Sign in

Kaitlin Samocha

@ksamocha.bsky.social
1.5K followers 244 following 70 posts

Assistant Investigator @ MGH / Broad / HMS. Focus on human genomics and modeling rare variation. She/her

PostsRepliesMedia
Reposted by Kaitlin Samocha
Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026
I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...
187109 0
Reposted by Kaitlin Samocha
Danny Miller, MD, PhD @danrdanny.bsky.social · 06/07/2026
Hi everyone! I'm excited to announce that our lab at UW will soon be recruiting a postdoc to work on DNA methylation signatures in rare disease. This will be a mostly computational position. Please share and reach out if interested! millerlaboratory.com
millerlaboratory.com
Miller Lab | University of Washington
Led by Danny E. Miller, MD, PhD, the Miller Lab uses long-read Nanopore sequencing to investigate the significance of structural genomic variation, methylation, and RNA in human disease, and to impro...
02317 0
Kaitlin Samocha @ksamocha.bsky.social · 29/06/2026
Live, laugh, l'oeuf 😂
100 0
Reposted by Kaitlin Samocha
Zornitza Stark @zornitza.bsky.social · 25/06/2026
📣 Out now @naturemedicine.bsky.social 🧬🤖 👉 rdcu.be/fqasl Our automated reanalysis tool Talos enables broad adoption and delivers timely + equitable #raredisease #diagnosis at scale! ♻️ Runs monthly on >10K datasets 🎯High specificity 💰Low running costs 🤗Open source @dgmacarthur.bsky.social
02311 0
Reposted by Kaitlin Samocha
Jack Kosmicki @jakphd.bsky.social · 25/06/2026
After 4 years, it's rather nice to finally present our work on genetic's model trait, height, in >1.4M WES/WGS samples (826k discovery; led by Adam Locke & Goncalo Abecasis where we found (amongst many other things) 207 genes (P<1.75e-9). A thread of findings below⬇️ www.medrxiv.org/content/10.6...
1187 0
Reposted by Kaitlin Samocha
prathitha.bsky.social @prathitha.bsky.social · 23/06/2026
Excited to share our new preprint, "Inference of elevated mutation rates and variant effects using 700k exomes"! - www.biorxiv.org/content/10.6... Using gnomAD v4, we estimate per-variant missense selection coefficients, and find loss-of-function (LoF) mutations with enhanced mutation rates.
biorxiv.org
Inference of elevated mutation rates and variant effects using 700k exomes
Genomic sequencing is now widely accessible for genetic diagnostics and is emerging as a component of newborn screening. This technological development generates the need to characterize incoming muta...
1127 0
Reposted by Kaitlin Samocha
European Society of Human Genetics @eshg.bsky.social · 13/06/2026
Attend the Leena Peltonen Award lecture now at #eshg2026 with Nicola Whiffin from Oxford University and learn About her recent discovieries in rare diseases and the broader inclusion of non-coding variants in clinical genetic testing that led to the Leena Peltonen Award. Congratulations!
0299 0
Reposted by Kaitlin Samocha
Zornitza Stark @zornitza.bsky.social · 13/06/2026
👏👏👏 fantastic to see @nickywhiffin.bsky.social win the Leena Peltonen award at #eshg2026 @eshg.bsky.social 👏👏👏
0176 0
Kaitlin Samocha @ksamocha.bsky.social · 12/06/2026
Excited to be at #ESHG2026 in the beautiful Gothenburg! For those of you attending and up for an extra game, check out the bingo cards 👇
010 0
Kaitlin Samocha @ksamocha.bsky.social · 30/03/2026
If you have more questions, you can check out our FAQ (gnomad.broadinstitute.org/help) or the Forum (discuss.gnomad.broadinstitute.org).
gnomad.broadinstitute.org
gnomAD
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from...
000 0
Kaitlin Samocha @ksamocha.bsky.social · 30/03/2026
We are always working to make the resource better and greatly appreciate the feedback we've received from the community!
