@TobyBaker97

PhD student in the Cancer Genomics Laboratory at the Francis Crick Institute. Studying the evolutionary trajectories of metastatic cancers.

Joined November 2019
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Tumor samples vary in purity and ploidy, both of which confound DNA methylation measures from bulk sequencing. We developed CAMDAC to clean up this signal. Here's our extended preprint with new insights from applying CAMDAC to TRACERx lung RRBS data: biorxiv.org/content/10.1101/…

Copy number-aware deconvolution of tumor-normal DNA methylation profiles

Aberrant methylation is a hallmark of cancer, but bulk tumor data is confounded by admixed normal cells and copy number changes. Here, we introduce Copy number-Aware Methylation Deconvolution...

biorxiv.org
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Millions of extra mutations retrieved in the non-unique regions of cancer genomes!? In the coding sequence of known cancer genes? In immunoglobulin genes in lymphoid tumours? And members of intriguing gene families? So thrilled this is finally out: nature.com/articles/s41587-0… 🥲🙃

A pan-cancer landscape of somatic mutations in non-unique regions of the human genome

Nature Biotechnology - Cancer mutations in non-unique sequences are identified by machine learning on short-read data.

nature.com
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CAMDAC: Copy number-Aware Methylation Deconvolution Analysis of Cancer live on GitHub at github.com/VanLoo-lab/CAMDAC! Run CAMDAC on tumour RRBS data & get tumour purity, allele-specific copy number and methylation rates free from normal contaminants. Preprint: tinyurl.com/y46zuvvw

GitHub - VanLoo-lab/CAMDAC

Contribute to VanLoo-lab/CAMDAC development by creating an account on GitHub.

github.com
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📰 @VanLooLab, @MaxGalder & the #PCAWG consortium have analysed tumours from over 2,600 patients. They found lots of genetic diversity in individual tumours, and confirmed that tumour evolution is driven by changes that benefit the cancer. @CellCellPress crick.ac.uk/news/2021-04-07_…

‘Patchwork’ tumours prevalent across multiple cancer types

Researchers at the Crick , as part of an international collaboration of scientists, have analysed the whole genomes of tumour samples from over 2,600 patients with different types of cancer. They...

crick.ac.uk
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Excited to share our new work published in @nature today by @darlanminussi @VanLooLab @HanghuiYe and Franziska michor on TNBC, in which we asked what happens after the initial burst of chromosome instability? nature.com/articles/s41586-0…
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Please join us for an afternoon of virtual talks on the 30th November starting at 12.30pm UK time: Somatic Evolution and Tumour Microenvironment Symposium 2020 crick.zoom.us/webinar/regist… 👌🙂
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📰 By analysing 47 million genetic changes in 2,658 tumours, a team led by our @VanLooLab and @emblebi has found that there can be genetic signs of cancer years earlier than we thought. ✏️ @ATJCagan | #pcawg | Read the full story ➡️ crick.ac.uk/news/2020-02-05_…
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