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Monogenic and polygenic inheritance become instruments for clonal selection
Analysis of blood-derived DNA from participants in the UK Biobank demonstrates that clonal expansions of acquired copy-neutral loss of heterozygosity mutations act on inherited alleles along a chromosome arm by modifying their allelic dosages.
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Jay Shendure
This paper by @s_mccarroll & colleagues is brilliant, particularly the observation that hematopoietic polygenic risk (PRS) predicts the direction of somatic copy number LOH. Apart from cancer-related implications, an amazing natural experiment for PRS!
nature.com/articles/s4158…. pic.twitter.com/r9kjNXgXiF
10d
Greater Seattle Coronavirus Assessment Network (SCAN) resumes COVID-19 testing – PUBLIC HEALTH INSIDER
SCAN is re-launching on Wednesday, June 10th, while upholding the spirit of #ShutDownSTEM. The study’s researchers move forward with their work, including outreach to underserved communities, and recognize the disproportionate impact that COVID-19...
Jay Shendure
Blog post on SCAN restart from @KCPubHealth that includes summary of safety data pulled together by @lea_starita and @LockwoodDNA
publichealthinsider.com/2020/06/10/gre… 4/4
23d
Seroprevalence of SARS-CoV-2 among children visiting a hospital during the initial Seattle outbreak
Children are strikingly underrepresented in COVID-19 case counts. In the United States, children represent 22% of the population but only 1.7% of confirmed SARS-CoV-2 cases. One possibility is that symptom-based viral testing is less likely to...
Massively multiplex single-molecule oligonucleosome footprinting
Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we...
Scientists baffled by decision to stop a pioneering coronavirus testing project
Researchers looking to make tests widely available worry as regulators freeze the team that first identified US community spread.
Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks
Agarwal and Shendure show that deep neural networks can strongly predict mRNA abundance
solely from promoter sequence. The residuals of these predictions facilitate inferences
about the regulatory influence of enhancers, heterochromatic domains, and...
Jay Shendure
Excited for work by the indomitable @vagar112, towards vision of predicting gene expression solely from primary sequence, finally out! Much of variance predicted by promoter seq; residuals help quantify influence of enhancers, heterochromatin, miRNAs, etc
46d
If 80% of Americans Wore Masks, COVID-19 Infections Would Plummet, New Study Says
There’s compelling evidence that Japan, Hong Kong, and other East Asian locales are doing it right and we should really, truly mask up—fast.
Seattle’s Leaders Let Scientists Take the Lead. New York’s Did Not
The initial coronavirus outbreaks on the East and West Coasts emerged at roughly the same time. But the danger was communicated very differently.
Preliminary support for a 'dry swab, extraction free' protocol for SARS-CoV-2 testing via RT-qPCR
The urgent need for massively scaled clinical or surveillance testing for SARS-CoV-2 has necessitated a reconsideration of the methods by which respiratory samples are collected, transported, processed and tested. Conventional testing for SARS-CoV-2...
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Jay Shendure
Preliminary support by @SRsrivatsan for a 'dry swab, extraction free' protocol for SARS-CoV-2 testing via RT-qPCR that would simplify workflows and facilitate scaling. Work led by the remarkable @lea_starita @HelenChuMD & @seattleflustudy @BrotmanBaty team
71d
What Viral Evolution Can Teach Us About the Coronavirus Pandemic
Can we read the virus’s evolutionary tree fast enough to make a difference as we race to limit its spread?
Sci-fate characterizes the dynamics of gene expression in single cells
Gene expression dynamics in single cells are tracked by labeling newly synthesized RNA in indexed cells.
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Jay Shendure
sci-fate! Another terrific single cell method by the remarkable @junyue_cao, combining combinatorial indexing and 4-thiouridine labeling for scalable, concurrent profiling of the whole and newly synthesized transcriptome
80d
New modeling reports suggest positive impact of social distancing measures on COVID-19 epidemic, but more progress needed – PUBLIC HEALTH INSIDER
Reductions in person-to-person contact through a variety of social distancing measures appear to be making a difference in slowing the spread of COVID-19 in King County, but those measures need to continue to succeed in decreasing and delaying the...
Introducing SCAN: the greater Seattle Coronavirus Assessment Network – PUBLIC HEALTH INSIDER
Washington state reported its first case of COVID-19 on January 21st. Since then, government officials and public health experts have been asking: How many more cases are there? And where will the virus show up next? These are important questions....
Jay Shendure
For more see excellent blogpost by @DocJeffD about SCAN: publichealthinsider.com/2020/03/23/int… 5/6
103d
Greater Seattle Coronavirus Assessment Network (SCAN)
SCAN is testing both healthy and sick people to see how the virus is spreading in the Greater Seattle area.
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Jay Shendure
Thrilled to be a part of the team launching the greater Seattle Coronavirus Assessment Network (SCAN) with @KCPubHealth @BrotmanBaty @UWMedicine @fredhutch @seattlechildren. Check it out: scanpublichealth.org 1/6
103d
2
Jay Shendure
And we're back! SCAN has resumed as a research study under a UW IRB from @HelenChuMD and Jan Englund modeled on @seattleflustudy. To participate in helping our community in @KingCountyWA understand what's going on with COVID-19, please see scanpublichealth.org. 1/4
23d
Personal Protective Equipment
The State of Washington is seeking to fill shortages of specific personal protective equipment (PPE) and infection-control products. The Department of Enterprise Services is seeking:
A coronavirus cautionary tale from Italy: Don’t do what we did - The Boston Globe
Many of us were too selfish to follow suggestions to change our behavior. Now we’re in lockdown and people are needlessly dying.
Seattle Flu Study - Swab and Send: Study Protocol for At-Home Surveillance Methods to Estimate the Burden of Respiratory Pathogens on a City-Wide Scale
Introduction. While seasonal influenza and other respiratory pathogens cause significant morbidity and mortality each year, the community-based burden of these infections remains incompletely understood. Understanding the prevalence, epidemiology,...
The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology
Introduction. Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterize, and potentially contain new and emerging influenza...