MIT Compbio Lecture 13 - Population Genetics (Fall 2019)

Описание: 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.