What did the largest trial of an early detection of cancer blood test show? erictopol.substack.com/p/the-larges...

Planning your afternoon poster session at #ashg25? Come say hello! This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬

Awesome work by @zornitza.bsky.social and collaborators showing the immediate value of WGS for newborn screening in a cohort of 1,000 Australian babies. Now we need larger, more diverse cohorts to show this approach can achieve population scale!

🤗 Out now @naturemedicine.bsky.social results of our genomic NBS study BabyScreen+ 👶🧬 👉 www.nature.com/articles/s41... 1,000 babies WGS using existing cards 600+ conditions 13 day TAT 16 diagnoses (vs 1 in std NBS) High clinical impact High parental acceptability

In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social ‬ & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n www.biorxiv.org/cgi/content/...

And now the fourth preprint from the TenK10K phase 1 dataset, led by @anglixue.bsky.social from @drjosephpowell.bsky.social's team - looking at genetic impacts on cell type-specific chromatin accessibility in 1,000 individuals who also have WGS and scRNA-seq!

I think 182 year old research articles should be free I want to read about the man

One for the reading pile and this scQTL x Disease in a MR framework feels a v powerful approach (more tissues / cell types please!) -

Another preprint from the TenK10K program! This work, led by @alberthenry.bsky.social and Anne Senabouth, leverages the unprecedented power of this WGS/single cell RNA-seq cohort to explore causal influences of blood gene expression on immune diseases and traits. Thread:

Our latest research is out today on ‪@medrxivpreprint.bsky.social: www.medrxiv.org/content/10.1... Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk. Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n

🚨 New preprint led by amazing duo @rociorius.bsky.social and @alexblakes.bsky.social in collaboration with @cassimons.bsky.social, @dgmacarthur.bsky.social and many other amazing folks! ❤️ We describe the clinical phenotype of a recessive NDD associated with biallelic variants in RNU4-2 🧬 See 🧵👇

New preprint! The outcome of a wonderful collaboration with @nickywhiffin.bsky.social’s team to define a new recessive syndrome associated with inherited variants in RNU4-2, the non-protein-coding gene that keeps on giving.

#HGSA2025 week kicks off with the OurDNA symposium tomorrow (with a preview of the OurDNA browser!) Register to attend online here👇

📣 We are recruiting! Please share!! Are you a bioinformatician / computational scientist who wants to apply your skills to understanding regulatory biology and improving rare disease diagnosis and treatment? 🧠 💻 🧬 🩺 We have two roles available 👇 🧵 1/4

Leena Peltonen School of Human Genetics in full-swing! @gosiatrynka.bsky.social @dgmacarthur.bsky.social @bpasaniuc.bsky.social @tuuliel.bsky.social @hilarycmartin.bsky.social @sashagusevposts.bsky.social @zkutalik.bsky.social @mashaals.bsky.social @alemedinarivera.bsky.social

This implies there is a huge literature of small microbiome association studies that is JUST NOISE. (As observed for these other fields)

About a hundred reasons not to use Excel. Yes, these are politely described as 'spreadsheet' horror stories, but we all know which bit of software we're really talking about. (HT @pgmj.bsky.social)

Peer review is not quite dead but it’s on life support and the current model of scientific publishing is a burning platform. healthydebate.ca/2025/06/topi...

Preprint out today! A team led by @tobioinformatics.bsky.social and Bradley Harris in @carlanderson.bsky.social ‘s lab has created the largest single-cell atlas of IBD tissues to date www.medrxiv.org/content/10.1...

Hey Australian genetics/genomics friends: the OurDNA Symposium will be in Sydney on 14 August, just before the HGSA meeting. Learn more about inclusive recruitment for genomics and get a preview of the OurDNA variant browser! events.humanitix.com/ourdna-sympo...

I wrote a new piece on how much progress has been made in treating childhood leukemia. The answer is: quite a lot! Before the 1970s, fewer than 10% of children diagnosed survived 5 years after diagnosis. Now most are cured and around 85% survive that long. ourworldindata.org/childhood-le...

I worry that not enough of a big deal is being made about how long-term the devastation of these budget cuts to our scientific and health agencies will be, beyond the absolute ruin they will cause in the acute period.

Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...

Jesus. Excellent work by Michael Le Page, and utterly infuriating scenario. As Michael points out, the press release from Colossal called these dire wolves throughout. But now they want to argue that they never claimed that. Scandalous, really. www.newscientist.com/article/2481...

