#gwas — Public Fediverse posts

Hey, gonna try my luck here with something technical:

Anyone has or knows of software or have public code to randomly select SNPs from a population or vcf file based on properties which as MAF, distance to TSS of nearest genes?

I can write something, but I'm hoping to save time here and can't find anything. I need it to do an enrichment analysis where I test real hits from the SNPs vs hits from the random ones.

#genomics #bioinformatics #gwas #academia #science #computationalbiology

[Edit] I think I finally have some winners WITH cell identities, though I had to dig for that part. Thanks!

Anyone working in #Genomics #SingleCell #RNASeq aware of a good data source for human kidney single-cell data that has *labeled* cell types.

We have a #GWAS that the target tissue would be kidneys. I'm stuck doing cell type analyses until I can find some labeled cell type data to connect back to the association data.

[Edit] I think I finally have some winners WITH cell identities, though I had to dig for that part. Thanks!

Anyone working in #Genomics #SingleCell #RNASeq aware of a good data source for human kidney single-cell data that has *labeled* cell types.

We have a #GWAS that the target tissue would be kidneys. I'm stuck doing cell type analyses until I can find some labeled cell type data to connect back to the association data.

[Edit] I think I finally have some winners WITH cell identities, though I had to dig for that part. Thanks!

Anyone working in #Genomics #SingleCell #RNASeq aware of a good data source for human kidney single-cell data that has *labeled* cell types.

We have a #GWAS that the target tissue would be kidneys. I'm stuck doing cell type analyses until I can find some labeled cell type data to connect back to the association data.

[Edit] I think I finally have some winners WITH cell identities, though I had to dig for that part. Thanks!

Anyone working in #Genomics #SingleCell #RNASeq aware of a good data source for human kidney single-cell data that has *labeled* cell types.

We have a #GWAS that the target tissue would be kidneys. I'm stuck doing cell type analyses until I can find some labeled cell type data to connect back to the association data.

[Edit] I think I finally have some winners WITH cell identities, though I had to dig for that part. Thanks!

Anyone working in #Genomics #SingleCell #RNASeq aware of a good data source for human kidney single-cell data that has *labeled* cell types.

We have a #GWAS that the target tissue would be kidneys. I'm stuck doing cell type analyses until I can find some labeled cell type data to connect back to the association data.

#gwas lookup: "Interpret GWAS variant associations across multiple genomics databases"

https://sashagusev.github.io/gwas_lookup/#pos=chr6%3A160540105&build=hg38

#bioinformatics #snp #gwas

SAIGE-GPU — Accelerating Genome- and Phenome-Wide Association Studies using GPUs Open Access

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btag032/8438945

"We developed SAIGE-GPU, a GPU-accelerated version of SAIGE that replaces CPU-intensive matrix operations with GPU-optimized kernels. The core innovation is distributing genetic relationship matrix calculations across GPUs and communication layers. "

#gwas #gpu #bioinformatics

Mapping genes for resilient dairy cows by means of across-breed genome-wide association analysis | BMC Genomics

Data processing and evaluation as well as statistica…
#NewsBeep #News #US #USA #UnitedStates #UnitedStatesOfAmerica #Genetics #AnimalGeneticsandGenomics #Autocorrelation #Dairycattle #general #GWAS #LifeSciences #LinkageDisequilibrium #MDS #Microarrays #MicrobialGeneticsandGenomics #PlantGeneticsandGenomics #Proteomics #resilience #Science #Variance
https://www.newsbeep.com/us/193938/

Mapping genes for resilient dairy cows by means of across-breed genome-wide association analysis | BMC Genomics

Data processing and evaluation as well as statistica…
#NewsBeep #News #US #USA #UnitedStates #UnitedStatesOfAmerica #Genetics #AnimalGeneticsandGenomics #Autocorrelation #Dairycattle #general #GWAS #LifeSciences #LinkageDisequilibrium #MDS #Microarrays #MicrobialGeneticsandGenomics #PlantGeneticsandGenomics #Proteomics #resilience #Science #Variance
https://www.newsbeep.com/us/193938/

