Alexander Rakitko
@alexrakitko.bsky.social
Genetic testing, population genetics, multifactor diseases, ML in HealthCare, Ph.D.
Reposted by Alexander Rakitko
Our paper on indirect assortative mating is now out in @natcomms.nature.com! In it, we provide refined definitions of terms used to explain partner similarity, develop statistical models, and find evidence of surprisingly high social homogamy for education.
Link: doi.org/10.1038/s414...
Link: doi.org/10.1038/s414...
June 6, 2025 at 6:01 PM
Our paper on indirect assortative mating is now out in @natcomms.nature.com! In it, we provide refined definitions of terms used to explain partner similarity, develop statistical models, and find evidence of surprisingly high social homogamy for education.
Link: doi.org/10.1038/s414...
Link: doi.org/10.1038/s414...
Reposted by Alexander Rakitko
📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41...
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
June 5, 2025 at 1:37 PM
📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41...
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Reposted by Alexander Rakitko
Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses www.nature.com/articles/s41...
Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses - Nature Communications
Here, the authors present efficient local ancestry inference algorithms to analyse the population of origin for each individual and variant in the UK Biobank, improving controls for population structu...
www.nature.com
March 22, 2025 at 11:12 AM
Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses www.nature.com/articles/s41...
Reposted by Alexander Rakitko
Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing www.biorxiv.org/content/10.1... 🧬🖥️🧪 Nextflow github.com/renatosantos...
March 4, 2025 at 9:00 PM
Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing www.biorxiv.org/content/10.1... 🧬🖥️🧪 Nextflow github.com/renatosantos...
Reposted by Alexander Rakitko
Happy to share a new preprint, to which I provided a minor contribution.
Using genetic data from ~100k human embryos, we found ~1k that were haploid or triploid.
We describe a thorough characterization of these embryos, with many interesting findings 🧵
1/9
www.biorxiv.org/content/10.1...
Using genetic data from ~100k human embryos, we found ~1k that were haploid or triploid.
We describe a thorough characterization of these embryos, with many interesting findings 🧵
1/9
www.biorxiv.org/content/10.1...
February 18, 2025 at 12:05 PM
Happy to share a new preprint, to which I provided a minor contribution.
Using genetic data from ~100k human embryos, we found ~1k that were haploid or triploid.
We describe a thorough characterization of these embryos, with many interesting findings 🧵
1/9
www.biorxiv.org/content/10.1...
Using genetic data from ~100k human embryos, we found ~1k that were haploid or triploid.
We describe a thorough characterization of these embryos, with many interesting findings 🧵
1/9
www.biorxiv.org/content/10.1...
Reposted by Alexander Rakitko
The long awaited European guidelines for the use of Polygenic score for primary prevention of cardiovascular diseases are out!
It took > 10 years from the first results proposing its use as additional screening factor among patients with intermediate CVD risk
academic.oup.com/eurheartj/ad...
It took > 10 years from the first results proposing its use as additional screening factor among patients with intermediate CVD risk
academic.oup.com/eurheartj/ad...
Clinical utility and implementation of polygenic risk scores for predicting cardiovascular disease: A clinical consensus statement of the ESC Council on Cardiovascular Genomics, the ESC Cardiovascular...
Abstract. Genome-wide association studies have revealed hundreds of genetic variants associated with cardiovascular diseases (CVD). Polygenic risk scores (
academic.oup.com
February 7, 2025 at 5:02 AM
The long awaited European guidelines for the use of Polygenic score for primary prevention of cardiovascular diseases are out!
It took > 10 years from the first results proposing its use as additional screening factor among patients with intermediate CVD risk
academic.oup.com/eurheartj/ad...
It took > 10 years from the first results proposing its use as additional screening factor among patients with intermediate CVD risk
academic.oup.com/eurheartj/ad...
Reposted by Alexander Rakitko
Did you know you can get DNA viruses from standard blood WGS done in large biobanks? (i didn’t). One point in favor of WGS vs WES
Yet another nice paper from Yuki’s group
www.nature.com/articles/s41...
Yet another nice paper from Yuki’s group
www.nature.com/articles/s41...
