This @CVIA_Journal study identifies COPD as a potential risk factor for AAA, supported by bidirectional MR, #eQTL integration, #SingleCellSequencing, and #PheWAS, and reveals shared #GeneticMechanisms and targets for #PrecisionMedicine.
#OpenAccess: tinyurl.com/2773qq59
Usamos análisis de #eQTL para examinar como los SNPs se relacionan a la expresión génica en #Habénula. 7 genes eQTLs fueron identificados como GDEs, y 16 eSNPs como SNPs de riesgo a la esquizofrenia en GWAS. 9 nuevos genes fueron colocalizados con el riesgo genético de esquizofrenia
We used #eQTL analysis to examine how SNPs relate to gene expression in #Habenula, 7 eQTLS genes were identified in differential expression, and 16 eSNPs were schizophrenia GWAS risk SNPs. Nine new schizophrenia colocalized genes with genetic risk were identified
Mentorship in action!
Dr. Jingyi Jessica Li and former PhD student Heather Zhou just published ClipperQTL, a fast, p-value-free eQTL method.
Now in Genome Biology:
🔗 genomebiology.biomedcentral.com/articles/10....
Congrats @jsb-ucla.bsky.social & Heather Zhou!
#eQTL #StatGenomics #FredHutch
Excited to share our method ClipperQTL published in Genome Biology.
Built on our p-value-free FDR control framework Clipper, ClipperQTL performs on par with FastQTL and runs up to 500× faster.
Big thanks to my former PhD student Heather Zhou!
genomebiology.biomedcentral.com/articles/10....
#eQTL
Top: Diagram of snRNA-seq analysis pipeline. Heterozygous Arabidopsis F1 plants were generated by crossing Col-0 to five different accessions. Pollen was collected from these five F1 plants and pooled, before nuclei isolation, barcoding, and cDNA synthesis using the 10x snRNA-seq protocol. After sequencing, nuclei from the five genotypes were demultiplexed, and meiotic recombination events were predicted. Gene expression and recombination patterns were then compared to identify eQTLs. Figure created using BioRender. Bottom: Fluorescent microscopy image of Arabidopsis thaliana pollen.
Expression quantitative trait locus (eQTL) mapping studies are limited by the need to study a large number of individuals. @labschneeberger.bsky.social &co develop a method to scale up #eQTL studies by performing single-nucleus #RNAseq of #Arabidopsis pollen @plosbiology.org 🧪 plos.io/4jPZOzD
Top: Diagram of snRNA-seq analysis pipeline. Heterozygous Arabidopsis F1 plants were generated by crossing Col-0 to five different accessions. Pollen was collected from these five F1 plants and pooled, before nuclei isolation, barcoding, and cDNA synthesis using the 10x snRNA-seq protocol. After sequencing, nuclei from the five genotypes were demultiplexed, and meiotic recombination events were predicted. Gene expression and recombination patterns were then compared to identify eQTLs. Figure created using BioRender. Bottom: Fluorescent microscopy image of Arabidopsis thaliana pollen.
Expression quantitative trait locus (eQTL) mapping studies are limited by the need to study a large number of individuals. @labschneeberger.bsky.social &co develop a method to scale up #eQTL studies by performing single-nucleus #RNAseq of #Arabidopsis pollen @plosbiology.org 🧪 plos.io/4jPZOzD
Top: Diagram of snRNA-seq analysis pipeline. Heterozygous Arabidopsis F1 plants were generated by crossing Col-0 to five different accessions. Pollen was collected from these five F1 plants and pooled, before nuclei isolation, barcoding, and cDNA synthesis using the 10x snRNA-seq protocol. After sequencing, nuclei from the five genotypes were demultiplexed, and meiotic recombination events were predicted. Gene expression and recombination patterns were then compared to identify eQTLs. Figure created using BioRender. Bottom: Fluorescent microscopy image of Arabidopsis thaliana pollen.
Expression quantitative trait locus (eQTL) mapping studies are limited by the need to study a large number of individuals. @labschneeberger.bsky.social &co develop a method to scale up #eQTL studies by performing single-nucleus #RNAseq of #Arabidopsis pollen @plosbiology.org 🧪 plos.io/4jPZOzD
HORNET is a comprehensive toolset for genome-wide causal gene discovery using multivariable #Mendelian randomization and #eQTL summary statistics. It corrects for confounding, LD bias, and missing data to enable robust identification of gene-trait associations across tissues.
For those who don't know it, I really think the fivex #eqtl/ #sqtl browser is one of the most useful and intuitive tools when doing detective work on a new #gwas hit.
fivex.sph.umich.edu
Much thanks to all its creators & @kauralasoo.bsky.social & team for the upstream work on the eqtl catalogue.
Problem: eQTL reveals disease alleles' function on gene expression, while it's been so puzzling🧐 that most #GWAS alleles do not colocalize with #eQTL. The traditional wisdom in the field is that eQTL regulate DNA transcription in the nucleus by altering regulatory sequences (2/n
Putting some finishing touches on a @Circ_Gen video abstract narrated by @mete_civelek.
#eQTL warrants celebratory fireworks, right?
