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MIT6_047f08_lec12_note12 - MIT OpenCourseWare...

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MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms .
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Lecture 12: Population Genomics I 6.047/6.878 Population Genomics I (Pardis Sabeti) 1 Introduction It is readily observable that a single species, while phenotypically discernible as a distinct group different from other species, often displays a great amount of phenotypic diversity of its own. In this lecture, we study the genetic basis of this diversity by considering polymorphisms and their evolution, basic population genetics, the fixation index, and haplotype analysis. 2 Polymorphisms Polymorphisms are DNA variations between different individuals of the same species. There are several types of polymorphisms, including single nucleotide polymorphisms (SNPs), vari- able number tandem repeats, insertions and deletions, large-scale polymorphisms, and copy number variants. In addition to helping explain the genetic basis of our diversity, under- standing polymorphisms is also medically relevant. These changes, when they affect critical genes, can result in severe clinical outcomes like sickle cell anemia (SNP), Huntington’s disease (triplet repeat), and cystic fibrosis (deletion). 3 Population genetics Consider a population of N individuals. At a given gene locus, there may be many possible alleles (polymorphisms). Each individual in the population has two alleles for every auto- somal gene locus, and the genotype of an individual refers to this collection of two alleles, taken over all loci of interest. The allele frequency of a particular allele is the proportion of all 2 N alleles of the population that are of that type, and the genotype frequency of a particular
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