Characterizing population distribution and determinants of distribution of parasitic organism

National Institute of Infectious Disease January 19, 2017 Infectious disease epidemiological problems addressed by molecular biology techniques (2016)               Tracking strains across time and geography Distinguishing endemic from epidemic disease occurrence Stratification of data to refine study designs Distinguishing pathovars vs commensal flora or saprophytes Identifying new modes of transmission Studying microorganisms associated with healthcare or institutional infections Surveillance and monitoring response to intervention Characterizing population distribution and determinants of distribution of parasitic organisms Identifying genetic basis for disease transmission Validating microdiversity genotyping methods applied to epidemiology Virus quasispecies population structure analysis Identifying direction and chain of transmission Identifying hidden social networks and transmission links Analyzing microbiomes to study non-infectious disease epidemiology Principles • Questions for parasite molecular epidemiology • Genetic biology of parasites – Genetic organization – Markers • Population genetics molecular techniques and analysis – How markers identify populations – How markers characterize populations Classification and Characteristics Protozoa • Single cell • Rapid replication • Commonly multiply in all hosts • Asexual reproduction common Helminths • Multicellular • Organs present • Rarely complete development in one host • Accumulation by exposure • Sexual reproduction common Protozoa • • • • Eukarotes (nuclear membrane, organelles) Single cell Intra- & extra cellular Asexual reproduction common Helminths • • • • Eukaryotes Multicellular Never intracellular Usually reproduce sexually Parasites Are Not Bacteria Cell size Parasites Are Not Bacteria Genome size Parasites Are Not Bacteria Cellular Organization Parasites Are Not Bacteria Genomic Organization Population = 20 Population = 200 Allele Frequency Allele Frequency Allele Frequency Genetic Drift Population = 2000 Hardy-Weinberg Equilibrium • Limitations – No population is infinite – Mating is almost never random – Mutation, migration and selection are always active in nature • Strengths – Despite this the majority of loci conform to HW proportions (sequencing) – Deviations correct themselves in 1-2 generations Hardy-Weinberg Equilibrium • • Implications – Allele frequencies (traits) not change in a stable population – Failure to conform to HWP is due to a severe violation of one of the assumptions Importance – Provides the ability to test whether or not a population has been changed in some way Hardy-Weinberg: The problem • If you know the frequency of an allele in a population, can you predict the frequency of genotypes? A Alleles A A A AAA A AAA A AA AAAA A A A A=50 A A AA AA a aaaa a aaaaaa a aaa a aaa a=50 a aaaa Genotypes AA Aa aa ? Hardy-Weinberg: The problem • If you know the frequency of an allele in a population, can you predict the frequency of genotypes? Alleles A a A=0.50 a=0.50 A=0.35 a=0.65 p2 + 2pq + q2 p2 + 2pq + q2 Genotypes AA Aa aa 0.25 0.50 0.25 0.12 0.46 0.42 A Quick Problem: 100 Aedes aegypti Genotyped • AA = 14 • Aa = 30 • aa = 56 Is this population in HWE? Goodness-of-Fit: Record the Observed Genotypic Frequency Genotype N observed Genotype Observed AA 14 0.14 Aa 30 0.30 aa 56 0.56 100 Sum Goodness-of-Fit Calculate the population allele frequency Genotype AA 14 Allele Counts A 28 Aa 30 30 30 aa 56 112 100 58 142 Sum Allele freq Observed 200 alleles 0.29 (p) Allele Counts a 0.71 (q) Goodness-of-Fit: Calculate expected genotype frequency • • Observed Allele Frequencies: A = 0.29, a = 0.71 HWE = p2+2pq+q2 Genotype N observed Genotype Observed HWE Calcs AA (p2) 14 0.14 0.29(0.29) Aa (2pq) 30 0.30 0.29(0.71)2 aa (q2) 56 0.56 0.71(0.71) 100 Sum Goodness-of-Fit: Calculate expected genotype frequency • • • Observed Allele Frequencies: A = 0.29, a = 0.71 HWE = p2+2pq+q2 df (degrees of freedom) = # of genotypes – – # independent genotype counts Genotype N observed Genotype Observed HWE Calcs Genotype Expected AA 14 0.14 0.29(0.29) 0.0841 Aa 30 0.30 0.29(0.71)2 0.4118 aa 56 0.56 0.71(0.71) 0.5041 100 Sum Goodness-of-Fit: Calculate chi-square • • • o  e 2   Observed Allele Frequencies: A = 0.29, a = 0.71 e HWE = p2+2pq+q2 df (degrees of freedom) = # of genotypes – – # independent allele counts Genotype df ,   N observed (o) Genotype Observed HWE expected Genotype Expected N expected (e) (o-e)2 AA 14 0.14 0.29(0.29) 0.0841 36 Aa 30 0.30 0.29(0.71)2 0.4118 42 144 aa 56 0.56 0.71(0.71) 0.5041 50 36 100 1 100 Sum df=1 Goodness-of-Fit: cont Calculate chi-square • • • o  e 2   Observed Allele Frequencies: A = 0.29, a = 0.71 e HWE = p2+2pq+q2 df (degrees of freedom) = # of genotypes – – # independent allele counts df ,   Genotype N observed N expected (o-e)2 2(1, 0.5) (o-e)2 / e AA 14 36 4.5 4.5 Aa 30 42 144 3.4 3.4 aa 56 50 36 0.7 0.7 100 100 Sum 8.6 df=1 pnon-random mating>other forms of selection>small population size>mutation • • • • Web Resources General: – http://www.web-books.com/MoBio/Free/TextBooks.htm – http://www.web-books.com/MoBio/Free/Contents.htm Glossary for genomics: http://www.genome.gov/glossary.cfm Microsatellites: – http://uwadmnweb.uwyo.edu/zoology/mcdonald/molmark/lectures/PopGen /PopGen6/PopGen6.html Population Genetics: – http://www.as.ua.edu/ant/bindon/ant570/pop_gen/population_genetics.htm (good general) – http://www.zoology.ubc.ca/~whitlock/bio434/LectureNotes/LectureNotes.ht ml (good general discussion) – http://wsrv.clas.virginia.edu/~rjh9u/abofreq.html (good discussion of HWE) – http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/popgen/ (Not so good Does have some basic HWE derivation and explanation) Population genetics resources Calculator for HWE: • http://www.genes.org.uk/software/hardy-weinberg.shtml • www.tufts.edu/~mcourt01/Documents/Court%20lab%20%20HW%20calculator.xls Additional examples for calculation of FST or Ne from genotyping data • www.uwyo.edu/dbmcd/popecol/Maylects/FST.html • www.life.uiuc.edu/ib/201/lectures/TheFSTstatistic.doc • Wang, J and Whitlock, M C (2003) Estimating effective population size and migration rates from genetic samples over space and time Genetics 163: 429-446 Population genetics programs: • Arlequin - http://lgb.unige.ch/arlequin/ • Genepop - on the Web http://genepop.curtin.edu.au/