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Shai Carmi

@shaicarmi.bsky.social

830 followers 200 following 310 posts

Associate professor at the Hebrew University of Jerusalem. Statistical, population, and medical genetics; preimplantation genetic testing. Views my own. http://scarmilab.org

scarmilab.org

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Shai Carmi @shaicarmi.bsky.social · Nov 10

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...

Slack

join.slack.com

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Reposted by Shai Carmi

April Wei @aprilwei.bsky.social · 1h

Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...

Inference of complex demographic history using composite likelihood based on whole-genome genealogies

Accurate parametric inference on complex demographic models is a continuing challenge in population genetics. Ancestral recombination graphs (ARGs) provide richer information than simple population ge...

www.biorxiv.org

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Shai Carmi @shaicarmi.bsky.social · 4d

What will be achieved first: in-vitro gametogenesis, or peace in the Middle East?

Reposted by Shai Carmi

Jonathan Sebat @sebatlab.bsky.social · 6d

Please repost: we are recruiting a postdoc for a project in my lab on genes and environment in autism

Jonathan Sebat @sebatlab.bsky.social · 11d

We are proud to be one of the 13 projects funded by the NIH Autism Data Science Initiative. Our project: "Elucidating the Interplay of Genes and Environment in Autism Using Genomic and Exposure Data from Large Populations" 🧵https://www.nytimes.com/2025/09/26/health/autism-research-trump-kennedy.html

Despite False Claims, Trump Funnels Millions Into Credible Autism Research

www.nytimes.com

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Shai Carmi @shaicarmi.bsky.social · 6d

It's not my expertise, but my understanding is that this is also very difficult.

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Shai Carmi @shaicarmi.bsky.social · 6d

where each chr has probability ~1/2 to end up in the egg. The probability of having exactly one copy of each of chrs 1,2,...,22,X is less than one in a million. Thus, the embryo will almost inevitably be aneuploid (and will either not be born or will be affected with disorders).
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Shai Carmi @shaicarmi.bsky.social · 6d

There is a lot of hype around this new paper. It's a great advance, but it will never result in the birth of a healthy baby. The reason is that in this method, chrs that end up in the egg are a random sample of the 46 somatic chrs,
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www.bbc.com/news/article...

Human skin DNA fertilised to make embryo for first time

US scientists testing the technique say it could help people overcome infertility and potentially allow same-sex couples to have a genetically related child.

www.bbc.com

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Shai Carmi @shaicarmi.bsky.social · 7d

Thanks. With mtDNA the coverage is very high anyway, isn't it?
And just to understand, did you go back to the original GVCF for each individual and each variant with ./. ?

Shai Carmi @shaicarmi.bsky.social · 7d

Hi hive mind - would appreciate feedback on the following.

I have ~3k whole-genomes, each called individually with GATK. I have 3k GVCFs.

I don't have enough resources for joint calling.

Should I use bcftools to merge into a multi-sample VCF? Or joint call in batches (say, 100) and then merge?

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Reposted by Shai Carmi

Seth D. Temple @sdtemple.bsky.social · 11d

The final thesis chapter is published OA at
@ajhgnews.bsky.social!
In short, we determine a valid significance level for a "selection" scan and apply it to 3 ancestry groups in 2 biobanks. 🧵 for updates from the helpful peer review.
www.sciencedirect.com/science/arti...

Multiple-testing corrections in selection scans using identity-by-descent segments

Failing to correct for multiple testing in selection scans can lead to false discoveries of recent genetic adaptations. The scanning statistics in sel…

www.sciencedirect.com

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Reposted by Shai Carmi

Robin Hofmeister @rjhfmstr.bsky.social · 11d

🚨 New preprint out!
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...

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Reposted by Shai Carmi

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 14d

Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity https://www.biorxiv.org/content/10.1101/2025.09.23.678138v1

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Reposted by Shai Carmi

sgravel.bsky.social @sgravel.bsky.social · 15d

To analyze millions of genetic variants, we need tools that are fast and memory efficient. Some of the most efficient tools have problems with numerical instability on dense sets of snps. Bercovich et al. figured out how to overcome a common source of instability: www.biorxiv.org/content/10.1...

