Shai Carmi
@shaicarmi.bsky.social
Associate professor at the Hebrew University of Jerusalem.
Statistical, population, and medical genetics; preimplantation genetic testing. Views my own.
http://scarmilab.org
Statistical, population, and medical genetics; preimplantation genetic testing. Views my own.
http://scarmilab.org
Pinned
Shai Carmi
@shaicarmi.bsky.social
· Nov 10
Slack
join.slack.com
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...
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...
Preprint by Gravel et al addressing an interesting question. Given carriers of a mutation and a population-scale pedigree, can we identify the most recent common ancestor of all carriers?
"20 carriers usually provide enough information to reliably identify a common ancestor 15 generations ago"
"20 carriers usually provide enough information to reliably identify a common ancestor 15 generations ago"
December 14, 2025 at 11:36 AM
Preprint by Gravel et al addressing an interesting question. Given carriers of a mutation and a population-scale pedigree, can we identify the most recent common ancestor of all carriers?
"20 carriers usually provide enough information to reliably identify a common ancestor 15 generations ago"
"20 carriers usually provide enough information to reliably identify a common ancestor 15 generations ago"
Reposted by Shai Carmi
Aligning gene trees with family trees https://www.biorxiv.org/content/10.64898/2025.12.11.693727v1
December 14, 2025 at 3:47 AM
Aligning gene trees with family trees https://www.biorxiv.org/content/10.64898/2025.12.11.693727v1
Fascinating work by Lipson, Skorecki et al, finally fully resolving the Y lineages of Jewish priests (Cohanim) using whole-Y sequencing.
Main finding: 45% of Jewish Cohanim (from all Jewish diasporas) have the same Y lineage, with origin ~3000 years ago, around the time of formation of Judaism.
Main finding: 45% of Jewish Cohanim (from all Jewish diasporas) have the same Y lineage, with origin ~3000 years ago, around the time of formation of Judaism.
Revisiting the lineages of the Cohanim using data from next-generation sequencing https://www.biorxiv.org/content/10.64898/2025.12.08.692646v1
December 11, 2025 at 8:18 AM
Fascinating work by Lipson, Skorecki et al, finally fully resolving the Y lineages of Jewish priests (Cohanim) using whole-Y sequencing.
Main finding: 45% of Jewish Cohanim (from all Jewish diasporas) have the same Y lineage, with origin ~3000 years ago, around the time of formation of Judaism.
Main finding: 45% of Jewish Cohanim (from all Jewish diasporas) have the same Y lineage, with origin ~3000 years ago, around the time of formation of Judaism.
Reposted by Shai Carmi
Revisiting the lineages of the Cohanim using data from next-generation sequencing https://www.biorxiv.org/content/10.64898/2025.12.08.692646v1
December 11, 2025 at 5:31 AM
Revisiting the lineages of the Cohanim using data from next-generation sequencing https://www.biorxiv.org/content/10.64898/2025.12.08.692646v1
Reposted by Shai Carmi
Have a smarter baby? You might, but it's not necessarily legal to advertise. Our look at the NYC subway ad campaign by IVF embryo profiling company Nucleus and how it collides with anti-discrimination statutes that apply to advertising on public property.
www.technologyreview.com/2025/12/05/1...
www.technologyreview.com/2025/12/05/1...
The ads that sell the sizzle of genetic trait discrimination
A startup’s ads for controversial embryo tests hit the New York City subway.
www.technologyreview.com
December 10, 2025 at 11:01 PM
Have a smarter baby? You might, but it's not necessarily legal to advertise. Our look at the NYC subway ad campaign by IVF embryo profiling company Nucleus and how it collides with anti-discrimination statutes that apply to advertising on public property.
www.technologyreview.com/2025/12/05/1...
www.technologyreview.com/2025/12/05/1...
Sperm banks should be much more strictly regulated. (particularly, only accepting donations from registered donors). The banks don't seem to make the slightest effort to avoid these cases.
www.bbc.com/news/article...
www.bbc.com/news/article...