100 0
Kaitlin Samocha @ksamocha.bsky.social · 30/03/2026
A huge thank you to the tireless gnomAD production and browser teams, who made this possible. Special thanks to Katherine Chao, Julia Goodrich, Phil Darnowsky, Ruchit Panchal, Kristen Laricchia, and Mike Wilson. More details + extra features can be found in the blog post.
111 0
Kaitlin Samocha @ksamocha.bsky.social · 30/03/2026
We are excited to share our gnomAD v4.1.1 release gnomad.broadinstitute.org/news/2026-03... Major changes: * Constraint scores on X and Y * Improved coverage correction * LOFTEE fix * Guidance on constraint cut-offs * New quality flag for low coverage/mappability genes @gnomad-project.bsky.social
gnomad.broadinstitute.org
gnomAD v4.1.1 | gnomAD browser
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from...
1112 0
Reposted by Kaitlin Samocha
Konrad @konradjk.bsky.social · 26/03/2026
To nominate disease genes, we introduce two discovery scores: ΔPEPPER flags genes where biological features predicts clinical impact beyond whats published, and DisPo highlights genes under strong constraint with limited literature. Together they prioritize hundreds of candidate genes for follow-up
101 0
Reposted by Kaitlin Samocha
Konrad @konradjk.bsky.social · 26/03/2026
We train a new model trained on biomedical literature (PEPPER_XGB). Mix LOEUF and PEPPER to make an OMELET, which outperforms either each individual model in identifying disease genes
222 0
Reposted by Kaitlin Samocha
Konrad @konradjk.bsky.social · 26/03/2026
We introduce LOEUF-MIS, combining pLoF and top 1% predicted deleterious missense constraint. This captures not just LoF but also gain-of-function and dominant-negative signals.
Precision-recall curves showing LOEUF-MIS outperforming other metrics
111 0
Reposted by Kaitlin Samocha
Konrad @konradjk.bsky.social · 26/03/2026
gnomAD v4's 5x sample increase benefits both common and rare disease: more common variants observed across ancestries improve diagnostic filtering, while more rare variants strengthen constraint metrics for disease gene detection
Figure 1a-b, growth of variation with sample size
111 0
Reposted by Kaitlin Samocha
Konrad @konradjk.bsky.social · 26/03/2026
Excited to share our new preprint on gnomAD v4! We present the full analysis of 730,947 exomes — new constraint metrics, improved LoF annotation (LOFTEE-2), LLM-based literature curation, and a unified framework for gene discovery and rare disease diagnosis. www.medrxiv.org/content/10.6...
medrxiv.org
Integrating 730,947 exome sequences with clinical literature improves gene discovery
Accurate estimates of allele frequencies aid in genetic discovery, including rare disease diagnosis, common disease investigations, and population genetics. Here, we present the Genome Aggregation Dat...
23717 0
Reposted by Kaitlin Samocha
Abraham Palmer @abepalmer.bsky.social · 06/01/2026
If you are submitting an NIH grant in February, you will be required to use SciENcv to prepare you biosketch. IT IS MUCH WORSE THAN YOU CAN POSSIBLY IMAGINE. Set aside *at least* 4 hours just to transfer an existing an biosketch into SciENcv.
2717792 0
Kaitlin Samocha @ksamocha.bsky.social · 07/01/2026
I guess we all decided to work on the biosketch at the same time?
100 0
Kaitlin Samocha @ksamocha.bsky.social · 07/01/2026
Ugh. This is the part I didn’t finish yet. The interface kept crashing and it was a nightmare to find things. I have a nicely curated MyBibliography elsewhere but it seems like it didn’t link to that one.
000 0
Kaitlin Samocha @ksamocha.bsky.social · 07/01/2026
Good to know. 🥲
000 0
Kaitlin Samocha @ksamocha.bsky.social · 07/01/2026
Is there an official "this is what it should look like" version floating around? I was working on it today and the preview looks weird, but maybe that is just the way it is.
