If you want to learn more about

- complex traits;
- #GWAS;
- #polygenic scores,

I have created a playlist in youtube with some great lectures and discussions from Broad Institute's Medical Population Genetics department.

Check it out: https://youtube.com/playlist?list=PLSTeUJbSJXfnUjstgtx2cTKWsCBJpnvGy

Scientists narrow down pool of potential #height #genes.

#development #GWAS #chondrocytes

https://medicalxpress.com/news/2023-04-scientists-narrow-pool-potential-height.html

New preprint by
Carl Veller and myself on the interpretation of population and family-based genome-wide association studies in the presence of confounding

https://www.biorxiv.org/content/10.1101/2023.02.26.530052v1

#GWAS interpretation is tricky, for three broad reasons: indirect effects of relatives, genetic confounding, and environmental confounding—where genetic confounding (long-distance LD) arises due to population structure, assortative mating, and selection. #EvolgenPaper

Genetic cause identified for #MIS_C. “Inborn errors of OAS–RNase L in SARS-CoV-2–related multisystem inflammatory syndrome in children.” #COVID #Genomics #GWAS h/t @holden https://www.science.org/doi/10.1126/science.abo3627

Decently exciting: trying to run my first #GWAS this month (hopefully), on fungicide tolerance in the phytopathogen Leptosphaeria maculans. Using PLINK 1.9, I guess it’s pretty good? Let me know if you have any essential tips or tricks!

(I know I need a kinship matrix or major PCAs plus phenotypic batch structure as covariates)

@benruisch How about a #gwas ,😛

Happy new year and a new "stupid" #GWAS question. Did someone ever try to control for PARENTAL socioeconomic status #SES (at conception) when running a GWAS? This type social environment was there before children's genome, right... I found a paper by Wu et al 2022 controlling for participants own household income and education to adjust for #regionaldifferences https://www.pnas.org/doi/full/10.1073/pnas.2117312119 Would such a control make sense and between family GWAS hits more similar to within #siblings GWAS?

RT @DrChoueiri@twitter.com

2/ First, we analyzed all-grade and high-grade irAEs in a cohort of 1,751 patients from @DanaFarber@twitter.com treated with ICIs, spanning >12 cancer types and evaluated the association of genome-wide loci with such events #GWAS.

🐦🔗: https://twitter.com/DrChoueiri/status/1603817690052935680

The advantage on #GWAS is that you can explore the genetic determinism of traits which are not polymorphic inside a population. Also it is not affected by #LinkedSelection and you can detect the precise sites which have shifted in directional selection.

Two shortcomings : 1) You can only study #homoplasy (i.e convergent traits). 2) You can only detect sites associated to a trait in protein coding genes (for now). (2/N).

Last december I discovered a great method that can detect shifts in the direction of #selection associated to
phenotypic traits.

doi.org/10.1093/molbev/msac247

I like to think of it is as a #Phylogenetic #GWAS. If you give a trait, for instance #echolocation, you can see which site in which protein coevolved with this trait. Afterwords, you can also verify that genes for which you find a #coevolution actually makes sense regarding the trait. (1/N)

"There is a flawed assumption that when designing a
genome-wide association study of disease, stratifying a standard genome panel sample by race helps to detect meaningful genetic
differences. Rather,
stratifying analyses by race, can introduce bias that reinforces essentialist
notions of biological race . biased samples
and standard genomic panels lead to ascertainment
bias when assessing non-European populations"
https://doi.org/10.1016/S0140-6736(22)02040-2
#GWAS #racebias #racialessentialism

Latest publication from when I was working at the UMC Utrecht: https://www.nature.com/articles/s44161-022-00171-0

Bulk #RNAseq of 654 patients with advanced carotid plaques. This data yielded five plaque types that correlate with clinical representation. And add an additional layer of information on top of the standard #histology.

Also #scRNAseq #GWAS #macrophages #SMC

#atherosclerosis #coronaryarterydisease (CAD)

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

"People don't mate randomly – but the flawed assumption that they do is an essential part of many studies linking genes to diseases and traits"

#GWAS #MR #Genetics #EpiVerse

https://theconversation.com/people-dont-mate-randomly-but-the-flawed-assumption-that-they-do-is-an-essential-part-of-many-studies-linking-genes-to-diseases-and-traits-194793

@dr_norb @dandelionhub @academicchatter
Funny thing though, impact factor is fake. With indexing of journals in online searches, there's no need for impact factors. <sarcasm>Oh no! People will have to read a paper and think about its merit. The horror</s> honestly, the number of Nature, Science, and PNAS #PopGen / #GWAS articles that have crap sampling or aren't ethically justifiable is unreal. We can do better.

#ImpactFactorIsFake

People don’t mate randomly – but the flawed assumption that they do is an essential part of many studies linking genes to diseases and traits https://theconversation.com/people-dont-mate-randomly-but-the-flawed-assumption-that-they-do-is-an-essential-part-of-many-studies-linking-genes-to-diseases-and-traits-194793 #GeneticEpidemiology #epidemiology #gwas #humangenome #genetics

Genome-wide association studies (#GWAS) have made clear that single-nucleotide variants (SNVs) that occur at multiple locations across the genome can be associated with a specific condition or trait, also known as a phenotype. Phenome-wide association studies (PheWAS) invert the idea of a GWAS by searching for phenotypes associated with specific SNVs across the range of thousands of human phenotypes, or the phenome”

Excellent insight piece in JAMA: https://jamanetwork.com/journals/jama/article-abstract/2787744

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

An impressive #medRXiv study in ~70k blood samples fails to detect association between #C4 genes and protein at birth and schziophrenia 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

#introduction
I am a #PhD student, and I would love to be in the loop about the following topics:
#fungicide #resistance #adaptation #GWAS #PopGen #Epigenetics #TE #genomics #EvolutionaryBiology #machinelearning #Epistasis #Phenomics #phenotyping #high #throughput #screening #genome #geneticnetworks #effectors #plantpathogen #gene #smallRNA #RNA #R #python #Bash #Linux #conda #GitHub and more!!

Interested in the genetics of #neurodegeneration and looking for an #internship in 2023? Help us better understand how genetic variants affect disease risk, e.g. by exploring large sets of #GWAS summary statistics: https://www.denalitherapeutics.com/job?id=4674434