MIT Compbio Lecture 13 - Population Genetics (Fall 2019) скачать в хорошем качестве

MIT Compbio Lecture 13 - Population Genetics (Fall 2019)

MIT Computational Biology: Genomes, Networks, Evolution, Health http://compbio.mit.edu/6.047/ Prof. Manolis Kellis Full playlist with all videos in order is here:    • Machine Learning in Genomics - Fall 2019   All slides from Fall 2019 are here: https://stellar.mit.edu/S/course/6/fa... Outline for this lecture: 1. Genetic variation: detection, quantification, and initial insights Brief history of genetics. Genome. Variation: SNPs, indels, CNVs, STRs. Detection: 1000Genomes project, ExAC, rare/common/neutral. Variant calling from sequencing reads, logistic regression, joint calling. 2. Haplotypes, Recombination, LD, Phasing Biology: meiosis, recombination, hotspots, PRDM9 protein/motif evol. Linkage Disequilibrium (D, D’, r2). Haplotype blocks, lengths. Phasing. 3. Human relatedness and ancestry painting 1000Genomes population differences. SNP sharing. IBD/heritability. Admixture, ancestry painting. PCA/MDS clustering (FST). PC correction 4. Human demographic history. History/evidence of migrations. Africa, India, Europe, Asia, Americas. Population size, dynamics, bottlenecks, expansion, effective pop size. Ancient DNA, Neanderthals, Denisovans. Gorilla/Chimp introgression. 5. Measuring human selection at multiple timescales Neutral evo, Hardy-Weinberg, Evidence of positive/directional selection Negative/purifying selection: SNP density, Derived allele freq, Heterozy.