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Rapid whole genome (
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🧬" title="DNA" aria-label="Emoji: DNA">) sequencing (rWGS) is one of the most exciting (and benevolent) collisions of #AI and #genomics I can think of.
rWGS can diagnose a critically ill child in minutes where previously it took years. https://www.illumina.com/company/news-center/feature-articles/project-baby-bear-interview.html">https://www.illumina.com/company/n...
rWGS can diagnose a critically ill child in minutes where previously it took years. https://www.illumina.com/company/news-center/feature-articles/project-baby-bear-interview.html">https://www.illumina.com/company/n...
A few years ago, Illumina ($ILMN) and Rady Children& #39;s Hospital ( @RadyGenomics) collaborated to offer sequencing services for diagnosing critically-ill infants and toddlers.
Roughly 70% of rare diseases are genetic and they can take five years to diagnose.
Roughly 70% of rare diseases are genetic and they can take five years to diagnose.
As sequencing costs dropped and #AI got faster, this collaboration became Project Baby Bear: a pilot study for rWGS& #39;s diagnostic yield, clinical utility, and health economics in practice.
Several innovative companies joined Rady& #39;s in creating a rapid diagnostic pipeline.
Several innovative companies joined Rady& #39;s in creating a rapid diagnostic pipeline.
@Clinithink contributed a natural language processing ( #NLP) system to scour medical literature and the patient& #39;s EHR. Traditionally, this process would be carried out manually. https://www.clinithink.com/life-science ">https://www.clinithink.com/life-scie...
Genomic data would be fed to Diploid& #39;s ( @diploidgenomics) AI-engine, MOON, which can suggest a causal #DNA variant out of ~45 million in just about five minutes.
This result would be verified on Fabric Enterprise; software by @FabricGenomics.
http://www.diploid.com/moon ">https://www.diploid.com/moon"...
This result would be verified on Fabric Enterprise; software by @FabricGenomics.
http://www.diploid.com/moon ">https://www.diploid.com/moon"...
After the pilot, Rady& #39;s rWGS was covered by Blue Shield of California (~$5,000).
Resurfacing, @ARKInvest believes #AI-accelerated #genomic diagnostics should be less expensive and more accessible in local hospitals. You shouldn& #39;t need to travel to receive the best care.
Resurfacing, @ARKInvest believes #AI-accelerated #genomic diagnostics should be less expensive and more accessible in local hospitals. You shouldn& #39;t need to travel to receive the best care.
So, where can we go from here?
A 2019 @AJHGNews article noted that the rare disease solve rate was <50% when using short read rWGS. The authors argued this rate could increase on long read systems given their ability to decipher hard-to-read variants. https://www.nature.com/articles/s10038-019-0671-8">https://www.nature.com/articles/...
A 2019 @AJHGNews article noted that the rare disease solve rate was <50% when using short read rWGS. The authors argued this rate could increase on long read systems given their ability to decipher hard-to-read variants. https://www.nature.com/articles/s10038-019-0671-8">https://www.nature.com/articles/...
For visual learners, @PacBio has a webinar on this topic ( https://tinyurl.com/y3ly77hg ).
Interestingly,">https://tinyurl.com/y3ly77hg&... Pacific Biosciences and Leiden University ( @LUMC_Leiden), another hospital using Diploid& #39;s MOON, have a long-read/diagnostic summit series called SMRT Leiden.
Interestingly,">https://tinyurl.com/y3ly77hg&... Pacific Biosciences and Leiden University ( @LUMC_Leiden), another hospital using Diploid& #39;s MOON, have a long-read/diagnostic summit series called SMRT Leiden.
Earlier this year, Invitae ( @Invitae) acquired Diploid to (a) accelerate and lower the cost of its whole exome/genome services and (b) to democratize access to MOON for children& #39;s hospitals of all sizes. https://ir.invitae.com/news-and-events/press-releases/press-release-details/2020/Invitae-Acquires-Diploid-Maker-of-Artificial-Intelligence-Engine-to-Enable-Clinical-Diagnosis-Using-Whole-Genome-Sequencing-in-Minutes/default.aspx">https://ir.invitae.com/news-and-...
Given the lower CapEx of PacBio sequencers and cost-declines associated w/ compute, we think some centers could profitably integrate decentralized long-read rWGS services, analyzable over the cloud w/ MOON.
Others have the flexibility to send samples to Invitae& #39;s central lab.
Others have the flexibility to send samples to Invitae& #39;s central lab.
Moreover, we think Invitae& #39;s integration of genetic counseling AI / clinical workflow management tools ( @cleargenetics), investments in telemedicine integration, and focus on rationalizing price, could galvanize rWGS adoption. https://ir.invitae.com/news-and-events/press-releases/press-release-details/2019/Invitae-to-Acquire-Clear-Genetics/default.aspx">https://ir.invitae.com/news-and-...
Altogether, rWGS is one of the most benevolent, impactful collisions of different areas of innovation and collaboration among various companies. #NGS #AI
Other Source(s):
https://www.radygenomics.org/tag/illumina/
https://www.radygenomics.org/tag/illum... href=" http://blog.diploid.com/
https://blog.diploid.com/">... href=" https://programs.pacificbiosciences.com/l/1652/2020-04-26/41txyd">https://programs.pacificbiosciences.com/l/1652/20... https://www.healthcarefinancenews.com/news/blue-shield-california-cover-whole-genome-sequencing-critically-ill-children">https://www.healthcarefinancenews.com/news/blue...
https://www.radygenomics.org/tag/illumina/
NOTE:
A lab/hospital using PacBio, or another long-read platform, would need an LDT/certification to use such a system for diagnostic purposes as none currently are FDA cleared/CE-marked for diagnostic purposes.
A lab/hospital using PacBio, or another long-read platform, would need an LDT/certification to use such a system for diagnostic purposes as none currently are FDA cleared/CE-marked for diagnostic purposes.
