JPM Healthcare Daily Roundup #JPM2021

The first day of the conference hasn't disappointed, especially if you're a fan of talking cubes. What is this mysterious object and what sorcery is inside?

See disclosures at the end.
The Tempus One, meant to be carried in a doctor's coat or sat at the bedside, is a physical manifestation of @TempusLabs' genomic and phenotypic data-lake. Oncologists can ask One all sorts of questions regarding their patients, though I'm unsure if it'll (...)
(...) just reflex you to a computer after a sufficiently difficult question. I'm sure we'll learn more soon. Has this sort of form-factor been tried before?

I'm just hoping it has adjustable humor/honesty settings like TARS from Interstellar.

Moving right along.
@10xGenomics inundated us w/ new product launches including:

CellPlex - a reagent/software package for sample multiplexing (four samples/channel, up to 60% cost reduction if fully loaded).

Low Throughput - Have 1,000 cells you'd like to run in a pilot study? You're in luck!
Fixed RNA Kit - point-of-collection tissue fixation, compatible w/ targeted or transcriptome workflows

Chromium X (that's an X, not a 10!) - a massive 1-million cell behemoth run on Next GEM, likely for the translational folks?

But, what about spatial #genomics? Read on.
The Visium FFPE Kit enables targeted/#transcriptome work to be run on FFPE samples w/ near fresh-frozen levels of gene sensitivity.

Have archived FFPE tissue on non-Visium slides? No worries, the Visium CytAssist can convert standard slides to Visium-compatible slides.
Coming in 2022, Visium evolves into Visium HD, with a resolution increase from 4X to 1,500X.

Interestingly, no real commentary on 'in situ' imaging. I guess no one wants to be the first to lay out their full range of specs (I eagerly await @agbt).

@GuardantHealth gave me a shock that it plans to move into tissue (!) profiling. I suppose this was an eventuality given that tissue isn't going anywhere - clinician habit, tissue/liquid concordance concerns, etc.

I don't think this will morph into a tumor-informed liquid test.
Finally, we heard about Guardant Reveal, a liquid-only #MRD assay for colorectal cancer (initially), the result of the ongoing Lunar 1 program.

It seems there's no escaping that adding #epigenetic (and fragmentomic) data overtop #ctDNA boosts detection sensitivity.

I missed the Seer talk, but took note that they gained non-exclusive rights to commercialize some of @thermofisher's and @bruker's mass spec portfolio.

#Proteomics, super-resolution optics, & cryoEM all seem like cool places to be right now, though earlier than #NGS.
@illumina's announcements are always fun, though some of my predictions didn't come true this year.

I was mulling a NovaSeq Dx launch, a clear $100-genome roadmap, or a small tool's acquisition to bolster long-read-esque capabilities. What we got was the following (...)
- A 2022 NovaSeq Dx launch window
- A lower-throughput (P1) flow cell for NextSeq 2000 (which is one of the prettiest sequencers I ever did see)
- A metric TON of IVD collaborations for TruSight and others (read: GRAIL MRD)
- A robust tool for backend multi-omics processing (ICA)
@GrailBio moved up its timeline to launch Galleri to 2Q 2021, possibly ahead of the acquisition and far ahead of any clinical utility data?

I'm unsure what the huge rush is, but maybe others have some ideas?
I'm still working my way through @TwistBioscience , @AdaptiveBiotech, and a few others. I'll return to keep adding little sprinkles here and there.

In the meantime, go OSU!

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More from @sbarnettARK

13 Jan
I've gotten a few questions about how the FDA regulates medical devices, chemical reagents, and diagnostic equipment.

Quick Thread 👇
First, understand there are two main regulatory pathways for diagnostic testing:

1. In-Vitro Diagnostic (IVD)
2. Laboratory Developed Test (LDT)

An IVD is an FDA-cleared diagnostic test sold as a self-contained kit.…
Companies wishing to sell IVDs must seek pre-market approval (PMA) from the FDA, which can take roughly 200 days. As I understand it, IVD's must be run on FDA-cleared diagnostic equipment, such as the NextSeq 550Dx, which is FDA-cleared and CE-marked (for Europe).
Read 10 tweets
10 Jan
Tomorrow kicks off the JP Morgan Healthcare Conference, one of the most information-dense and exciting weeks for biotechnology.

Though I’ll miss annual lab tours, I’m excited not to have my shoes destroyed amidst all the shoulder-to-shoulder crowds.
Unlike last year, I’m going to try to give a daily news recap once the US trading session closes (inspired by @aurmanARK). My hope is to aggregate input from folks who can offer alternative takes.
We’ve got our #mARKetUpdate webcast on Tuesday, where I’ll be talking more about my recent blog on earlier #cancer detection as well as plans for including community feedback in the forthcoming white paper.…
Read 6 tweets
5 Jan
A Thread (🧵)

Let's discuss long-read #sequencing, optical mapping, and the implications of a recent study (linked below).

Please view my disclosures at the end. I've intentionally made this thread more technical as I think it's necessary.…
First, let's deconstruct the paper's title: "De Novo Assembly of 64 Haplotype-Resolved Human Genomes of Diverse Ancestry and Integrated Analysis of Structural Variation".

De novo (Latin: "Of New") assembly involves sequencing a genome without the help of a reference.
Assembling a #genome de novo is like solving a jigsaw puzzle without using the picture on the front of the box. You could start with the corners, assemble the edges, and try to fill in the rest using color- or shape-matching methods.

Let me use an analogy.
Read 31 tweets
18 Nov 20
Long-read #NGS obeys Wright's Law.

For every cumulative doubling in sequence data generated across its install base, @PacBio has been able to lower (consumables) costs by roughly 30%, as shown below.

What could this imply about the future of long-read #sequencing?
First, let's acknowledge a Catch-22. Does PacBio need to (a) derive knowledge from platform utilization to lower sequencing costs or (b) lower costs first in order to unlock greater platform utilization?

At present, we believe it's more of the latter. Why?
PacBio's HiFi chemistry and Sequel II optics are relatively nascent (2019). This suggests a lot of near-term headroom left for optimization in these areas.

It's crucial that all long-read users, not just the top 1%, have access to this innovation.…
Read 15 tweets
20 Oct 20
Besides #immunotherapy, how can #CRISPR be used to treat cancer?

Researchers at @CNIOStopCancer just published an exciting proof-of-concept showing how CRISPR can delete cancer-causing gene fusions, selectively killing cancer cells.

I'll elaborate.…
First, let's discuss what gene fusions are. As shown below, fusions result when two genes crash into each other and fuse together.

The resulting protein product is a hybrid. It has some features of Protein A and some of Protein B.

This usually is very bad.
We know that cancer-causing (#oncogenic) fusions have been found in nearly all cancer types. They're more common in pediatric cancers, but still are present in as many as 15-20% of adult cancers.

If present, fusions often are the main drivers of tumor growth.
Read 12 tweets
24 Sep 20
Interesting, Exact Sciences ($EXAS) is halted and spiking up ~15%, likely because of what's going on at the Cowen liquid biopsy conference. I will provide updates.
This is the first time, to my knowledge, Exact has seriously discussed multi-cancer liquid biopsy instead of just colorectal cancer screening via Cologuard. They presented preliminary data evaluating a blood-based multi-cancer test.
The cohort was relatively small, but showed sensitivity of ~85% (true-positive rate) and specificity of ~95% (true-negative rate). This is definitely the highest sensitivity I've seen from a test like this, but also the weakest specificity. Granted, this is early data.
Read 4 tweets

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