For once I did not spend much time on biological networks (maybe inadvisable at a course whose subtitle contains the words "network modeling"), but instead presented SMuGLasso, a sparse multitask group lasso for GWAS in diverse populations that we developed with Asma Nouira and that was published just last week. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012734

SMuGlasso groups SNPs by LD blocks (as done by Alia Dehman, Christophe Ambroise and Pierre Neuvial in 2015), and treats genetically homogeneous subpopulations of a heterogeneous data set as different but interlinked tasks. An additional sparsity constraints allows us to identify population-specific loci.

On simulations, we show that SMuGLasso has much better recall than classical GWAS (at the expense of more false positives, but fewer than other comparison partners).

On real data, we observe that SMuGLasso recovers all the genes identified by a classical GWAS, as well as some that were identified by a meta-GWAS that included our dataset. All in all, only 2 of the 27 identified genes look likely to be false positives.

#machineLearning #genomics #GWAS

"GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations"

https://www.biorxiv.org/content/10.1101/2025.09.03.674075v1?rss=1

#gwas #sv #cnv #structuralvariation

What determines the human gut fungal community? Emily van Syoc, @erdavenport @symbionticism &co present the first #GWAS of human genetic loci that influence the relative abundance of gut #fungi, linking these to disease risk #mycobiome @PLOSBiology https://plos.io/42bCKou

#GWAS #PopulationGenomics #BIAS #PRS academic.oup.com/gigascience/...

EraSOR: a software tool to eli...

#GWAS #PopulationGenomics #BIAS #PRS https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad043/7199403

We are just one week away from Let’s Get Quizzical: Trivia, #Bioblitz & Food by the Gorge, happening on Saturday, August 30, 2025, from 11 AM to 5 PM at #GorgeEsquimaltPark - right outside the Gorge Nature House.

This exciting, #free #FamilyFriendly event is packed with activities for all ages:

🧠 Sustainable Smarts #Trivia – Three rounds of engaging trivia with fantastic #prizes from local favourites like HAVN, Axe & Grind, and Quazar’s Arcade + some of Esquimalt's finest, Warm Gift Shop, Errant Empire, and 4Cats Esquimalt!

🌿 Bioblitz #CommunityScience – Join guided walks and help document local plants, bugs, birds, and more on iNaturalist.

🐞 #BugWalk & #PlantWalks – Led by the #GWAS team to connect you with the biodiversity of our beautiful #GorgeWaterway.

🎟️ Passport to Science Wrap-Up – Explore hands-on science with our friends from Passport to Science, Victoria Bug Zoo, Centre of the Universe, and more!

And, of course… delicious food all day long:
🍦 Hazel’s Ice Cream – Serving cold treats and smiles.
🌯 Greek on the Street – Flavour-packed eats and street-side classics.
🥗 Naked Dressings – Fresh, healthy bites made with love.

Whether you are coming for the science, the food, the trivia, or simply to enjoy the community atmosphere, there is something for everyone. So, choose your favourite method of Active Transportation and come get quizzical on Saturday, August 30!

Support Your Local #NatureHouse
This #fundraiser helps support much-needed improvements to the Gorge Nature House, enabling us to continue providing #environmental #education and #CommunityPrograms for years to come.

Mark your calendars, bring your friends and family, and come celebrate the Gorge with us!

