’m excited to share the 2 newest Neonatal diabetes genes: RNU4ATAC and RNU6ATAC. These genes encode snRNA components of the minor spliceosome and biallelic variants in them cause monogenic autoimmune diabetes. If you are at #EASD, come to Matt Johnson’s talk Tuesday @4pm in Milan hall to hear more.
The minor spliceosome is a master immune regulator
Pathogenic variants in non-coding genes are emerging as critical contributors to human rare diseases. We identified 19 individuals with early-onset diabetes (diagnosed <5 years) and additional clinica...
www.medrxiv.org
September 15, 2025 at 8:28 AM
I’m excited to share the 2 newest Neonatal diabetes genes: RNU4ATAC and RNU6ATAC. These genes encode snRNA components of the minor spliceosome and biallelic variants in them cause monogenic autoimmune diabetes. If you are at #EASD, come to Matt Johnson’s talk Tuesday @4pm in Milan hall to hear more.
Reposted by Josep Mercader
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
September 12, 2025 at 7:00 PM
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
Reposted by Josep Mercader
Delighted to amplify my talented PhD student’s work! Check it out for a great way to streamline and harmonize Tractor analyses.
🚨 New preprint! Traditional GWAS often exclude admixed individuals, missing ancestry-enriched genetic signals. We built Tractor Nextflow Workflow - a modular, scalable pipeline that automates phasing, LAI, and Tractor GWAS, alongside comprehensive documentation.
Preprint: doi.org/10.1101/2025...
Preprint: doi.org/10.1101/2025...
Tractor Workflow Pipeline: A Scalable Nextflow Framework for Local Ancestry-Aware Genome-Wide Association Studies
The routine exclusion of admixed individuals from traditional Genome-Wide Association Studies (GWAS) due to concerns about spurious associations has hindered genetic analyses involving multiple ancest...
www.biorxiv.org
September 13, 2025 at 12:47 AM
Delighted to amplify my talented PhD student’s work! Check it out for a great way to streamline and harmonize Tractor analyses.
Reposted by Josep Mercader
Reposted by Josep Mercader
Gut hormones suppress bone turnover and resorption. Some new acute studies in #T2D academic.oup.com/jcem/advance...?
The separate and combined effects of GIP, GLP-1 and GLP-2 on markers of bone turnover in type 2 diabetes
AbstractContext. Oral glucose tolerance test (OGTT) induces greater acute suppression of bone resorption than isoglycaemic intravenous glucose infusions (I
academic.oup.com
August 29, 2025 at 2:53 PM
Gut hormones suppress bone turnover and resorption. Some new acute studies in #T2D academic.oup.com/jcem/advance...?
Reposted by Josep Mercader
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 🧵:
Reposted by Josep Mercader
Are electronic health records (EHR) more predictive of disease onset than polygenic scores? Can we transfer EHR-based prediction models between countries? Our study on these questions using 3 biobank-based studies with N>845K, is out in @natgenet.nature.com today:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Cross-biobank generalizability and accuracy of electronic health record-based predictors compared to polygenic scores - Nature Genetics
Comparison of electronic health record-based phenotype risk scores (PheRS) and polygenic scores (PGS) across 13 common diseases and three biobank-based studies indicates that PheRS and PGS may provide...
www.nature.com
August 27, 2025 at 2:15 PM
Are electronic health records (EHR) more predictive of disease onset than polygenic scores? Can we transfer EHR-based prediction models between countries? Our study on these questions using 3 biobank-based studies with N>845K, is out in @natgenet.nature.com today:
www.nature.com/articles/s41...
www.nature.com/articles/s41...