RT @: @chrisdwhelan presenting on the transformative potential of #proteomics in #UKBiobank for accelerated genetic targets and better treatment options for #health find out about the project here: https://ukbiobank.ac.uk/learn-more-about-uk-biobank/news/uk-biobank-launches-one-of-the-largest-scientific-studies…

If you are interested in #PhD #AI #machinelearning #retina #ophthalmology #ukbiobank

Check out this fully funded PhD at University of Leicester working with Dr Mervyn Thomas

Institute for Precision Health PhD Studentships | Postgraduate research | University of Leicester
https://le.ac.uk/study/research-degrees/funded-opportunities/iph

Deadline approaching this weekend

Experimenting with running analyses on the UK Biobank cloud platform (RAP). By my estimates a case/control GWAS of the TOPmed imputation in 380k samples, with minor allele count < 20 as the only QC and 11 covariates, would cost about £90 to run.

that is actually cheaper than it would cost on my institutional cluster if I had to pay for every core hour...but I don't. #UKBiobank

I've made a Nextflow workflow for processing UK Biobank phenotype releases into a DuckDB database.

- fields are organised into tables by category
- built-in data dictionary
- work with the whole dataset in R/python without loading it all into memory.

https://github.com/mja/ukb-release-nf #UKBiobank #DuckDB #Nextflow

asked #biostars https://www.biostars.org/p/9554494/ #UKBiobank #dnanexus #wdl "UKBiobank / DNANexus. Working with WDL and directories."

Polygenic architecture of rare coding variation across 400,000 exomes https://www.medrxiv.org/content/10.1101/2022.07.06.22277335v2 #genomics #genome #burden #exome "Here, we quantify the heritability explained by gene-wise burden of rare coding variants and compare the genetic architecture of common and rare variation across 22 common traits and diseases in 400,000 #UKBiobank exomes"

More evidence of increased risk of new cardiovascular disease and death after #Covid19 #UKBiobank

https://news-sky-com.cdn.ampproject.org/c/s/news.sky.com/story/amp/unvaccinated-covid-patients-at-greater-risk-of-death-for-at-least-18-months-after-infection-12789515

A lot of that was already happening with COVID19 Latiflow/PCR testing, so we now have an educated population that knows how to do it, so we have a chance of turbo-boost biobanking projects like the #UKBiobank with systematic sample collections with regular intervals.

In a place like the UK, where the #UKBiobank has detailed information of about 500,000 people's health and various 'omic profiles of their blood and other samples, and given the fact that DNA/RNA Sequencing is getting cheaper and cheaper,

Tidying up my pre-holidays yak shaving, which was to extract a full UK Biobank data release, group fields into tables for each category, and store all the tables in a DuckDB database (bonus is the data dictionary also gets stored as a table).

Thousands of fields at your fingertips without loading the whole dataset into memory. #UKBiobank #DuckDB

https://www.nature.com/articles/s41588-022-01225-6 "Powerful, scalable and resource-efficient meta-analysis of #rareVariant associations in large whole genome sequencing studies" #wgs #genetics #genomics #bioinformatics #MetaSTAAR performs rare variant meta-analysis at scale and produces results comparable to using pooled data. We further demonstrate that MetaSTAAR is scalable to biobank-scale cohorts through meta-analysis of #TOPMed WGS data and #UKBiobank WES data of ~200,000 samples.

The UK Biobank had to remind everyone by email that they should not upload patient data to Github. This reminds me of the emails I used to get from my apartment reminding people not to flush random items such as noodles & diapers down the toilet. #ukbiobank #privacy #security

RT @jsantoyo@twitter.com

Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. #UKbiobank #GenotypeInputation #WGS @biorxivpreprint@twitter.com
https://www.biorxiv.org/content/10.1101/2022.11.28.518213v1

🐦🔗: https://twitter.com/jsantoyo/status/1605331678779637763

Low coverage WGS + UKB imputation reference panel (based on 150k whole genomes) is a great combo.

RT @jsantoyo@twitter.com

Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. #UKbiobank #GenotypeInputation #WGS @biorxivpreprint@twitter.com
https://www.biorxiv.org/content/10.1101/2022.11.28.518213v1

🐦🔗: https://twitter.com/jsantoyo/status/1605331678779637763

We updated our manuscript "Lipoprotein profile and metabolic fine-mapping of genetic lipid risk loci" using 98,000 samples of the #UKBiobank
#Nightingale
data on#medRxiv
https://medrxiv.org/content/10.1101/2022.06.12.22276286v2 - here the new key figure, annotated by my colleague Hani Najafi-Shoushtari

RT @uk_biobank@twitter.com

We hope you enjoyed the #UKBiobank winter Scientific Conference as much as we did yesterday! #thankyou to all our fantastic speakers and everyone who joined online and in London! If you you missed it catch up on all the talks now here: https://video.silverstream.tv/event/gZQeUBcM #UKBSC22

🐦🔗: https://twitter.com/uk_biobank/status/1601184337197641728

RT @uk_biobank
Researchers in Sydney @syd_health found that several one minute bursts of activity is associated with reductions in premature death through using #UKBiobank activity data @M_Stamatakis #research #health https://twitter.com/syd_health/status/1600988069272113152

RT @uk_biobank@twitter.com

1 week until the #UKBiobank Scientific Conference - open to all! Join us to find out how our data can facilitate your research to tackle major health issues facing us - book your place today! http://ow.ly/SZiq50LPKZF #UKBSC22

🐦🔗: https://twitter.com/uk_biobank/status/1598256900608516098

https://www.biorxiv.org/content/10.1101/2022.11.28.518213v1 #lowCoverage #ngs #genomics #ukBiobank "#Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes" "The release of whole genome sequencing data for 150,119 UK Biobank (UKB) samples represents an unprecedented opportunity to impute lcWGS with high accuracy. However, despite recent progress, current methods struggle to cope with the growing numbers of samples and markers in modern reference panels, resulting in unsustainable computational costs. "

Question for folks working in the UK Biobank -- Is there a variable that just indicates whether a participant ever tested positive for #COVID19?

I know there's the seroprevalence / blood sampling substudy, but wondered about just straight self-report? #UKBB #UKBioBank