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QTL mapping and GWAS (Bioinformatics S8E2)

Quantitative trait locus (QTL) mapping and Genome Wide Association Analysis (GWAS) with examples in the R Programming language and R/qtl. Learn about association analysis, LOD scores, Additive and Dominant effects, Multiple testing, and QTL/GWAS visualisations such as Manhattan plots. Lectures @ https://dannyarends.nl/bioinformatik/ Programming Assignments and Answers @ https://dannyarends.nl/bioinfo/ Playlist:    • Bioinformatics for Plant and Animal s...   This is a live-stream recording of the MSc and PhD lecture series: Bioinformatics for plant and animal sciences, given digitally during the Covid19 pandemic at the Humboldt University in Berlin organized and lectured by Dr Danny Arends. Chapters: 00:00 Welcome and intro into linkage analysis 00:53 Creating a genetic linkage map 02:18 Linkage analysis using QTL the effect scan 04:54 Additive markers, each additional allele has the same effect size 05:38 Dominance at markers, one allele is enough for the whole effect size 06:44 Over dominance and under dominance, mixture of alleles shows an additional effect 07:40 Group mean + std deviations allows for statistical likelihood tests on genotypes 09:37 P-value to LOD score conversion 11:15 Mapping categorical quantitative trait loci with ANOVA in R 13:10 Mapping additive quantitative trait loci using single linear regression 14:09 Mapping additive and dominant quantitative trait loci using multiple linear regression 19:09 Fast and robust multiple testing by Bonferonni adjustment 22:40 Example LOD curve for blood pressure in RIL mice (data-set from R/QTL) 27:31 Confirming Quantitative Trait Locus mapping in plants via Near Isogenic Lines (NILs) 32:56 Genome wide association via GWAS, a different pattern (minor allele effects) 34:11 Manhattan plots in GWAS linkage groups towers of association 35:57 Human populations and theory behind intro of mutations into a population 36:26 AIL generations after F2, allow for GWAS like fine mapping (fat-mass example) 39:10 Recap overview of the lecture so far 40:37 Single single linear regression mapping of a QTL locus using the R/qtl hyper data-set Thanks for taking an interest in my channel 😄If you've made it this far down, support me by giving a like or subscribing. Join me during my live streams Thursday afternoons on Twitch @   / dannyarends   This work is licensed under version 3.0 of the Creative Commons CC-BY license. For more information see http://creativecommons.org/licenses/b... #bioinformatics #computationalbiology #lectureseries #programming #playlist #molecularbiology #englishstream #msc #phd #livestream #assignments #statisticsfordatascience #academia #academicyoutube #qtl #gwas #quantitativeanalysis #qualitativeanalysis #heritability #anova #homologous #snps #backcross #f2 #rils #linkage #linkageanalysis #experimentalcrosses #traits #complextrait #mendelian #vntrs #rlpf #geneticmap #additive #dominant #manhattanplot #lodscore #mutations #bonferonni #multipletesting #regression