🧬Can chemotherapy response in aggressive breast cancer be predicted from the tumor “ecosystem”? New @nature.com study shows that single-cell RNAseq and spatial transcriptomics can predict response to chemotherapy in triple-negative breast cancer (model reaching AUC = 0.84).

🧬New preprint from David Reich and colleagues examines the population history of the first Caribbean inhabitants, which has been difficult to reconstruct because very few early human remains are known. www.biorxiv.org/content/10.6... #PopulationGenetics #CaribbeanIslands #aDNA

🧬When the world is shaken by disasters on a planetary scale, it may be time to duplicate the genome💥🌍🌱 In a new paper in @cellcellpress.bsky.social, researchers analyzed 470 genomes of flowering plants and suggest that whole-genome duplication may act as an evolutionary emergency mode. 🧵⤵️

🧬CroCoDeEL is a new tool for detecting cross-sample contamination in metagenomic data.🐊🦠 The idea behind CroCoDeEL is simple and elegant. Imagine different cocktails poured into a row of glasses...🧵 www.nature.com/articles/s41... #Microbiome #Metagenomics #Contamination

🧬New @Nature paper suggests that the human gut microbiome may be shaped by evolutionary events that look surprisingly similar to global epidemics.🦠🧵 www.nature.com/articles/s41... #Microbiome #Genomics #Evolution #PopulationGenetics

🧬Cool paper on the evolution of water lilies.🌺 What I liked most was how they adapted to aquatic life. The authors found 481 genes that water lilies have lost, including: rdcu.be/fhdEb #WaterLily #Evolution #Genetics #Adaptation

Water lily complete genomes illuminate the innovations of water lilies and early angiosperms

Nature Plants - This study decodes gapless genomes for three water lily species, discovering genetic keys to fertilization, floral colour and scent, and offering a molecular roadmap for how early...

rdcu.be

🧬New massive study of more than one trillion variant–trait associations suggests that drug-target success may lie in the middle ground between low and high pleiotropy. 💊 🧵 platform.opentargets.org www.biorxiv.org/content/10.6... #GWAS #OpenTargets #Pleiotropy #DrugDesign #ComplexDiseases

Bitter truth or sweet AI lie? A new @Nature paper shows that making LLMs more “warm” and polite can actually make them less accurate. Warm-tuned models made +8.6% more errors on medical questions. And the effect got much worse when the user was emotionally vulnerable. www.nature.com/articles/s41...

Training language models to be warm can reduce accuracy and increase sycophancy - Nature

Experiments on five different language models show that training language models to produce warmer responses can undermine the accuracy of their output, especially when users express feelings of sadne...

nature.com

A new preprint! A short case report in forensic genetics. Skeletal remains discovered in a cave in central Israel were thought to match a person of Ashkenazi Jewish origin missing since 1948. The authorities were confident about the identification, but... 1/3 www.biorxiv.org/content/10.6...

🧬A new @Nature study of 258 ancient genomes from Germany shows that Early Medieval southern Germany was not formed by a simple barbarian replacement of the Roman population.🏺 www.nature.com/articles/s41... #aDNA #RomanEmpire #Admixture #PCA #PopulationGenetics #PedigreeReconstruction

Demography and life histories across the Roman frontier in Germany 400–700 ce - Nature

Analysis of 258 ancient genomes from southern Germany reveals a major demographic shift during the late fifth century, yet family structures persisted from Late Roman times, demonstrating cultural con...

nature.com

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...

📣 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.

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...

nature.com

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...

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...

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...

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

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...

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 ...

nature.com

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...

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...

nature.com

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...

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

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