Post-doc @UMich in the @KoschmannLab. Research: intro-operative/rapid sequencing, high-accuracy cf-tDNA sensing. @nanopore hacker. He/him 🏳️🌈
Ann Arbor, MI
Joined June 2011
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SUPER excited for this project to finally be out in
@CommsBio! Important updates since the pre-print include replicates, flowcell re-use, live basecalling/analysis, and ddPCR validation. @nanopore will end up in-OR (not if but when). A few notes below...
Somatic variants for the intraoperative evaluation of tumor mutations can be detected in less than 30 minutes, using rapid DNA extraction, in silico optimized LAMP amplification, and a LAMP product analysis tool: LAMPrey. @jackwadden nature.com/articles/s42003-0…
Such an amazing experience to present to this group at #SNO2023! Come say hi at my poster later (BIOM-58) to talk about how we are rapidly and accurately sequencing a variety of sample types (tumor, csf, blood, biopsy wash water) using @nanopore
Excellent Presentation by @jackwadden from @KoschmannLab at SNO2023 (@NeuroOnc) on Nanopore sequencing plasma for H3K27M!
Jack Wadden retweeted
Fanstastic line up of insightful talks at the first ever @UMRogelCancer #liquidbiopsy symposium by @jackwadden @andi_cani @TewariLab with special guest speaker @max_diehn
Even after one day, I'm *SO* happy I came to #NanoporeConf. Amazing networking. If you're here, come nerd out with me about hyper-accurate concatemeric consensus seq, ultra-rapid (<30min) seq, weird isothermal amplification techniques, and liquid biopsy using @nanopore!
I'll be hanging around my poster (#59) from 11:30-12:40. We're showcasing our approach for MRD and cancer monitoring. Concatemer consensus sequencing is so accurate we can track VAFs down to ~0.05%
Day two at #NanoporeConf! Kicking things off listening to the Data for Breakfast talks. Kudos to @nanopore for committing to open sourcing their code! About halfway through adding support for duplex basecalling of lamplicons to dorado for even more accurate cf-tDNA detection
Excited to listen to @billytcl, @Carolinmsa, and @adbeggs talk about utility of @nanopore for liquid biopsy #NanoporeConf #LC23
Here we go! So excited to be at my first London Calling. I’m here presenting my poster (#59) on our same-day, LAMP-based ctDNA RMD monitoring technique. Come say hi! I’m the one with the big scar on my head @nanopore #NanoporeConf
Jack Wadden retweeted
The incredible Drs. @CarlKoschmann &
@NazarianLabs presenting at the @PNOCFoundation @PNOC_kids @act_dmg in SF! So proud!
Jack Wadden retweeted
At #AACR23, @jackwadden shared his research developing a new protocol to identify brain tumours in less than an hour, right in the operating room. He discussed his protocol's potential to impact surgical-decision making, in the future. Learn more👇
Super excited to be at #AACR23 presenting my poster on needle wash diagnostics. We’re sequencing cell-free waste water DNA from biopsy needles and finding exciting potential for clinical diagnostics *AND* research. Come say hi at section 38 poster 18 (#2115)
Featuring some older ultra-rapid LAMP @nanopore results. We were able to amplify DNA from raw, unprocessed wash water and call clinically relevant mutations within 1hr of sample hands on! We can go a lot faster these days 😜
Briefly switching gears from my liquid biopsy work back to ultra-rapid @nanopore sequencing. This is a three target panel with 1,000x coverage over all three targets ***within 30mins*** of tissue hands on. Continuously amazed by this tech and kit14 improvements!
Also was able to ask why they deprecated 260bp/s models in favor of 400bp/s or higher speeds. Answer seemed to boil down to: market for super high accuracy but low throughout was small. Unfortunately this is me rn.
13) SOO thankful for my @UMichCSE PIs for letting me go out on this long limb. Also for the training and mentorship from @robertpdickson and @CarlKoschmann. I'm now full-time in the @KoschmannLab and fully hooked on @nanopore for rapid cancer Dx