Sperm from donor with cancer-causing gene was used to conceive almost 200 children
Some children have already died and only a minority who inherit the mutation will escape cancer in their lifetimes.
www.bbc.com
December 10, 2025 at 10:22 AM
Sperm banks should be much more strictly regulated. (particularly, only accepting donations from registered donors). The banks don't seem to make the slightest effort to avoid these cases.
www.bbc.com/news/article...
www.bbc.com/news/article...
A lot has been written about AI in academia. But I think there's one overlooked problem.
Say AI makes it easier to write grants (probably correct).
However, grants are zero-sum games. If you can write more grants, everyone can. In the end, you do more work, but gain nothing.
Say AI makes it easier to write grants (probably correct).
However, grants are zero-sum games. If you can write more grants, everyone can. In the end, you do more work, but gain nothing.
December 10, 2025 at 9:29 AM
A lot has been written about AI in academia. But I think there's one overlooked problem.
Say AI makes it easier to write grants (probably correct).
However, grants are zero-sum games. If you can write more grants, everyone can. In the end, you do more work, but gain nothing.
Say AI makes it easier to write grants (probably correct).
However, grants are zero-sum games. If you can write more grants, everyone can. In the end, you do more work, but gain nothing.
Reposted by Shai Carmi
Job AD. Research Directions:
1. Selection in early development; Pop gen methods applied to new technologies, i.e. scDNA-seq with D. Shao
2. Study of hypermutability and selection using population cohorts with E. Koch
3. Evolution of Mutagenesis with M. Penenell & @jgschraiber.bsky.social
1. Selection in early development; Pop gen methods applied to new technologies, i.e. scDNA-seq with D. Shao
2. Study of hypermutability and selection using population cohorts with E. Koch
3. Evolution of Mutagenesis with M. Penenell & @jgschraiber.bsky.social
POSTDOCTORAL RESEARCHER - McDermott Center HG&D - Seplyarskiy Lab
Discover POSTDOCTORAL RESEARCHER - McDermott Center HG&D - Seplyarskiy Lab and other PostDoc jobs in Dallas, TX and apply online today!
jobs.utsouthwestern.edu
December 8, 2025 at 5:31 PM
Job AD. Research Directions:
1. Selection in early development; Pop gen methods applied to new technologies, i.e. scDNA-seq with D. Shao
2. Study of hypermutability and selection using population cohorts with E. Koch
3. Evolution of Mutagenesis with M. Penenell & @jgschraiber.bsky.social
1. Selection in early development; Pop gen methods applied to new technologies, i.e. scDNA-seq with D. Shao
2. Study of hypermutability and selection using population cohorts with E. Koch
3. Evolution of Mutagenesis with M. Penenell & @jgschraiber.bsky.social
Reposted by Shai Carmi
Polygenic embryo screening is being marketed commercially – but how do IVF clinicians view it?
• General approval is low (12%)
For specific uses:
• 59% approved of health-related embryo selection
• 6% approved of trait-based selection
🧵 Survey findings in NPJ Genomic Medicine
• General approval is low (12%)
For specific uses:
• 59% approved of health-related embryo selection
• 6% approved of trait-based selection
🧵 Survey findings in NPJ Genomic Medicine
December 1, 2025 at 8:24 PM
Polygenic embryo screening is being marketed commercially – but how do IVF clinicians view it?