Learn More →
http://triviabythegorge.eventbrite.com

Unable to make the event but still want to support the cause?
No problem – Donate today!
https://www.gorge.ca/donate?link_id=14&can_id=885c887d51f4f2992844bbc18a1523b7&source=email-one-week-until-lets-get-quizzical-trivia-bioblitz-food-by-the-gorge&email_subject=_-one-week-until-lets-get-quizzical-trivia-bioblitz-food-by-the-gorge-_&&

#Saanich #VictoriaBC #Esquimalt #YYJ #Songhees #VancouverIsland #VanIsle #PacificNorthwest #PNW #Nature #HandsOnLearning #CitizenScience #YYJParks #AllAges #InclusiveEvents #AccessibleEvents #FreeEvent #FunAtThePark #Naturalists #LearnAboutNature #CommunityEvent #CommunityBuilding

Need an overview before the webinar? Here are 2 links from the DecodeME website:

1. Initial DecodeME DNA Results:

https://www.decodeme.org.uk/initial-dna-results/

2. X marks the spot where ME/CFS biology can be discovered:

https://www.decodeme.org.uk/x-marks-the-spot/

@mecfs

#MEcfs #PwME #DecodeME #GWAS

🚨 DecodeME Genetic Results Webinar tomorrow, Thursday, Aug 14, 2:30 PM BST

Register here:
https://us02web.zoom.us/webinar/register/WN_C82NbFK_TYGnJ_T6edmV-w#/registration

(registration link will show time in your time zone)

Note from DecodeME:
"There are limited spots to join on Zoom (registering does not guarantee a spot).

Don’t worry though, we will be recording it and we will also be sharing it live on Facebook at the time."

@mecfs

#MEcfs #PwME #DecodeME #GWAS

💊 Think your prescription changes are random? Your genes might be calling the shots.

🔗 Genome-wide associations spanning 194 in-hospital drug dosage change phenotypes highlight diverse genetic backgrounds in concurrent drug therapy. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.042

📚 CSBJ Smart Hospital: https://www.csbj.org/smarthospital

#Genomics #Polypharmacy #PersonalizedMedicine #Pharmacogenomics #DrugSafety #GWAS #PrecisionMedicine #Pharmacology #Genetics #MedTech

"Lack of ME research because of ‘medical misogyny’, says top scientist"

https://www.thetimes.com/uk/scotland/article/chris-ponting-misogyny-me-research-c09hp0hfg

"Professor Chris Ponting, who led a groundbreaking study into the disease (DecodeME) says it is 'highly stigmatised and incredibly female-biased'"

"…clinicians and scientists should be asking why his work was not done 15 years ago"

#MEcfs #PwME #GWAS #Genetics #DecodeME

Association of myalgic encephalomyelitis / chronic fatigue syndrome (#ME / #CFS) with genetic mutations found. Preprint. #GWAS https://www.research.ed.ac.uk/en/publications/initial-findings-from-the-decodeme-genome-wide-association-study-

#Stutter associated with mutations in specific neurologically important genes.
#gwas
https://www.science.org/content/article/genome-wide-study-makes-quantum-leap-understanding-stuttering

SciTech Chronicles.. . . . . .May 8th, 2025

https://bit.ly/stc051425

#vertebra #imaging #tegu #oVert #LMR #Maganese #prismatic #lithium-ion #obsessions #compulsions #GWAS #hypothalamus #Bespoke #protein #catalysts #"de novo protein design" #"smart fabric" #comfort #durability

SciTech Chronicles.. . . . . .May 8th, 2025

https://bit.ly/stc051425

#vertebra #imaging #tegu #oVert #LMR #Maganese #prismatic #lithium-ion #obsessions #compulsions #GWAS #hypothalamus #Bespoke #protein #catalysts #"de novo protein design" #"smart fabric" #comfort #durability

Huge meta-analysis identifies many new mutations that influence #osteoarthritis in different joints. Several of the pathways involved contain proteins that are already drug targets in other diseases -> potential new osteoarthritis treatments. #GWAS https://www.nature.com/articles/s41586-025-08771-z

OK brains trust: does anyone know a tool to simulate a set of genetic variants given a GRM, such that simulated samples have a very similar GRM? #quantgen #gwas #genomics

Following the NASEM report, we updated the population descriptors and piloted what is currently reported in the literature. You are still on time to participate in our survey regarding population descriptors
📝 tinyurl.com/yc6wwx53
📷 Share with
#gwas
colleagues

NEWS! Check our wrap-up about #ashg24 https://shorturl.at/WcTiz

Something is missing? Let us know!

