Bobby Bentham @rbentham.bsky.social · 21/02/2025Thanks! It’s all of Genomics England >90k WGS samples but only ~15k of which are from tumours 100
Reposted by Bobby BenthamEric Topol @erictopol.bsky.social · 18/02/2025Using whole genome sequencing to derive circulating T cell fraction, an immune system metric that has prognostic importance for cancer. And B cell fraction for risk of cancer. www.nature.com/articles/s41... 38715
Bobby Bentham @rbentham.bsky.social · 18/02/2025www.ucl.ac.uk/news/2025/fe...ucl.ac.ukNew tool reveals disruption of immune cells in blood is linked to cancer outcomesThe immune systems of cancer patients are highly disrupted, with those who have a higher number of immune cells in their blood having a better survival rate, finds a new study that uses a pioneering t... 010
Bobby Bentham @rbentham.bsky.social · 18/02/2025And a final thanks to our funders without which none of this work would have been possible: @cancerresearchuk.org, @wellcometrust.bsky.social and Rosetrees as well as most importantly all the patients & participants. 021
Bobby Bentham @rbentham.bsky.social · 18/02/2025A huge thanks to my co-authors, especially my PI Prof. Nicholas McGranahan for guiding all of this and @charlesswanton.bsky.social who gave his support throughout. Thanks also to @genomicsengland.bsky.social , @cruk-cityoflondon.bsky.social , UCL Cancer Institute, and @crick.ac.uk 131
Bobby Bentham @rbentham.bsky.social · 18/02/2025Finally, we directly compared the prognostic value of circulating vs. tumour infiltrating T cells in cancer patients 🔹 Circulating T cells were more prognostic than infiltrating 🔹 Circulating B cells were also prognostic, but only non-class-switched IgM/D B cells contributed to this signal. 100
Bobby Bentham @rbentham.bsky.social · 18/02/2025ImmuneLENS also enables the study of tumour microenvironment and cancer evolution. 🧬 In the 100KGP cohort we identified driver mutations enriched in T cell–replete tumours vs. T cell–depleted tumours, suggesting that different cancer drivers may have immune-suppressive or immune-evasive roles. 110
Bobby Bentham @rbentham.bsky.social · 18/02/2025In blood samples, ImmuneLENS scores reflect circulating T cell fractions, a proxy for the neutrophil-to-lymphocyte ratio. 🔹 In cancer patients, circulating T cell fractions were significantly lower than in healthy individuals. 🔹 We also observed notable sex-based differences. 110
Bobby Bentham @rbentham.bsky.social · 18/02/2025We applied ImmuneLENS to the 100,000 Genomes Project (100KGP) from Genomics England —a WGS cohort lacking orthogonal immune data—creating an important new resource for researchers. 🚨 Now, you can investigate immune content in this or any other WGS dataset! 110
Bobby Bentham @rbentham.bsky.social · 18/02/2025ImmuneLENS follows the same principles but improves the model to better reflect V(D)J recombination, leveraging the uniform coverage of WGS, it: ✅ Measures T and B cell fractions ✅ Detects class switching in B cells ✅ Predicts V and J segment usage 📢 Now Available: github.com/McGranahanLa... 120
Bobby Bentham @rbentham.bsky.social · 18/02/2025🚀 Our paper introducing ImmuneLENS, a new tool that measures T and B cell fractions from WGS data. This builds on our previous method, T cell ExTRECT, that used a signal from V(D)J recombination to measure T cells. Out today in @naturegenet.bsky.social : doi.org/10.1038/s41588-025-02086-5 🧵👇nature.comImmuneLENS characterizes systemic immune dysregulation in aging and cancer - Nature GeneticsImmune lymphocyte estimation from nucleotide sequencing (ImmuneLENS) infers B cell and T cell fractions from whole-genome sequencing data. Applied to the 100,000 Genomes Project datasets, circulating ... 2127
