Want to check your ancient DNA study for chromosomal aneuploidies? RChASM is now available for R, to screen for autosomal and sex chromosomal aneuploidies, such as Down syndrome on data from 0.0014X coverage.
We also wrote a step-by-step tutorial with examples:
jonotuke.github.io/RChASM/artic...
Have you ever wondered how many archaic populations contributed DNA to modern humans? We know about Neanderthals and Denisovans, but the fossil and genetic evidence suggests a much more complex history!
www.biorxiv.org/content/10.6...
Great perspective by @philipcball.bsky.social.
Elementary genetics teaching (HS/college) focuses on Mendelian traits (single gene => single trait). However, it is now clear that polygenicity and pleiotropy are the norm. Curriculum must change accordingly.
www.sciencedirect.com/science/arti...
... phase the array data to generate two haplotypes for each individual.
5) Predict Lp(a) as the sum of the AoU-based model predictions for the two haplotype.
The method works well (r^2=46%) with minimal population differences, indicating it captures relevant rare and structural variation.
3/3
1) In All of Us, group individuals by SNP-based haplotypes flanking the LPA locus.
2) Assign each AoU participant the Lp(a) level predicted by a sequencing-based model previously developed in the UK biobank.
3) Assign each haplotype the mean predicted Lp(a) level.
4) In the target cohort,
2/3
An interesting novel paradigm for phenotype prediction.
Lp(a) is associated with heart disease. It's highly heritable, but it's mostly influenced by repeat polymorphism, requiring sequencing data.
For array data, the authors propose the following pipeline:
1/3
www.medrxiv.org/content/10.6...
Two studies performed GWAS on gut microbiome composition. One study used dataset A (Sweden) with replication in B (Norway). The other used dataset B and replicated in A. Both published in Nature Genetics.
Unbelievable.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Two post-doc post in ARG space and loads of internal and external collaboration
Postdoctoral Research Associate in quantitative genomics
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
Postdoctoral Research Associate in quantitative genetics and breeding
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs).
If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.
New preprint! with @a-solernunez.bsky.social
Rethinking a textbook example of human adaptation "AMY1 copy number evolution in light of demographic history"
Once population structure is accounted for, the classic starch–agriculture narrative becomes much less clear
www.biorxiv.org/content/10.6...
Rare disease piece in @theatlantic.com, how carriers of recessive conditions can have medical problems, making them more than 'carriers'. Gift link below.
www.theatlantic.com/health/2026/...
I overall agree with the conclusions: it is important to acknowledge the limitations of shallow phenotyping, and the tradeoffs between power and specificity should be further studied.
My only criticism is perhaps too much trust in the clinical interview diagnosis - is it truly a gold standard?
The authors recommend using statistical imputation to generate estimated high-quality diagnoses from shallow but multi-dimensional biobank data.
The authors also note that if a polygenic score for a specific disorder is not only more accurate for the target disorder, but it is also more accurate for other disorders, it may just capture more of the heritable confounders.
This means that it is very difficult to interpret evidence of pleiotropy between disorders. More generally, these confounders complicate the interpretation of the GWAS results and make it difficult to learn new biology.
Specifically, shallow phenotyping studies may detect SNPs that associate with confounders.
Genetic correlations between deep/shallow phenotyping cohorts for same disorder are indeed <1.
Also, these associations are often shared across disorders, creating the impression of a shared genetic basis.
In some studies, diagnosis is based on clinical interviews (gold standard), whereas in others (e.g. 23andMe-based) it is self-reported ("Have you ever been diagnosed with clinical depression?")
The latter studies are larger, but what they actually measure is unclear and may also be heritable.
Very interesting perspective article by @caina89.bsky.social et al on genetic studies in psychiatry.
The authors argue that studies increasingly rely on "shallow" phenotyping (self-reported), leading to biases in estimation of genetic relationships between disorders.
www.nature.com/articles/s41...
Put your skates on & register for this #ESHRE webinar ⛸️
Polygenic embryo screening (#PES): practice is moving fast—ethics need to catch up.
Join this #ESHRE webinar on public views, patient experiences & clinical concerns worldwide.
🗓️ 10 February 2026 | 17:00 CET
🔗 www.eshre.eu/Education/We...
🧬 Now published in Bioinformatics Advances: "pygenstrat: A Python package for EIGENSTRAT data processing" by @dilekopter.bsky.social
Full article available: https://doi.org/10.1093/bioadv/vbag022
It took scientists 11 years to compute 1-2/3=1/3
Indeed.
(1/2) The preprint of our perspective on genetic estimates of relatedness in animal populations is out! Big Congratulations to Annika!
doi.org/10.32942/X28...
A systematic review of 2,861 articles shows that, even in 2025, 75% of such studies use microsatellites. And most use only a few!
#PopGen
Given several new followers here, I'm posting the link to our Slack group "genetic genealogy science".
We post and discuss manuscripts on phasing/imputation, IBD, recombination, demographic inference, ancient DNA, ancestry/admixture, etc.
All are welcome.
join.slack.com/t/geneticgen...
New Year, New Paper! #PolygenicEmbryoScreening
We examined the interaction of rare and common variation for breast cancer in the context of PES, with three key findings detailed in posts below...
Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs https://www.biorxiv.org/content/10.64898/2026.01.07.698223v1
Previous work suggested that the role of genes in educational attainment was higher in contemporary Estonia than during the Soviet era. With a tenfold larger dataset, our new preprint finds limited evidence to support this.
www.biorxiv.org/content/10.6...
Good (long) coverage here:
www.science.org/content/arti...
Sampling and sequencing of male-line descendants is underway.
Global patterns of natural selection inferred using ancient DNA https://www.biorxiv.org/content/10.64898/2026.01.07.697984v1
There are 2x2 haplotype comparisons between pairs of genomes. For half-sibs, one comparison will have kinship 0.25 and the others zero. For avuncular pairs, two will be ~0.125. The maximal haplotype-haplotype kinship shows clear distinction between half-sibs (pink) and avuncular pairs (light blue).