🙌 Thanks, ASHG, for giving us the floor to share updates with #genetics community, delivered by our colleague @mariacerezo.bsky.social

#OpenAccess #gwas #gwasdatahero

Stronger together @ebi.embl.org @NIH

#Genomics #SingleCell #GWAS #Genetics

Anyone out there using tools to convert GWAS outputs to likely affected genes to potential cell types in single-cell RNA-Seq data?

There are a few options I've looked through and they... are not easy to deploy or use. The answer I've gotten so far in other networks is "no great options," but I'm not so sure that's true anymore.

Unlocking the #genetic secrets of #strawberries for superior fruit quality.

#agriculture #GWAS #QTL

https://phys.org/news/2024-08-genetic-secrets-strawberries-superior-fruit.html

New lab preprint: GWAS on crossover dynamics in pigs led by Cathrine Brekke. We explored individual variation in rate, positioning and interference and found a few significant loci in females🐷:

📈👯‍♀️ Rate & interference associated with RNF212 (+ small rate effects at CTCF & REC114/REC8/CCNB1IP1)

📌 Broad-scale positioning at MEI4, SYCP2, PRDM9 (+ small effects at ZCWPW1 & ZCWPW2)

#meiosis #pigs #GWAS #recombination #meiosis4eva

https://biologists.social/@biorxivpreprint/112673500288980099

Are you going to #eshg? Join our workshop TODAY
https://shorturl.at/zYurA and learn how to:

📰Prepare your data for submission to the
@gwascatalog
and
@PGSCatalog

✅Access harmonised #gwas #SumStats and scores

🧮Calculate scores from existing PGS in new samples using PGSC_calc?

Are you going to #eshg? Join our workshop TODAY
https://shorturl.at/zYurA and learn how to:

📰Prepare your data for submission to the
@gwascatalog
and
@PGSCatalog

✅Access harmonised #gwas #SumStats and scores

🧮Calculate scores from existing PGS in new samples using PGSC_calc?

Are you going to #eshg? Join our workshop TODAY
https://shorturl.at/zYurA and learn how to:

📰Prepare your data for submission to the
@gwascatalog
and
@PGSCatalog

✅Access harmonised #gwas #SumStats and scores

🧮Calculate scores from existing PGS in new samples using PGSC_calc?

Sweet trade-offs: Unraveling the #genetic puzzle of #strawberry flavor and yield.

#genomics #agriculture #QTL #GWAS

https://phys.org/news/2024-05-sweet-offs-unraveling-genetic-puzzle.html

Research reveals key #genetic factors in snap #bean pod traits.

#phaseolus #GWAS #agriculture

https://phys.org/news/2024-05-reveals-key-genetic-factors-snap.html

Гений Бетховена: генетическая предрасположенность или случайность

Одним из аспектов, изучаемых генетикой, является наследственность. Физиологические особенности, такие как цвет глаз, цвет волос, рост, комплекция, предрасположенность к определенным заболеваниям, могут передаваться из поколения в поколение. Учитывая это, ученые также пытались понять, существуют ли какие-то генетические факторы, влияющие на навыки человека. Если родители обладают удивительными, к примеру, математическими навыками, передастся ли это их ребенку? Многие ученые уверены, что да, однако полноценных материальных подтверждений этому мало. Порой результаты исследований и вовсе говорят об обратном. Ученые из Медицинского центра Вандербильтского университета (США) изучили ДНК великого композитора Людвига ван Бетховена, извлеченное из его волос, и попытались оценить его генетическую предрасположенность к музыке. Как ученые искали музыкальный дар Бетховена, что им удалось найти, и есть ли связь между генетикой и навыками? Ответы на эти вопросы мы найдем в докладе ученых.

https://habr.com/ru/companies/ua-hosting/articles/803511/

#Бетховен #музыка #навыки #талант #генетика #ДНК #секвенирование_генома #PGI #GWAS #человек #мозг #способности

