Manolis Kellis
@manoliskellis1·24.9K subscribers·255 videos
MIT CompBio Lecture 13 - Population Genomics
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October 23, 2018
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October 23, 2018
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1:23:43Now PlayingMIT Computational Biology: Genomes, Networks, Evolution, Health
Prof. Manolis Kellis
Fall 2018
Lecture 13 - Population Genomics
1. Genetic variation: detection, quantification, and initial insights
- SNPs, indels, copy-number, structural, short tandem repeats.
- 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
- 23andMe parent-child vs. sibling 50%. 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.
Slides for Lecture 13:
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