Excited to be in Milan for #eshg2025! If you’re interested in leading analysis of large, diverse cohorts with WGS and cellular genomic data in Australia, I’d be keen to chat - we’re looking to fill a variety of senior comp bio roles: populationgenomics.org.au/careers/ #eshg25

🤗 Hugely excited to share our work on automating iterative reanalysis in #raredisease, preprint out: www.medrxiv.org/content/10.1... 🤖🧬 github.com/populationge... A superb collaboration with @dgmacarthur.bsky.social @cassimons.bsky.social @heidirehm.bsky.social @ksamocha.bsky.social and many more!

The Cambridge Companion to Workday The Routledge Handbook of Dual-Factor Authentication The Oxford Handbook of Figuring Out How To Add A Signature To This PDF, Why The Hell Is This So Difficult

This is the best graph I've seen in a while 📊

What happens to science under autocracy? The rise of the National Socialist Party in 1930s Germany provides an (admittedly extreme) example. Prior to the early 1930s, scientists at German institutions won a third of Nobels. 10 years later, that number was 5%, and has never recovered.

KJ Muldoon, a 9½-month-old boy with a rare condition, made medical history by receiving the first custom gene-editing treatment. The technique used has the potential to help people with thousands of other uncommon genetic diseases. Read more: nyti.ms/44H77pg

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

Release of DeepVariant and DeepSomatic v1.9 DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h). DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models. github.com/google/deepv...

As grant money starts drying up, it's more important than ever not to waste it on paying publishers' open access "article processing fees" when we can host PDFs for free. Tom Morgan and I wrote a paper on this, forthcoming at Science and Public Policy. Accepted draft here: osf.io/preprints/os...

Weird intersection of math & centrifuge balancing: Visual proof that it's possible to balance a 24-position centrifuge rotor for any number of equally-filled tubes EXCEPT 1 and 23. Some of these are anxiety-inducing, though. (🧑‍🎨: aliyoh, labrats subreddit)

These boxes are not moving. A mind-bending optical illusion by Japanese artist Jagarikin.

We've worked on eQTLs and CRISPR for 10+ years now, and 4 years ago I hypothesized about their orthogonal strengths and weaknesses, for a review paper with @dgmacarthur.bsky.social. It’s exciting to finally have enough empirical data for a systematic analysis. www.science.org/doi/10.1126/...

Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇 www.biorxiv.org/content/10.1...

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...

Two things that are true at the same time: 1. The massive cuts to science funding in the US is a terrible blow that can't be patched by efforts elsewhere. 2. It's great that the EU and many individuals countries are stepping up; it helps science and many US scientists willing/able to relocate.

1/n 🚨Very excited to share our recent work!🚨 To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro. www.biorxiv.org/content/10.1...

I think a lot about what Carl Sagan said in one of his final interviews.

🎉 This paper has been a long time and a labour of love (and hardship) for multiple group members, but, finally: we MPRA'ed 25k introgressed variants (Denisovan and Neanderthal) segregating at allele frequencies > 0.15 in humans today to evaluate their potential to regulate gene expression.

Talk about impactful: ReNu syndrome linked to the RNU4-2 variation was discovered this time last year & now a global community has grown around those affected by the disease: www.renusyndrome.org/map

Very excited to share our preprint led by M. Levin @skoyama.bsky.social J. Woerner & with S. Damrauer assessing genome-wide pleiotropy of >1,000 clinical traits across ~1.7M individuals with nearly 30K locus-trait associations! www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social

Just a little update for the busy, from the world of science: 1) There's no life on K2-18b 2) Vaccines cause adults 3) They are not Dire Wolves Carry on.

An astonishing headline reporting on new observations from a team led to Nikku Madhusudhan claims they’ve found ‘hints of life’ on a planet orbiting a dwarf star some 124 light years away. What’s going on? (1/n) www.bbc.co.uk/news/article... 🔭 🧪

What does openRxiv mean for bioRxiv/medRxiv? How did biologists embrace preprints? And what's the future of the scientific article? Fun talking with @jontytownson.bsky.social at #biologists100 www.youtube.com/watch?v=L5O2...

its amazing how chatgpt knows everything about subjects I know nothing about, but is wrong like 40% of the time in things im an expert on. not going to think about this any further