Mapping genetic influences on the infant brain: A chat with Rebecca Knickmeyer

https://www.spectrumnews.org/opinion/q-and-a/mapping-genetic-influences-on-the-infant-brain-a-chat-with-rebecca-knickmeyer/

#diffusiontensorimaging #genetictesting #brainimaging #autism #GWAS #Q&A #MRI

Mapping genetic influences on the infant brain: A chat with Rebecca Knickmeyer

https://www.spectrumnews.org/opinion/q-and-a/mapping-genetic-influences-on-the-infant-brain-a-chat-with-rebecca-knickmeyer/

#diffusiontensorimaging #genetictesting #brainimaging #autism #GWAS #Q&A #MRI

Mapping genetic influences on the infant brain: A chat with Rebecca Knickmeyer

https://www.spectrumnews.org/opinion/q-and-a/mapping-genetic-influences-on-the-infant-brain-a-chat-with-rebecca-knickmeyer/

#diffusiontensorimaging #genetictesting #brainimaging #autism #GWAS #Q&A #MRI

Mapping genetic influences on the infant brain: A chat with Rebecca Knickmeyer

https://www.spectrumnews.org/opinion/q-and-a/mapping-genetic-influences-on-the-infant-brain-a-chat-with-rebecca-knickmeyer/

#diffusiontensorimaging #genetictesting #brainimaging #autism #GWAS #Q&A #MRI

Now out in G3: "Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems", our GWAS of bone quality traits (and body mass, because, you know, if you weigh a chicken you have to GWAS it) in laying hens. With collaborators from SLU, the Roslin Institute and University of Granada. @DJ_de_Koning

https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkac302/6855652

#GWAS #QuantitativeGenetics #AnimalScience #AnimalGenetics

No evidence for link between #complement C4 and #schizophrenia!

An impressive #medRXiv study in ~70k blood samples fails to detect association between #C4 genes or protein at birth and schizophrenia later in life. This is interesting because the strongest genome-wide association for schizophrenia, found in the #MHC region, has so far been attributed to C4. May the search for other loci continue, I cannot wait to see the #GWAS mystery of schizophrenia unfold!

https://www.medrxiv.org/content/10.1101/2022.11.09.22281216v1

Mutations disrupting chromatin interactions contribute to autism

https://www.spectrumnews.org/news/mutations-disrupting-chromatin-interactions-contribute-to-autism/

#SimonsSimplexCollection #whole-genomesequencing #denovomutations #geneexpression #sequencing #autism #News #GWAS

Maternal genetics may confound studies of autism’s link to prenatal factors

https://www.spectrumnews.org/news/maternal-genetics-may-confound-studies-of-autisms-link-to-prenatal-factors/

#antidepressants #commonvariants #schizophrenia #environment #pregnancy #anxiety #autism #News #ADHD #GWAS

Information loss may weaken autism genetic scores

https://www.spectrumnews.org/news/information-loss-may-weaken-autism-genetic-scores/

#autism #News #GWAS #SNPs

Autism and the complete human genome: Q&A with Evan Eichler

https://www.spectrumnews.org/opinion/autism-and-the-complete-human-genome-qa-with-evan-eichler/

#whole-genomesequencing #copynumbervariation #denovomutations #geneexpression #genetictesting #genenetworks #rarevariants #epigenetics #15q11-13 #Opinion #16p11.2 #GWAS #QA

X chromosome exerts extra influence on brain development

https://www.spectrumnews.org/news/x-chromosome-exerts-extra-influence-on-brain-development/

#commonvariants #geneexpression #brainimaging #theoryofmind #sequencing #brainsize #autism #cortex #News #GWAS #SNPs #MRI #sex

Mutations in the noncoding genome contribute to autism

https://www.spectrumnews.org/news/mutations-in-the-noncoding-genome-contribute-to-autism/

#SimonsSimplexCollection #whole-genomesequencing #denovomutations #geneexpression #News #GWAS