Manolis Kellis
@manoliskellis1·24.9K subscribers·255 videos
MIT Compbio Lecture 13 - Population Genetics (Fall 2019)
Posted
October 22, 2019
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6,250
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October 22, 2019
6,250
95
3
1.57%
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1:18:54Now PlayingMIT Computational Biology: Genomes, Networks, Evolution, Health
Prof. Manolis Kellis
Full playlist with all videos in order is here
All slides from Fall 2019 are here
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.
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