Andrew Beggs

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!

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.

👉 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 -

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

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.

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.

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.

🧧🧧🧧🧧 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.

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

🚨🚨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...

Thank you it was really nice to be there!

Because it got people’s attention!

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

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.

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.

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.

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...

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.

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.

It is, @jostockton.bsky.social pointed me to this and it’s been very handy:

gringer.gitlab.io/presentation...

We’re all here don’t worry!

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!

Yes it is me on here from Twitter..