• General approval is low (12%)
For specific uses:
• 59% approved of health-related embryo selection
• 6% approved of trait-based selection
🧵 Survey findings in NPJ Genomic Medicine
• General approval is low (12%)
For specific uses:
• 59% approved of health-related embryo selection
• 6% approved of trait-based selection
🧵 Survey findings in NPJ Genomic Medicine
Reposted by Shai Carmi
Interested in pleiotropy dissection but not sure where to start, which methods are useful, which studies offer illustrative examples, or how to robustly validate your results? Look no further 👀 rdcu.be/eSfAZ
Dissecting pleiotropy to gain mechanistic insights into human disease
Nature Reviews Genetics - Genome-wide association studies of increasing scale have revealed the prevalence of pleiotropic genetic variants that affect multiple traits. In this Review, the authors...
rdcu.be
November 28, 2025 at 1:10 PM
Interested in pleiotropy dissection but not sure where to start, which methods are useful, which studies offer illustrative examples, or how to robustly validate your results? Look no further 👀 rdcu.be/eSfAZ
Reposted by Shai Carmi
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
November 25, 2025 at 8:27 PM
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
Reposted by Shai Carmi
The 2026 EMBL symposium 'Reconstructing the human past using ancient and modern genomics' is live with a fantastic invited speaker lineup!
Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.
Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.
Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
November 19, 2025 at 1:41 PM
The 2026 EMBL symposium 'Reconstructing the human past using ancient and modern genomics' is live with a fantastic invited speaker lineup!
Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.
Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.
Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
Reposted by Shai Carmi
This comment made me wonder: what kinds of cases or research goals/questions would geneticists generally consider scientifically useful/interesting/valid when it comes to looking at the genomes of long-dead famous people?
November 17, 2025 at 10:01 AM
This comment made me wonder: what kinds of cases or research goals/questions would geneticists generally consider scientifically useful/interesting/valid when it comes to looking at the genomes of long-dead famous people?
More details emerge on this affair.
1. A paper has been submitted to a "high profile" journal. I think no editor in their right mind should take it, but I have no hope.
2. Details on the psychiatric PRS analysis were reported by the investigator.
edition.cnn.com/2025/11/13/s...
1. A paper has been submitted to a "high profile" journal. I think no editor in their right mind should take it, but I have no hope.
2. Details on the psychiatric PRS analysis were reported by the investigator.
edition.cnn.com/2025/11/13/s...
November 14, 2025 at 9:13 AM
More details emerge on this affair.
1. A paper has been submitted to a "high profile" journal. I think no editor in their right mind should take it, but I have no hope.
2. Details on the psychiatric PRS analysis were reported by the investigator.
edition.cnn.com/2025/11/13/s...
1. A paper has been submitted to a "high profile" journal. I think no editor in their right mind should take it, but I have no hope.
2. Details on the psychiatric PRS analysis were reported by the investigator.
edition.cnn.com/2025/11/13/s...
One of my core principles is to defend the freedom of sequencing the DNA of everyone for every purpose.
This should not mean it is always a good (or responsible) idea.
And at least post a preprint before going on TV (reminding me of the Columbus fiasco).
www.independent.co.uk/news/science...
This should not mean it is always a good (or responsible) idea.
And at least post a preprint before going on TV (reminding me of the Columbus fiasco).
www.independent.co.uk/news/science...
Hitler had genetic sexual disorder, new DNA analysis reveals
Findings also debunked myth that Nazi dictator had Jewish ancestry
www.independent.co.uk
November 13, 2025 at 6:27 AM
One of my core principles is to defend the freedom of sequencing the DNA of everyone for every purpose.
This should not mean it is always a good (or responsible) idea.
And at least post a preprint before going on TV (reminding me of the Columbus fiasco).
www.independent.co.uk/news/science...
This should not mean it is always a good (or responsible) idea.
And at least post a preprint before going on TV (reminding me of the Columbus fiasco).
www.independent.co.uk/news/science...
Reposted by Shai Carmi
Straight onto the reading list: Forensic genetics in the omics era www.nature.com/articles/s41...
Forensic genetics in the omics era - Nature Reviews Genetics
Recent advances in forensic genetics have improved the range, precision and reliability of forensic information obtainable from biological trace material. The author reviews how non-targeted and ...
www.nature.com
November 9, 2025 at 5:12 PM
Straight onto the reading list: Forensic genetics in the omics era www.nature.com/articles/s41...
