In what has been a labor of love & joyful collaboration, we are super excited to share our preprint on recommendations towards the ethical and accurate use of population descriptors generated from a survey by trainees, for trainees. www.biorxiv.org/content/10.6...

Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers

Despite the importance of population descriptors in human genomics research, many scientists struggle to translate evolving ethical guidelines into their computational workflows. To characterize this ...

biorxiv.org

New in @nature.com! “GREGoR: Accelerating Genomics for Rare Diseases” highlights how the GREGoR Consortium is advancing rare disease discovery through data sharing, multi-omics, and next-gen sequencing across 7,500+ individuals in 3,000+ families. 🧬 www.nature.com/articles/s41...

GREGoR: accelerating genomics for rare diseases - Nature

The GREGoR consortium provides foundational resources and substrates for the future of rare disease genomics.

nature.com

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...

Specificity, length and luck drive gene rankings in association studies - Nature

Genetic association tests prioritize candidate genes based on different criteria.

nature.com

I am super proud to present our new manuscript “Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores” www.medrxiv.org/content/10.1...

Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores

Background: SpliceAI is a deep learning algorithm that predicts whether genetic variants are likely to affect splicing. Precomputed spliceAI predictions for all theoretical SNVs and small indels were ...

medrxiv.org

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.

The American Journal of Human Genetics@ajhgnews.bsky.social · last yr.

📣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

Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪

Rachel Ungar@raungar.bsky.social · last yr.

Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪

Roshni is one of the best people to work with, academia is so lucky to have her as a professor!

Roshni Patel@roshnipatel.bsky.social · last yr.

Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.

You've never seen anything like this before. Come see for yourself! mitnano.mit.edu/events/studi...

Michal Caspi Tal, PhD@immunofever.bsky.social · last yr.

Want to see the universe within? Join us at MIT where you'll get to peak under our microscopes at the bacteria that cause #Lyme disease and even get to view YOUR own capillaries to see a bit of what we look at in our clinical study MAESTRO. July 24th RSVP: mitnano.mit.edu/events/studi...

Have you worked with human genetics data? Consider taking this short survey to help us better understand how folks are using population descriptors! 🧬💻🧪

Rachel Ungar@raungar.bsky.social · last yr.

Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪

It's officially online, learn more about the interplay between the X-chromosome, rare variants, sex, and gene expression! 🧬💻🧪

American Society of Human Genetics (ASHG)@geneticssociety.bsky.social · last yr.

@raungar.bsky.social, @sbmontgom.bsky.social, & co. examine the impact of rare variants & sex on gene expression across the X-chromosome & autosomes, identifying 700+ rare variants w/ predicted functional differences in males & females: www.cell.com/hgg-advances... #ASHG @hggadvances.bsky.social

Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️

This survey was put together by several fellow trainees and friends who are dedicated to the ethical conduct of human genetics research. Tagging some below! @christacaggiano.bsky.social @roshnipatel.bsky.social @raungar.bsky.social @dianexue.bsky.social @jpflores.rbind.io

Are you an early-career researcher working on the computational analysis of population-level human genetics data? We want to hear from you about if, how, and why you use population descriptors in your research! Fill out our short survey: forms.gle/SCiNUq71wgi5... 🧬💻🧪

I wrote a thing. I am eternally grateful for my editor, who took the original draft and helped me narrow down my key points into a more effective piece with a broader reach. Also, thanks to the editorial & legal teams, who maintained the message while protecting us in this fraught moment.

Nature@nature.com · last yr.

Scientists must push back against the threat of rising white nationalism and the dangerous and pseudoscientific ideas of eugenics https://go.nature.com/4jGqiUc

Happy to share our work characterizing functional rare SVs in rare diseases with long-read genome sequencing and transcriptomic outlier data: genome.cshlp.org/content/earl...

New preprint w/ @soumyakundu.bsky.social @sbmontgom.bsky.social @anshulkundaje.bsky.social ! Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families. doi.org/10.1101/2025...

Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart

Whole genome sequencing has identified over a billion non-coding variants in humans, while GWAS has revealed the non-coding genome as a significant contributor to disease. However, prioritizing causal...

biorxiv.org

The Stanford Center for Biomedical Ethics was asked to be the Montgomery Lab's valentine this year via an IRB, and we delightfully approved their request!

Are you a scientist interested in science communication but don’t know where to start? Ever wonder how a graduate student has time for outreach projects? Check out SCOPE! An org @vangeliqueallen.bsky.social and I created! First panel on creating children’s books and podcasts is today at 1pm ET 😊🧪

Interested in rare variants, the X-chromosome, sex-differences, pharmacogenetics, or transcription factors? You might be interested in our new manuscript where we identified >700 functional rare variants with a difference in effect by sex in GTEx! bit.ly/x_rv_sex #genomics #multiomics 💻🧬

Functional impact of rare variants and sex across the X-chromosome and autosomes

The human X-chromosome contains hundreds of genes and has well-established impacts on sex differences and traits. However, the X-chromosome is often excluded from many genetic analyses, limiting broad...

biorxiv.org

What do you mean when you say that you've #shared your #data broadly? @jonathanmoreno.bsky.social and I published a new data sharing framework in @naturegenet.bsky.social along with #bioethics challenges for #genomics in the #ai era. www.nature.com/articles/s41... @pennmedresearch.bsky.social

If anyone happens to need it this week for...reasons...this is the best graphic on the complexity of human sex determination I've ever seen. I use it in an undergrad course on gene regulatory mechanisms. Shoutout to @unamandita.bsky.social! www.scientificamerican.com/article/beyo...

