Bobby Bentham

Thanks! It’s all of Genomics England >90k WGS samples but only ~15k of which are from tumours

Using 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...

New tool reveals disruption of immune cells in blood is linked to cancer outcomes The 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...

www.ucl.ac.uk/news/2025/fe...

And 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.

A 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

Finally, 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.

ImmuneLENS 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.

In 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.

We 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!

ImmuneLENS 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...

ImmuneLENS characterizes systemic immune dysregulation in aging and cancer - Nature Genetics Immune 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 ...

🚀 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
🧵👇