We can use #deeplearning to learn from our #genomes and predict personal risk of #disease! New method and framework called EIR led by amazing @Arnor_Sig !.

Developed and built by Arnor Sigurdsson from the group, EIR helps researchers work with real-world health data at scale. 📦 📖

🚨 Cool news! Our EIR framework for modeling multi-modal biomedical data has been featured in the first blog post from the new @PyTorch Ecosystem WG!. 🔗 #PyTorch #EHR #Genomics #AI4Health #OpenSource #FoundationModels.

RT @andganna: We have 2-3 group leader positions opening up @FIMM_UH !!. We are looking for outstanding candidates in human genetics and pr….

RT @andganna: We are looking for a post-doc/research fellow working on non-bullshit, reality-centered AI. Meaning: unique nationwide EHR….

25/.And much more, have a look at the paper and thanks to all contributors and co-authors!.@MichaelBenros Thorfinn Korneliussen, Lasse Danielsen, Martin Sikora, Morten Allentoft, Eske Willerslev.

24/.In summary:.✅ CCR5delta32 arose once, >6,700 years ago.✅ It spread via Bronze Age demographic expansions.✅ Underwent strong positive selection.✅ Is now a globally relevant variant in medicine.All from an ancient immunogenetic adaptation.

23/.Our spatiotemporal model estimates a rapid westward diffusion of CCR5delta32, covering 60���100 km² per generation. Its spread likely paralleled the expansion of Steppe-related ancestry into Europe in the Early Bronze Age.

22/.Only Haplotype A (with CCR5delta32) was under positive selection. This suggests the deletion conferred an adaptive advantage—possibly by modulating immune tolerance in denser Neolithic populations.

21/.Its frequency rose rapidly during the Late Neolithic and Bronze Age — then plateaued. Strong positive selection from 8,000-2,000 years BP, particular Eastern and Caucasus Hunter Gatherers

20/.Applying HAPI to 934 ancient genomes revealed that CCR5delta32 originated once in the Western Steppe ~6,700–9,000 years ago.

19/.Importantly, we benchmarked HAPI against GATK and vg graph-genomes:.✅ HAPI called 63% more ancient genomes.✅ Maintained high precision even at 0.3× coverage.👉 This enables robust indel detection in challenging aDNA datasets.

18/.HAPI: Haplotype Aware Probabilistic modeling of Indels.Use entire haplotype information to call deletion in ancient samples

17/.We identify two ancestral haplotypes (B and C) that were widespread long before CCR5delta32 emerged on the haplotype B.

16/.Bonus technical details:.We found that CCR5delta32 sits on a specific haplotype — “Haplotype A” — comprising 86 tightly linked variants. We developed a probabilistic genotyper for ancient genomes: HAPI. This allowed us to robustly call CCR5delta32 in low-coverage ancient DNA.

15/.Thanks for reading!.Paper (open access): Lead authors: @RavnKirstine, @Leonardo_Cob, Rasa Muktupavela, @Rosemeis91, @EvanIrvingPease, @simonrasmu.Affiliations: @UCPH_Research.

14/.So if you’re one of the millions of Europeans who carry this variant—.You share a direct genetic link to a single ancient human whose mutation reshaped immune defenses across Europe.

13/.HIV appeared in the 20th century. That a Neolithic mutation offers protection against a modern virus is a testament to #evolution’s strange, #serendipitous logic.

12/.Think of allergic reactions or COVID-19:.It’s often not the virus, but the immune system overreacting, that causes the most damage. CCR5delta32 may have helped tune immune balance in a world where infections were more common.

11/.Here’s the wild part:.A #mutation that damages an immune gene sounds bad. But in the context of evolving human societies, it might’ve been a life-saving #adaptation.

10/.After year 0, we no longer see signs of a positive selection. But by then, the variant was well established in Northern Europe—and it remains there today.