Beyond XX and XY: The Extraordinary Complexity of Sex Determination

A host of factors figure into whether someone is female, male or somewhere in between

scientificamerican.com

So excited to read this preprint after Maggie's amazing plenary at ASHG. Congrats @maggie-arriaga.bsky.social and team 🥳 A transcriptome first approach identifies pathogenic variants in RNU4ATAC and highlights the RNU6ATAC as a putative new disease gene 🧬🖥️ A 💪 day for snRNA preprints!!

Maggie Arriaga@maggie-arriaga.bsky.social · 2y ago

What if one variant can cause splicing outliers transcriptome-wide? In our preprint, we show how examining transcriptome-wide patterns of splicing outliers can both diagnose individuals with rare spliceopathies and uncover novel disease-gene relationships! (www.medrxiv.org/content/10.1...)

Our team identified a new putative disease-gene using a transcriptome-first approach! 💻🧬

Maggie Arriaga@maggie-arriaga.bsky.social · 2y ago

What if one variant can cause splicing outliers transcriptome-wide? In our preprint, we show how examining transcriptome-wide patterns of splicing outliers can both diagnose individuals with rare spliceopathies and uncover novel disease-gene relationships! (www.medrxiv.org/content/10.1...)

🚨 Excited to announce the Marker paper for the GREGoR Consortium! arxiv.org/abs/2412.14338 Accelerating #RareDisease diagnostics with cutting-edge #Genomics and global data sharing of omics and deep phenotyping from ~7500 individuals on NHGRI AnVIL and much more to come! 🧬

GREGoR: Accelerating Genomics for Rare Diseases

Rare diseases are collectively common, affecting approximately one in twenty individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in DNA seq...

arxiv.org

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies

Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...

biorxiv.org

Paper came out this past week! Using MAVEs to reduce variant classification disparities in underrepresented populations and demonstrating AI bias in computational predictors rdcu.be/d2kCn Previous tweetorial: x.com/MoezDawood/s... Previous post by @ee-reh-neh.bsky.social: bsky.app/profile/ee-r...

Irene Gallego Romero@ee-reh-neh.bsky.social · 2y ago

New work! Wherein we (as in, the AVE ODIC working group) looked at clinical variant classification across genetic ancestry groups in gnomAD and AoU and what we found... is exactly what you might expect, after decades of Eurocentric research. But we also show there's a better way forward! 🧬🖥️

It was so fun to chat with the amazing @jpflores.bsky.social about our class, incentives in science, and some of our favorite food!

jp flores (he/him)@jpflores.rbind.io · 2y ago

In this episode, I interviewed Dr. Roshni Patel (@roshnipatel.bsky.social) & Dr. Rachel Ungar (@raungar.bsky.social), former students (now postdocs!) that developed the course "Introduction to Genetics, Ethics, & Society" @ Stanford. I'm so lucky to learn from and know them!

This is now published! www.cell.com/cell-genomic...

Increasing equity in science requires better ethics training: A course by trainees, for trainees

Despite the widespread impacts of human genetics research, few researchers are trained to evaluate how their work impacts and is impacted by society. In response, Patel et al. describe how a group of ...

cell.com

Rachel Ungar@raungar.bsky.social · 3y ago

Roshni Patel and I are thrilled to share our paper on the trainee-led course on genetics, ethics, and society that was developed at Stanford: www.biorxiv.org/content/10.1... (1/9) 🧬💻🧪

It's been a minute since I've been on here, wanted to update that this is now published! www.cell.com/ajhg/fulltex... We saw genome build choice impacting RNA-seq results for ~4% of all genes, and ~39% of all quantified genes from six biospecimen types.

Impact of genome build on RNA-seq interpretation and diagnostics

A genome build is the reference sequence to which RNA-sequencing reads are aligned. We found changing the human genome builds (hg19, hg38, and CHM13) impacts interpretation of approximately 39% of gen...

cell.com

Rachel Ungar@raungar.bsky.social · 3y ago

Have you ever wondered how genome build is impacting your RNA-seq results? I am excited to share our new paper on medRxiv investigating the impact of hg19, hg38, and chm13 on six routinely-collected biospecimens: www.medrxiv.org/content/10.1... (1/8) 🧬💻👩‍💻🧪

Congratulations to my mentee Maggie Maurer, an ASHG Trainee Research Excellence Pre-Doctoral Winner. She discovered a new disease gene in her rotation project last year! The critical method for this project was shared with us by collaborator Vijay Ganesh and clinical work was done by Rodrigo Mendez.