Jonathan Keats, PhD 🇨🇦

Hard day I suspect. If that ends up being the diagnosis make sure to find a reputable myeloma center, outcomes are so much better now overall but management and outcomes are better in centers with disease experts

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...

As an integrated kit, really system with informatics TSO is impressive for a panel offer. What surprised me recently paying to validate clincal WGS findings was the list price per sample cost is a lot more than whole exome kits

New prognostic systems for multiple myeloma in the context of contemporary therapies Recent clinical trials in both transplant eligible and ineligible newly diagnosed multiple myeloma utilising three and four drug combinations have demonstr

New prognostic systems for multiple myeloma in the context of contemporary therapies url: ashpublications.org/blood/articl...

Sarcastic me: Ah I feel so bad for him… Honest me: please don’t give this piece of shit a platform, hope no one hires him as it just helps is platform of spewing crap appear academic in origin

This is yet another amazing outcome of large public datasets like the UK bio bank. Suspect having a high serum BAFF level means you don’t have many plasma cells, wonder if those people have frequent infections

Dysregulated immune proteins in plasma in the UK Biobank predict multiple myeloma 12 years before clinical diagnosis TO THE EDITOR:

Dysregulated immune proteins in plasma in the UK Biobank predict multiple myeloma 12 years before clinical diagnosis, regardless of MGUS status, amazing work!: ashpublications.org/bloodadvance...

Sauber only had two bottles of champagne, both Mercedes and Aston Martin sent them all of theirs so the team could celebrate properly!

A very hard fought well deserved podium for both team and driver
#BritishGP

But not all mutations block all anti-BCMA therapies from binding and we at @tgenresearch.bsky.social and @cityofhope.bsky.social are integrating the known binding of these agents into our whole genome sequencing reports to ensure patients get the therapy that will work best for them at that point

This is great news for patients to add one more highly effective agent. And importantly provides more opportunities for personalized medicine in myeloma. We are learning more and more each day how tumors evolve the mutate to prevent these drugs from binding.

Drug approval timeline from 2003 to 2025, showing when therapies were first approved, the type of therapy, the target of the therapy (if known and singular), with the scientifically used common names

Drug approval timeline from 2003 to 2025, showing when therapies were first approved, noting the type of therapy and showing the advertised trade names

Yesterday the FDA approved the third T-cell engager against BCMA, Lynozyfic (linvoseltamab) from Regeneron, following on the earlier EMA approval this spring. This is the 20th drug approved to treat #myeloma in just over 20 years. For those that are interested here is the updated approval timeline.

But can you cluster inserts of sufficient length to see the benefit? One major change for the X vs 6K is the preferential clustering of smaller inserts. However, the original Xleap advert when it was codenamed was longer read lengths

Suggests that NK cell numbers, and percentage of different types correlates with if patients achieve MRD negativity with daratumumb based combination.

Interesting paper #myelomasky
The bone marrow NK-cell profile predicts MRD negativity in patients with multiple myeloma treated with daratumumab-based therapy url:https://ashpublications.org/blood/article-abstract/doi/10.1182/blood.2024026455/535791/The-bone-marrow-NK-cell-profile-predicts-MRD

Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986

We are proud to announce that the International Myeloma Society/International Myeloma Working Group Consensus Recommendations on the Definition of High-Risk Multiple Myeloma has been published by the Journal of Clinical Oncology! ascopubs.org/doi/10.1200/...

Don’t worry this one was developed in China and a lot of good science and scientists exist in other countries that have the other 7+ billion people on the planet. But agree US leadership is at risk but science won’t stop

Long-Term (≥5-Year) Remission and Survival After Treatment With Ciltacabtagene Autoleucel in CARTITUDE-1 Patients With Relapsed/Refractory Multiple Myeloma CARTITUDE-1 evaluated ciltacabtagene autoleucel (cilta-cel) in patients with heavily pretreated relapsed/refractory multiple myeloma (RRMM). We describe overall survival (OS), ≥5-year progression-free...

ascopubs.org/doi/10.1200/... considering the patient population this is extremely impressive, 1/3 of patients progression free at 5 years, glad to have @cityofhope.bsky.social physician Dr. Myo Htut as one of the coauthors. I for one believe cures are possible in #myeloma @tgenresearch.bsky.social

Awesome summary

Using sequencing replicates of the normal cell line COLO829BL, we found that SAVANA shows 13- and 82-times higher specificity than the second and third-best performing algorithms (391x higher than the worse performing one). In practice, this means 10s-1000s less false positives..

One major issue with the X compared to 6k is the increase in failures on turn around that create read2 polyG, easy to spot if you turn on show mate unmapped in IGV and causes a pileup issue in chr2 in a large polyG, but do worry it causes false mapping of read1 in some cases then FP variants

Agree, I suspect it was optimized with the older chemistry, nice to speed runs a bit but would rather get a bit more data. Appreciate the feed back

Are you turning off the adaptive loading option? We never seem to get past the low to mid 70s for P1 rate, even when you load more the loading time just gets shorter

Release DeepVariant 1.9.0 · google/deepvariant DeepVariant: In this version we have updated our training scheme for the HG002 sample with the newly released HG002-T2T truth set which improves accuracy against that truth set. Our labeling metho...

Release of DeepVariant and DeepSomatic v1.9

DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h).

DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.

github.com/google/deepv...

Nanopore direct RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between regulatory features Understanding the interactions between various mRNA features—such as RNA modifications, poly(A) tail length, and splicing—has been highly sought after but remains largely elusive. Here, Kim and Savill...

Excited to share our first study using nanopore direct RNA seq to comprehensively characterize RNA features. We believe that our deep and high coverage datasets should be a nice resource for the field! www.cell.com/cell-genomic...

Like the old Agilent microarrays, we use to strip and get at least two good runs and a third or fourth for development testing.

Imagine an election and you are only voting for your congressional rep, nothing else

Paper only votes, hand counts

Exercise your right to vote today, Canadians! Own your democracy! 🇨🇦🗳️