Reposted by Shai Carmi
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes
Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with L...
www.biorxiv.org
November 7, 2025 at 2:33 PM
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A meta-analysis of the impact of polygenic risk score disclosures on health outcomes. 27 RCTs, max follow up 12 months.
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
Effects of polygenic risk score communication on health outcomes: systematic review and meta-analysis
Abstract Objective. The purpose of this systematic review and meta-analysis is to summarize evidence from all RCTs to-date on the efficacy of polygenic risk score (PRS) communication in changing healt...
www.medrxiv.org
November 7, 2025 at 8:33 AM
A meta-analysis of the impact of polygenic risk score disclosures on health outcomes. 27 RCTs, max follow up 12 months.
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
Interesting story in this preprint.
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
Multi-lineage natural gene therapy mediated by embryonic triploid mosaicism in the context of Fanconi anaemia
Fanconi anemia is a rare inherited bone marrow failure syndrome caused by inactivation of genes in the Fanconi anemia/BRCA DNA repair pathway. We report a patient with X-linked Fanconi anemia, and aty...
www.medrxiv.org
November 5, 2025 at 8:04 AM
Interesting story in this preprint.
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
Reposted by Shai Carmi
Excited to help host the 54th European Mathematical Genetics Meeting in Davos, Switzerland, next spring!
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
November 4, 2025 at 2:05 PM
Excited to help host the 54th European Mathematical Genetics Meeting in Davos, Switzerland, next spring!
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Reposted by Shai Carmi
New from FinnGen!! 🚀🚀🚀
FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!!
All results are open for browsing & download:
👉 labvalues.finngen.fi.
🧬🧬🧬
Have fun!! 🏄🏄♀️🏄♂️
FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!!
All results are open for browsing & download:
👉 labvalues.finngen.fi.
🧬🧬🧬
Have fun!! 🏄🏄♀️🏄♂️
October 24, 2025 at 12:09 AM
New from FinnGen!! 🚀🚀🚀
FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!!
All results are open for browsing & download:
👉 labvalues.finngen.fi.
🧬🧬🧬
Have fun!! 🏄🏄♀️🏄♂️
FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!!
All results are open for browsing & download:
👉 labvalues.finngen.fi.
🧬🧬🧬
Have fun!! 🏄🏄♀️🏄♂️
Reposted by Shai Carmi
Online now!
📄Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
🧑🤝🧑 @shaicarmi.bsky.social @eva-hoffmann.bsky.social & co
📄Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
🧑🤝🧑 @shaicarmi.bsky.social @eva-hoffmann.bsky.social & co
Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
Ploidy abnormalities affect over 1% of human embryos. Haploidy typically results from
absent sperm DNA, while triploidy mainly arises from maternal meiosis II errors. Triploidy
also shows a linear mat...
www.cell.com
October 20, 2025 at 5:32 PM
Online now!
📄Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
🧑🤝🧑 @shaicarmi.bsky.social @eva-hoffmann.bsky.social & co
📄Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
🧑🤝🧑 @shaicarmi.bsky.social @eva-hoffmann.bsky.social & co
Reposted by Shai Carmi
FLARE2: local ancestry inference with poorly-matched reference panels https://www.biorxiv.org/content/10.1101/2025.10.13.681993v1
October 14, 2025 at 5:34 PM
FLARE2: local ancestry inference with poorly-matched reference panels https://www.biorxiv.org/content/10.1101/2025.10.13.681993v1
Hebrew University graduate wins Economics Nobel prize.
Not bad for one day :)
www.nobelprize.org/prizes/econo...
www.nobelprize.org/events/nobel...
Not bad for one day :)
www.nobelprize.org/prizes/econo...
www.nobelprize.org/events/nobel...
October 13, 2025 at 12:36 PM
Hebrew University graduate wins Economics Nobel prize.
Not bad for one day :)
www.nobelprize.org/prizes/econo...
www.nobelprize.org/events/nobel...
Not bad for one day :)
www.nobelprize.org/prizes/econo...
www.nobelprize.org/events/nobel...