Discover and read the best of Twitter Threads about #wgs
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1/ Happy Friday!
Today I am celebrating #scicomm! As of this week, I have contributed 21 articles to the @ASMicrobiology Bugs & Drugs blog! Here's a recap of some of these articles for those who love clinical #microbiology
#IDTwitter @ASCLS @CUAnschutz #MedEd @JClinMicro
Today I am celebrating #scicomm! As of this week, I have contributed 21 articles to the @ASMicrobiology Bugs & Drugs blog! Here's a recap of some of these articles for those who love clinical #microbiology
#IDTwitter @ASCLS @CUAnschutz #MedEd @JClinMicro
2/ First, just a quick note on writing for @ASMicrobiology. Volunteering my time to write has been one of the highlights of the last 2 yrs for me! So grateful for the amazing Bugs & Drugs team, especially @JulieMarieWolf @JClinMicro @ScienceInTheDMV who took a chance on me.
3/
YELLOW FEVER AND FRACTIONAL DOSES
#Publichealth piece discussing the yellow fever outbreak of 2015/16 in Africa & highlighting the amazing work of researchers working on fractional #vaccine dosing. It's an amazing story, full of impressive characters.
asm.org/Articles/2021/…
YELLOW FEVER AND FRACTIONAL DOSES
#Publichealth piece discussing the yellow fever outbreak of 2015/16 in Africa & highlighting the amazing work of researchers working on fractional #vaccine dosing. It's an amazing story, full of impressive characters.
asm.org/Articles/2021/…
As short-read #sequencing (SRS) costs begin to drop again, undoubtedly fueled by a resurgence in competition, I suspect many liquid biopsy providers will add blood-based whole-genome sequencing (WGS) to supplement, or replace, the deep targeted sequencing paradigm.
With a few exceptions, most clinical-stage diagnostic companies build patient-specific panels by sequencing the solid tumor, then downselecting to a few dozen mutations to survey in the bloodstream.
I don't think this approach is going anywhere anytime soon.
I don't think this approach is going anywhere anytime soon.
However useful, this deep-sequencing approach suffers from several challenges:
1. It requires access to tissue.
2. It requires the construction of patient-specific PCR panels.
3. It requires significant over-sequencing ($$$).
4. It introduces a third layer of error (PCR).
1. It requires access to tissue.
2. It requires the construction of patient-specific PCR panels.
3. It requires significant over-sequencing ($$$).
4. It introduces a third layer of error (PCR).
Delighted to share our new study nature.com/articles/s4158… introducing PhasED-Seq out today @NatureBiotech.
A fantastic collaboration from @StanfordMedicine led by Dave_Kurtz & Joanne Soo with @max_diehn to help transform #cancer interception & monitoring by improving #LiquidBiopsy #ctDNA detection of #MRD.
I received an email from @NebulaGenomics today, with a discount code for a $299 genome sequencing offer. Which made me wonder: are they using the already cheaper @MGI_BGI #DNBSEQTx sequencing for this? It would mean they can run it at cost or make a small profit from it.
Then you realise there is "analysis" charge on top of the $299 which you can't untick, so the $299 #WGS 30x genome goes up to $499. Still, at $499, you would find it difficult to make money if you were @NebulaGenomics and you were using something like an @illumina #NovaSeq
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.
biorxiv.org/content/10.110…
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.
biorxiv.org/content/10.110…
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.
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.
Let me use an analogy.
I'm very pleased to announce our publication "Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk paediatric cancer" online today in @NatureMedicine rdcu.be/b76h9 Here's a tweetorial of the main findings 1/22
This research was 7 years in the making & is the first major publication from #ZeroChildhoodCancer, a joint initiative of @KidsCancerInst and Kids Cancer Centre @Sydney_Kids. #Zero is now a national precision medicine program, including all 8 hospitals and 23 research partners /2 
What value does deciphering the whole genome hold for guiding clinical care of children with high-risk cancer? LOTS. Does it provide more accurate diagnoses, more treatment options, better risk stratification? YES. Can it be done fast enough to have a clinical impact? YES. /3
Excited to share our work @NatureMedicine offering a novel framework [MRDetect] for ultra-sensitive cancer monitoring through whole genome mutational integration of cfDNA go.nature.com/2XmxJZv
1/
#LiquidBiopsy #WGS #cfDNA #MachineLearning
👇👇👇
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#LiquidBiopsy #WGS #cfDNA #MachineLearning
👇👇👇
Therapy monitoring is a central pillar of modern medicine. And yet, in many areas of oncology, we lack sensitive monitoring tools for residual disease detection. ctDNA carries the potential to change this, but is scarce in low-burden disease.
The central paradigm in the field aims to overcome ctDNA scarcity through deep targeted sequencing of informative sites. However, we show that limited number of fragments imposes a hard ceiling on cfDNA deep targeted sequencing, with sensitivity limited ~1:1,000 per site.
1/13 While #COVID19 warrants our attention and swift, concerted action, we cannot forget about the existing high global burden diseases like #tuberculosis.
2/13 In ”Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases” preview.tinyurl.com/vyhckyc, @crobinhold1 @Valafarlab & I provide a roadmap for navigating #Illumina coverage bias when #sequencing Mtb #genomes
3/13 We use a #phylogenomic filtering step to remove evolutionary signals isolating systematically low coverage and provide lists of #Illumina #blindspots for seven #sequencing workflows (lib prep + instrument) at single-base resolution
We are excited to share our pub in #EvolutionaryApplications bit.ly/2GH3tzr comparing relatedness estimates for pairing recommendations in critically #endangered #birds from #Aotearoa #NZ 🇳🇿. See this #SciComm 🧵 for more! #Conservation #Genomics #ConGen #ConSERTeam 1/13
Around the 🌏, #conservation breeding programmes strategically pair the least related individuals to enhance recovery. This is like #Tinder for threatened species, only more information goes into pairing than swiping ⬅️ or ➡️. See my #3MT for more! 2/13
It’s important to get the relatedness value right for pairing, because mating between close relatives can result in negative fitness consequences, like ⬇️ hatching success 🐣(see bit.ly/3b4IILO). 3/13