200 0
Reposted by Kaitlin Samocha
Nik Baya @nbaya.bsky.social · 06/01/2026
Why do some individuals defy their polygenic score? In the largest study of its kind (402k UKB individuals; 7 continuous traits + 3 diseases), we asked: If your phenotype deviates from common-variant polygenic score prediction, what's driving that difference? www.medrxiv.org/content/10.6...
25027 0
Kaitlin Samocha @ksamocha.bsky.social · 15/12/2025
Huge congratulations on your next step! Sounds like an amazing opportunity. :)
120 0
Reposted by Kaitlin Samocha
Sasha Gusev @sashagusevposts.bsky.social · 30/11/2025
Massive single-cell study by Kanai et al (www.medrxiv.org/content/10.1...): - Once statistical power is high, constrained genes have more (though weaker) eQTLs. - Chromatin-QTLs near constrained genes have "normal" effect sizes, colocalize more with disease, but exhibit attenuated peak-gene effects.
1349 0
Reposted by Kaitlin Samocha
Kartik Chundru @chundru.bsky.social · 08/11/2025
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”
biorxiv.org
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...
24619 0
Reposted by Kaitlin Samocha
European Society of Human Genetics @eshg.bsky.social · 04/11/2025
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...
nature.com
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),…
02315 0
Kaitlin Samocha @ksamocha.bsky.social · 16/10/2025
I haven't found it printed but there is a PDF link here: www.ashg.org/wp-content/u...
ashg.org
011 0
Reposted by Kaitlin Samocha
Pragati Kore @pragskore.bsky.social · 06/10/2025
📃 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).
nature.com
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.
1298 0
Reposted by Kaitlin Samocha
Matthew Neville @mattneville.bsky.social · 08/10/2025
Now published! Our paper on: (1) Accurate sequencing of sperm at scale (2) Positive selection of spermatogenesis driver mutations across the exome (3) Offspring disease risks from male reproductive aging [1/n] www.nature.com/articles/s41...
nature.com
Sperm sequencing reveals extensive positive selection in the male germline - Nature
A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.
38650 0
Reposted by Kaitlin Samocha
Nicky Whiffin @nickywhiffin.bsky.social · 31/07/2025
📣 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
Image of an old building in Oxford with the heading 'postdoc opportunities' and the text 'computational approaches to improve rare disease diagnosis and treatment' and 'Big Data Institute, University of Oxford'
14443 0
Reposted by Kaitlin Samocha
Nicky Whiffin @nickywhiffin.bsky.social · 18/08/2025
Isn't genetics cool??? Within only 145 nucleotides(!) of a non-coding RNA (RNU4-2) - different variants in distinct regions / structures cause three distinct disorders!!! (all discovered within the last 18 months) 🤯🤓🧬❤️
Schematic of the U4 and U6 snRNAs with coloured annotations to note nucleotides linked to different disorders:
- Teal in the T-loop and Stem III for ReNU syndrome (Chen et al. Nature 2024 and Greene et al. Nature Medicine 2024)
- Red for variants causing a recessive NDD in Stem II, the k-turn and Sm protein binding sites (De Jonghe et al. medRxiv 2025 and Rius & Blakes medRxiv 2025)
- Yellow for the central loop and Retinitis pigmentosa (Quinodoz et al. medRxiv 2025)
16213 0
Reposted by Kaitlin Samocha
James Fasham @jamesfasham.bsky.social · 24/05/2025
🗣️ Quote of #ESHG2025 (so far) "Who licks bone !?!" 🦴 - Johannes Krause Anyone have that on your bingo card? Well apparently archeologists do, to distinguish bone from stones and it causes problems in DNA sequencing. 🤔
12810 0
Kaitlin Samocha @ksamocha.bsky.social · 24/05/2025
We are just wrapping up day 1 at #ESGH2025 in beautiful Milan. For those who want some extra fun while listening to the great science, you can play bingo.👇 I know multiple of these have already occurred.
