iiinova — where your digital self keeps evolving

Andrew Beggs @adbeggs.bsky.social · 13/04/2025

Whilst you’re here can I just point out we do all this work with no core funding… just the genorosity of donors, so if anyone would like to core fund us to continue what we think is cool science! Thank you for reading!

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Andrew Beggs @adbeggs.bsky.social · 13/04/2025

We're looking for partners as this has the potential to really expand the range of samples Nanopore sequencing can access, and could work on any ligation based technology too.

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Andrew Beggs @adbeggs.bsky.social · 13/04/2025

👉 Detection of variants that we would expect to see in this control, at appropriate variant allele frequencies So the next thing to do is to validate this method further -

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Andrew Beggs @adbeggs.bsky.social · 13/04/2025

The next images show: 👉 A sensible fragment distribution that we would expect with FFPE samples 👉 Q20 base accuracy 👉 Preservation of base level methylation and hydroxymethlation WITHOUT enzymatic modification or copying

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Andrew Beggs @adbeggs.bsky.social · 13/04/2025

The first image shows the different between the input before and after our mods - as you can see there is a near 10x increase in flowcell output.

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Andrew Beggs @adbeggs.bsky.social · 13/04/2025

So here's the Horizon HD832 FFPE control, taken from FFPE tissue curl to LSK114 library, with the proprietary tech we have developed in the lab (hard wet work from Luke Ames and Joanne Stockton) over the last year.

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Andrew Beggs @adbeggs.bsky.social · 13/04/2025

This was thought to because the DNA blocks the pores and it wouldn't give a whole genome with decent coverage - really important for access to historical clinical trial samples.

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Andrew Beggs @adbeggs.bsky.social · 13/04/2025

🧧🧧🧧🧧 So another exciting finding for the weekend before I go on vacation. *FFPE Ligation Sequencing for ALL!* For a long while it was thought that ligation (i.e. native DNA) sequencing on @nanoporetech.com was difficult, if not impossible.

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Andrew Beggs @adbeggs.bsky.social · 25/03/2025

Amazing bit of cleaning tech this morning @unibirmingham.bsky.social - our robot overlords have clearly arrived 😂

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Andrew Beggs @adbeggs.bsky.social · 19/03/2025

🚨🚨JOB ALERT We’ve got a new job going developing AI algorithms for molecular classification of H&E images of ovarian cancer. Led by Elaine Leung you’ll get to learn cutting edge techniques and travel overseas More details here: edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

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Andrew Beggs @adbeggs.bsky.social · 03/03/2025

Thank you it was really nice to be there!

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Andrew Beggs @adbeggs.bsky.social · 09/02/2025

Because it got people’s attention!

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Andrew Beggs @adbeggs.bsky.social · 09/02/2025

Please, get in touch with me if you'd like to consider a move to Birmingham (especially those of you in the US who are suffering from NIH cuts). More information on the scheme is here: fellowsandchairs.birmingham.ac.uk

fellowsandchairs.birmingham.ac.uk

125th Anniversary Fellows and Chairs | University of Birmingham

This is 125 years of NobelPrize-winning research.This is your opportunity to become one of our 125th Anniversary Fellows and Chairs.

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Andrew Beggs @adbeggs.bsky.social · 09/02/2025

We're looking for high quality candidates wanting to set up their own lab or bring over an existing lab to Birmingham, where you'll have access to state of the art facilities and ~ 6M diverse patient population accross the Midlands.

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Andrew Beggs @adbeggs.bsky.social · 09/02/2025

We want to expand our offering in these areas and will be looking for academics (non-clinical) at Professor, Assoc. & Assistant Professor levels to fill these gaps.

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Andrew Beggs @adbeggs.bsky.social · 09/02/2025

Want to join us in Birmingham?! In a few months the University of Birmingham will be re-opening its 125th Anniversary Chair and Fellows Scheme. One of our strengths currently in the lab is organoid modelling, genomic medicine and Nanopore sequencing, especially in cancer.

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Andrew Beggs @adbeggs.bsky.social · 07/02/2025

Really delighted to show our first attempts at growing Wilms Tumour organoids (left) and the kidney (right) from paediatric patients by @maxpedsurg.bsky.social ,Zeynep Kaya and Kaitlin Marley. Funding from @littleprincesses.bsky.social Project here: www.littleprincesses.org.uk/news/innovat...

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Andrew Beggs @adbeggs.bsky.social · 06/02/2025

Trying to improve somatic cancer genomic testing in the NHS at the moment feels like an Esherian/Penrose staircase. Always falling. Immensely painful. It is almost as if we want to go backwards as a healthcare system.

giphy.com

m c escher falling GIF - Find & Share on GIPHY

Discover & share this m c escher falling GIF with everyone you know. GIPHY is how you search, share, discover, and create GIFs.

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Andrew Beggs @adbeggs.bsky.social · 04/02/2025

We’re all here don’t worry!

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Andrew Beggs @adbeggs.bsky.social · 30/01/2025

We’ve been doing it for a little while anyway 😉but we thought we should make it official - we are now certified service providers for @nanoporetech.com sequencing For service work contact Genomics Birmingham - lnkd.in/e_nmh2Ki For research and collaboration enquiries - email me!

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Andrew Beggs @adbeggs.bsky.social · 28/01/2025

Yes it is me on here from Twitter..

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