Blood DNA virome associates with autoimmune diseases and COVID-19 - Nature Genetics
Analysis of the blood DNA virome in patients with COVID-19 and autoimmune disease associates endogenous HHV-6 (eHHV-6) and high anellovirus load with increased disease risk, most notably for systemic ...
www.nature.com
January 8, 2025 at 8:39 AM
Did you know you can get DNA viruses from standard blood WGS done in large biobanks? (i didn’t). One point in favor of WGS vs WES
Yet another nice paper from Yuki’s group
www.nature.com/articles/s41...
Yet another nice paper from Yuki’s group
www.nature.com/articles/s41...
Reposted by Alexander Rakitko
I am excited that our *hapla* framework for fast and scalable haplotype clustering in phased genotype data has been published in Nature Communications!
GitHub: github.com/Rosemeis/hapla
Paper: www.nature.com/articles/s41...
GitHub: github.com/Rosemeis/hapla
Paper: www.nature.com/articles/s41...
Leveraging haplotype information in heritability estimation and polygenic prediction - Nature Communications
Here the authors develop a framework to leverage haplotype information through clustering for heritability estimation and polygenic prediction. Their approach estimates disease risk more accurately th...
www.nature.com
January 7, 2025 at 10:05 AM
I am excited that our *hapla* framework for fast and scalable haplotype clustering in phased genotype data has been published in Nature Communications!
GitHub: github.com/Rosemeis/hapla
Paper: www.nature.com/articles/s41...
GitHub: github.com/Rosemeis/hapla
Paper: www.nature.com/articles/s41...
Reposted by Alexander Rakitko
Nice analysis by PRS company Genomics plc, quantifying the potential reduction in mortality due to PRS screening. Assuming people at high risk for 7 diseases get early access to prevention/detection, they estimate saving 95 lives for each 100k people.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
December 30, 2024 at 6:50 PM
Nice analysis by PRS company Genomics plc, quantifying the potential reduction in mortality due to PRS screening. Assuming people at high risk for 7 diseases get early access to prevention/detection, they estimate saving 95 lives for each 100k people.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Alexander Rakitko
New metabolomic aging clock trained on 168 metabolites in UK Biobank (N=225,212)⏲️
👉R2 up to 0.35
👉associations with frailty index, telomere length, self-rated health
👉prediction of all-cause mortality
1/3
👉R2 up to 0.35
👉associations with frailty index, telomere length, self-rated health
👉prediction of all-cause mortality
1/3
December 22, 2024 at 6:49 PM
New metabolomic aging clock trained on 168 metabolites in UK Biobank (N=225,212)⏲️
👉R2 up to 0.35
👉associations with frailty index, telomere length, self-rated health
👉prediction of all-cause mortality
1/3
👉R2 up to 0.35
👉associations with frailty index, telomere length, self-rated health
👉prediction of all-cause mortality
1/3
Reposted by Alexander Rakitko
It's the era of large-scale biobanks❗️
🧬GWAS summary stats from meta-analyses of:
👉MVP (N=630K)
👉FinnGen (N=420K)
👉UK Biobank (N=500K)
...for 330 clinical outcomes
Unparalleled resource for phenome-wide explorations of genetic variation🔗: mvp-ukbb.finngen.fi
🧬GWAS summary stats from meta-analyses of:
👉MVP (N=630K)
👉FinnGen (N=420K)
👉UK Biobank (N=500K)
...for 330 clinical outcomes
Unparalleled resource for phenome-wide explorations of genetic variation🔗: mvp-ukbb.finngen.fi
December 17, 2024 at 7:57 PM
It's the era of large-scale biobanks❗️
🧬GWAS summary stats from meta-analyses of:
👉MVP (N=630K)
👉FinnGen (N=420K)
👉UK Biobank (N=500K)
...for 330 clinical outcomes
Unparalleled resource for phenome-wide explorations of genetic variation🔗: mvp-ukbb.finngen.fi
🧬GWAS summary stats from meta-analyses of:
👉MVP (N=630K)
👉FinnGen (N=420K)
👉UK Biobank (N=500K)
...for 330 clinical outcomes
Unparalleled resource for phenome-wide explorations of genetic variation🔗: mvp-ukbb.finngen.fi