LD Matrix Approximations for Scalable Analysis of High-dimensional Genetic Data

Linkage disequilibrium (LD) matrices are an essential part of many statistical genetics methods. However, their high dimensionality makes their computation and storage impractical for large genomic da...

www.biorxiv.org

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Reposted by Shai Carmi

sgravel.bsky.social @sgravel.bsky.social · 15d

To predict genetic risk for an individual, which score should you use? The one learned from a cohort that best matches by ancestry? Or by sex, or age, or environment? Shadi Zabad proposes to combine scores taking all these into account. www.biorxiv.org/content/10.1...

Personalized polygenic risk prediction and assessment with a Mixture-of-Experts framework

With the increasing availability of high quality genomic data from diverse cohorts, polygenic scores (PRS) have become a mainstay of genetic analyses of complex traits and diseases. Despite their prol...

www.biorxiv.org

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Shai Carmi @shaicarmi.bsky.social · 17d

Some days it feels as if Netanyahu and Trump are competing who can destroy their country faster or while inflicting the most pain

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Reposted by Shai Carmi

Robel Alemu @robel-alemu.bsky.social · 20d

Excited to share our preprint on PGI portability across ancestries—now on bioRxiv. With co-authors @aysuo.bsky.social, @paturley.bsky.social, @alextisyoung.bsky.social, and @Dan_J_Benjamin. Preprint: doi.org/10.1101/2025... Thread below for details.

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Shai Carmi @shaicarmi.bsky.social · 21d

Oh I see now. But wasn't it a supervised ADMIXTURE run? In such a case the ancestral groups are defined by the training data regardless of sample size.

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Shai Carmi @shaicarmi.bsky.social · 22d

Not sure I agree - in the plot you can see that EAS ancestry is inferred for even fewer UAE people.

Anyhow I wouldn't overinterpret given that the best solution is to simply use a more suitable reference panel.

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Shai Carmi @shaicarmi.bsky.social · 22d

Yeah I was also wondering about that. I guess it's tagging some Asian ancestry. But why not use HGDP, with plenty of local populations.

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Shai Carmi @shaicarmi.bsky.social · 26d

Interesting work. "we analyzed viral load of 31 DNA viruses in human blood and saliva using whole-genome sequencing from UK Biobank (n=490k), SPARK (n=13k), and All of Us (n=415k)... genetic variation at dozens of loci associated with load of seven viruses"

www.biorxiv.org/content/10.1...

Genes and environment profoundly affect the human virome

Many viruses have adapted to persist in infected humans for life. Variable host control of their abundance (or load) can lead to clearance or disease. Here, we analyzed the viral load of 31 DNA viruse...

www.biorxiv.org

Shai Carmi @shaicarmi.bsky.social · 26d

It was perhaps a bit sloppy phrasing. The more precise point is that when comparing siblings, the environment is no longer a confounder for the relation between genotype and phenotype.

Shai Carmi @shaicarmi.bsky.social · 27d

Using 30k sibling pairs from Mexico city, the authors find that indigenous American ancestry is associated with lower height (-1.5SD) and higher type 2 diabetes risk

There were no associations with other traits, including education.

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Shai Carmi @shaicarmi.bsky.social · 27d

Here, the authors suggest to study pairs of siblings in admixed populations.

Due to the randomness of Mendelian inheritance, sibs differ in their ancestry proportions. At the same time, they have a nearly identical environment.

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Shai Carmi @shaicarmi.bsky.social · 27d

Brilliant paper by Visscher et al.

Populations differ in traits/disease burden. Are these differences due to genetics?

Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.

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www.medrxiv.org/content/10.1...

Direct effect of genetic ancestry on complex traits in a Mexican population

Human populations differ in disease prevalences and in average values of phenotypes, but the extent to which differences are caused by genetic or environmental factors is unknown for most complex trai...

www.medrxiv.org

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Shai Carmi @shaicarmi.bsky.social · 28d

We hope people find the app useful! For technical details, see the preprint.

Led by Liraz Klausner, a PhD student. Also contributed: Ateret Revital, @toddlencz.bsky.social

Here are the links again:
App:
polygenicembryo.shinyapps.io/pestimate/
Preprint:
www.medrxiv.org/content/10.1...

polygenicembryo.shinyapps.io

Shai Carmi @shaicarmi.bsky.social · 28d

We showed (mathematically and numerically) that using a fixed number of births (e.g., the mean number of births per IVF cycle) still overestimates the risk reduction (see Figure). It is important to account for the randomness of embryo transfer outcomes.

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