genomic.social/@a bsky.app/profile/alexphd.bskโฆ Director @cancervariants, VR lead @GA4GH. NHGRI Genomic Innovator. I ๐ open science.
Columbus, Ohio
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Very exciting progress on @ClinGenResource Somatic oncogenicity assessment of NTRK fusions, being presented NOW at #AMP22. Drop by poster G025 (Genetics section) to learn more from @jasonmsaliba about this product of the ClinGen NTRK fusions group!
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Updates to the @CIViCdb resource being presented by @KilanninK RIGHT NOW at #AMP22! Come visit poster G047 in the Genetics section!
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6yo had pinewood derby race today. 3rd place (of 10) first graders, 8th place overall across K-5, very happy.
Comes home, immediately designs car for next year. Looks just like 1st place car this year.
The recipe for success? Red paint, wood, wheels.
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Saw the rare "Anonymous Nyan Cat" in a collaborative Google Doc today. I consider this a good omen for the project.
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Just watched โdonโt look upโ and did a quick search about the movie. What more fitting response to this movie could you find than the top โPeople also askโ questions?
At some point I came to the conclusion that homemade latkes are 100% what #Hanukkah is about and I stand by that assertion.
Thankful for a spouse (and assist from kids) that made a surprise batch for dinner tonight!
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In conjunction with a computed identifier algorithm (Figure 4), the value object design principle enables computed identifiers for VRS objects.
Consequently, Variation from sequences with multiple identifiers (e.g. RefSeq, GENCODE, etc.) resolve to the same computed identifier!
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As value objects, VRS Variation objects representing the same variation on the same sequence are identical anywhere, without prenegotiation between services. This has important implications for federated knowledge exchange.
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Each of these classes is formally specified in a technical terminology and information model, which serves as the foundation of the specification.
This information model is the heart of what makes VRS uniquely suited to computability: value object representation.
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With VRS, you can represent each concept explicitly: a tandem duplication is a form of molecular variation (Allele) and is distinct from systemic variation (Copy Number). VRS also supports SNVs, indels, haplotypes, ranged locations, and cytogenomic variation (paper Figure 2).
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For example, a variant ("NC_000001.10:g.(?_1950843)_(1961741_?)dup") was submitted as a tandem duplication using HGVS to a public database.
Buried as free-text in the submission description there is important context: this was intended to represent a copy number gain.
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Why do we need VRS?
Current standards for representing variation are optimized for human readability. This can sometimes result in conceptual ambiguity, creating challenges for computational search and aggregation of variation across genomic databases and knowledgebases.
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VRS is all about how computers exchange data about biomolecular variation.
Want a compact, easy-to-read structure for describing variants? Use HGVS, ISCN, or SPDI nomenclatures.
Want a computable framework for variation that is precise and extensible? Thatโs what VRS is for.
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@Marc_GeneDoc giving a great talk on the gaps in precision health we need to fill at @GA4GH #9thPlenary. Loved this slide near the end describing the virtuous cycle of Precision Health in a Learning Healthcare System: "We guarantee we'll get it wrong or your money back!"
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This is what Outlook for Mac is like for me. Today, I found out I can reply, forward, or *1984*.
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I choose to believe that @MeCookieMonster is also a prolific web admin and has inadvertently alarmed @BenLangmead on #WorldKindnessDay.
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From the Climate Change Report Card. US gets a score of "Barely Trying", alongside Saudi Arabia and Russia.
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The above is great!
But, if you go to the SPARQL endpoint directly from that result page (shown here), and add the &format=json attribute to the URL...
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After 2 weeks of largely avoiding work emails while on PTO, my first day back appears particularly daunting...
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Turned on this @Apple eMate 300 after a couple decades in storage to teach my kids how to type. Apparently my software licenses need updating. First order of business: connecting this to another computer via serial port...
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Timely.
Will be curious to see what #SocialDistancing measures have been implemented in the courthouse, during the early growth phase of the disease.
๐คthat I am told not to report...
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I think that they are being lenient about that now. From this: youtube.com/watch?v=jLmBi5wvโฆ
When you think that you are #reviewer3 but the manuscript is rejected because the other reviewers had even more extensive concerns.
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That feeling when you submit your conference abstract 10 minutes before the deadline after spending 90 minutes entering authors and affiliations.
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First snow of winter in St. Louis! Hard to focus on work with such nice, thick snow falling outside.
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Great night out with the @GA4GH Genomic Knowledge Standards group after a successful working conference! Definitely looking forward to the plenary and our upcoming variant representation schema.
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Highlighting the "Mo' money, mo' problems of genomics", @lea_starita at #AACR19 describes the alarming growth of observed variants of unknown significance over the last decade, and zooms in on the current state of BRCA1 (according to ClinVar):
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Got settled in at my hotel in preparation for #AACR19, and walked over to @MaxLagers to try their beer selection.
10/10 would kick off a conference this way again.
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Introduction to VMC by @reecehart at #GEMJW19 starts with a discussion of coordinate systems and object types. Extremely motivating example of representation for precise variants by the @GA4GH Genomic Knowledge Standards workstream.
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I'm >1000 lines of code into a PR to fix a one-sentence comment in a paper review, and this is all I can think of:
xkcd.com/1425/
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.@ewanbirney shares all public details for 7th @GA4GH plenary in closing remarks. Looking for a host city!
Did this start recently, like the last day or two? I haven't had this problem in years, and all of a sudden my phone has been lighting up too. I use Project Fi, and enabled their "Filter Spam Calls" feature, and it stopped most. Since then, one call did slip through, though.
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