150 0
Reposted by Kaitlin Samocha
Alex Hoischen @ahoischen.bsky.social · 24/05/2025
Buongiorno Milano! Ready for a great day 1 of #eshg2025? Packed program of excellent science 8.30am-8.00pm - plus networking event till 9.30pm to meet many friends, colleagues and collaborators! …andiamo @eshg.bsky.social @eshgyoung.bsky.social
0156 0
Reposted by Kaitlin Samocha
Zornitza Stark @zornitza.bsky.social · 23/05/2025
🤗 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!
medrxiv.org
Scalable automated reanalysis of genomic data in research and clinical rare disease cohorts
Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necess...
12413 0
Reposted by Kaitlin Samocha
deciphergenomics.bsky.social @deciphergenomics.bsky.social · 07/05/2025
Human Developmental Cell Atlas (HDCA) expression data is now displayed. Expression is displayed in 12 sections of a 6-7 post-conception week human embryo, alongside a sagittal view which displays the region of the embryo represented by each section @mhaniffa.bsky.social
0177 0
Reposted by Kaitlin Samocha
Nicky Whiffin @nickywhiffin.bsky.social · 02/03/2025
A few weeks ago, I had an incredibly emotional call with James Coney, a writer for the Sunday Times whose son Charlie was in the @genomicsengland.bsky.social 100k project and was recently diagnosed with ReNU syndrome. This beautiful article tells their story ❤️ www.thetimes.com/article/0bcc...
thetimes.com
My son Charlie — and the breakthrough that changed our lives
James Coney and his wife, Sarah, struggled not knowing why their 12-year-old was born with a severe learning disability. In their darkest moments, they blamed themselves. Then, out of the blue, came a...
511040 0
Kaitlin Samocha @ksamocha.bsky.social · 21/02/2025
Yes, I've done this once before for a paper (listing in the system only first and last authors). It is easy to get those handful of people to approve additional authors in the future if the journal requires it. Not sure if recommended, but it saved time.
010 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
Projects like this can’t be completed without many others: thanks to Mark Daly for continued mentorship across the years; critical support and work from @anneotation.bsky.social, @konradjk.bsky.social, Predrag Radivojac; the Hail team; and everyone associated with @gnomad-project.bsky.social. 10/10
010 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
If this work feels familiar, it is because it is building off older work from our team originally released for ExAC. I view this iteration as more of a franchise reboot instead of a sequel – we have new leads, but similar themes. 9/10
110 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
As with all gnomAD-led projects, we’ve already shared the data and code. Regions are displayed for v2 on the gnomAD browser, the code can be seen on Github (github.com/broadinstitu...), and MPC scores are available for download. 8/10
100 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
There is still much more to learn: using 125k exomes, our median region size is ~450bp and we see a relationship between transcript length and the number of regions we can identify due to statistical power. 7/10
100 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
Finally, missense constraint information was incorporated into a deleteriousness metric named MPC (Missense deleteriousness Prediction by Constraint), which separates case from control de novo missense variants well with similar performance to ML models like AlphaMissense. 6/10
100 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
In collaboration with Predrag Radivojac and team, we demonstrated that coding bases with < 20% of their expected missense variation achieve moderate support for pathogenicity (PM1) following ACMG/AMP guidelines that can be used for clinical classification. 5/10
100 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
Missense depleted regions show an enrichment of (1) de novo missense variants in neurodevelopmental disorder cases compared to controls, (2) partitioned common variant heritability for >260 independent traits from the UK Biobank, and (3) ClinVar pathogenic (P/LP) variants. 4/10
100 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
Why try to find subgenic regions that are specifically missense constrained? Splitting up genes reveals patterns of negative and neutral selection that are obscured when looking gene-wide, including highlighting regions that have a large number of known pathogenic variants. 3/10
100 0
Kaitlin Samocha @ksamocha.bsky.social · 20/04/2024
Co-led by the fabulous Katherine Chao and Lily Wang, we used gnomAD v2 and a recursive search to identify ~28% of canonical transcripts that were split into multiple missense constraint regions (measured by variable missense depletion in gnomAD). 2/10
100 0