Malachi Griffith

We should definitely add to the list of things we need to catch up on!

Adding @obigriffith.bsky.social who is much more involved than I. We have several long running collaborations relating to canine and feline cancer genomics and development of improved treatments for companion dogs in collaboration with vet oncologists: Dr. Shirley Chu and Dr. Jeff Bryan.

But the authors do not name the assay used so its unclear...

While looking for more details I also noticed that they include highlighted copies of full PDFs for 11 other papers as Supplementary Data. These correspond to a literature review. I'm surprised the journal allowed that.

The paper is a case report about a single pediatric case. From the wording there it almost sounds like the tumor has all three variants. That would be notable, but is not commented on in the paper. I suspect instead the result comes from an assay that doesn't resolve or report a specific AA change.

Came across this paper as the source of an evidence submission in CIViC for clinical significance of V600 mutation in secondary histiocytic sarcoma. A couple things stood out. First, that they report ("Mutation in exon 15 of BRAF V600 (V600E, V600K and V600R) was detected") doi.org/10.1186/s128....

Single-cell T-cell receptor repertoire profiling in dogs - PubMed Spontaneous cancers in companion dogs are robust models of human disease. Tracking tumor-specific immune responses in these models requires reagents to perform species-specific single cell T cell receptor sequencing (scTCRseq). scTCRseq and integration with scRNA data have not been demonstrated on c …

I don't think so? ... There are 5-6 competing reference genome builds if that helps. :). To do single cell TCRseq in dogs we had to create our own 10x compatible reagent. pubmed.ncbi.nlm.nih.gov/38649520/

CIViC automatically makes connections to relevant resources that aid interpretation: ClinGen Allele Registry, GNOMAD, ClinVar, MyVariantInfo, OpenCRAVAT, various computational predictors, etc.

Once entered into CIViC by a curator (both the clinical/experimental evidence and genomic variant identity) they appear in a provisional status. An additional CIViC curator (with editor training) reviews and approves the curations.

These evidence lines describe the clinical significance of MEN1 resistance mutations for the therapy collectively as well as evidence for specific variants such as MEN1 T344M.

They follow up with extensive molecular diagnostics, in vitro functional work, in vivo models, and computational predictions to characterize somatic resistance variants that emerge under treatment with revumenib. The paper supports 8 structured evidence records in CIViC: civicdb.org/sources/5461...

MEN1 mutations mediate clinical resistance to menin inhibition - Nature Somatic mutations in MEN1 are identified in patients with leukaemia treated with a novel chromatin-targeting therapy, and the mechanism by which these mutations mediate therapeutic resistance&nbs...

A nice paper that acts as a great exemplar for curation of clinical variant information in CIViC (civicdb.org). www.nature.com/articles/s41.... The authors report on a clinical trial (evaluating the menin inhibitor revumenib in acute leukemia).

I also submitted a help desk ticket and got the same auto-reply. But a few hours ago, I got a human reply stating that they are aware of the problem and working to resolve it.

Yes, you can delegate to another person with an account. Our grants team has a shared account set up. Go to your profile settings to find this option. We are doing this for the Other Support doc. Grants team exports from another system and then imports it to Sciencv.

For convenience, here is the notice grants.nih.gov/grants/guide... describing the requirement to use sciencv for all submissions *on or after Jan 25, 2026*. Quite a few things are due on Jan 25. For those submissions we must use this system for Biosketch and Other Support docs.

It was working more smoothly last week but over the past three days I have been getting constant errors. Almost unusable. Since every submitted application will require use of this system (starting Jan 25) presumably it is experiencing a significant increase in users that it is unable to handle.

If you are submitting an NIH grant in February, you will be required to use SciENcv to prepare you biosketch.

IT IS MUCH WORSE THAN YOU CAN POSSIBLY IMAGINE.

Set aside *at least* 4 hours just to transfer an existing an biosketch into SciENcv.

DGIdb Feature Sets Evaluation Below is a list of proposed features currently under consideration for inclusion in the next major release of DGIdb. Each feature is grouped by category and includes a brief description. We ask that y...

Help the DGIdb development team understand how we can better promote hypothesis generation and interaction data sets for the biomedical and clinical research community. Take 5 minutes to share how you use DGIdb and what we can improve for your research:

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The ITCR Training Network (ITN) www.itcrtraining.org develops training materials for informatics and research.

We have a short survey ~3-9 min about your experience & preferences for learning as a researcher. Previous engagement not required!

xiar7j-itn.shinyapps.io/itn_follow_up/

📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!

🔹Join a research group in our department
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Apply here: t.co/B7SLZzQFKu

GA4GH April Connect 2026 registration and session proposal submissions are now open!

The meeting will take place from 14 to 17 April 2026 in Montreal, Canada. We invite the GA4GH community to submit session proposals by 30 January.

Learn more: broadinstitute.swoogo.com/connect26/10...

(2026) RNA-seq Analysis: Saskatoon, SK - Bioinformatics.ca

It will also be delivered in parallel using a distributed in-person model in Saskatoon. bioinformatics.ca/workshops-al...

(2026) RNA-seq Analysis: Toronto, ON - Bioinformatics.ca

Excited to announce that we will be delivering a Canadian Bioinformatics Workshop (CBW) covering RNA-seq analysis and general bioinformatics this summer in Toronto. Hosted by Ontario Institute for Cancer Research (OICR). bioinformatics.ca/workshops-al...

The open access resource CIViCdb.org (Clinical Interpretation of Variants in Cancer) has just passed 11,000 evidence statements! That's 11k times a domain expert reviewed a paper and used the CIViC curation interface to create a structured entry for clinical relevance of a specific somatic variant.

Our first curated draft somatic structural variant benchmark for the new GIAB PDAC tumor cell line HG008-T is at ftp-trace.ncbi.nlm.nih.gov/ReferenceSam..., based on extensive short+long read sequencing data described in doi.org/10.1101/2024.... Feedback to improve future versions is very welcome!