Lecture 2: Applied Genomics Overview
Key Concepts Covered
Hardy-Weinberg Equilibrium
Population genetics foundation - allele frequencies (p, q, r) in populations remain constant under specific conditions.
Quantitative Genetics (QG)
Study of traits controlled by multiple genes. Used for calculating breeding values in agriculture and understanding complex human traits.
The Human Genome
- ~3 billion base pairs
- <5% codes for proteins (the rest: regulatory, structural, "junk")
- Massive scale creates computational challenges
QTL (Quantitative Trait Loci)
Genomic regions associated with quantitative traits - linking genotype to phenotype.
Genomics Definition
Study of entire genomes - all DNA sequences, genes, and their interactions.
Sequencing Accuracy
Modern sequencing: <1 error per 10,000 bases
Comparative Genomics
Comparing genomes across species to understand evolution, function, and conservation.
Applied Genomics (Why we're here)
Analyze genomes and extract information - turning raw sequence data into biological insights.
Major Challenges in Genomic Data
- Storage - Billions of bases = terabytes of data
- Transfer - Moving large datasets between systems
- Processing - Computational power for analysis
Sequencing Direction Note
Sanger sequencing: Input = what you're reading (direct)
NGS: Reverse problem - detect complement synthesis, infer template