Lecture 26 - Genetics and Epidemiology Flashcards
Uses of comparative genomics
1)
2)
3)
1) Rational vaccine design
2) Novel drug targets
3) Diagnosis using DNA sequencing
Example of comparative genomic population sample
1000 N. meningitidis samples from meningococcal patients
Uses of population analysis
1)
2)
1) Trace evolution (resistances, virulence determinants)
2) Trace spread
Read mapping
1)
2)
3)
1) Used to compare the genomes of different bacteria
2) Instead of sequencing the entire genome by constructing a contig (de novo asembly), compare reads to a reference genome
3) Match reads with reference, look for SNPs
Phylogenetics
Inferring phylogeny from a set of taxa
Estimate the evolutionary relationship between taxa
Epidemiology
Science of evaluating occurrence, determinants, distribution, control of health and disease in a set human population
Example of population dynamics
Evolution due to the new selective pressure of a vaccine
Phylogeography
Used to map how strains spread in space Combine phylogenetics (evolution) with location of outbreaks
How did the 2011 Haiti cholera outbreak occur? 1) 2) 3) 4)
1) Cholera strain was identified as an Asian strain
2) Nepalese soldiers subcontracted sewage disposal to local company.
3) Sewage was dumped in an open pit, which flowed into drinking water during rains
4) A 2bp difference was found between current Nepalese cholera and Haitian outbreak strain (using genomics)
MRCA
Most recent common ancestor