Optimal Haplotype Block-Free Selection of Tagging SNPs for ...

Optimal Haplotype Block-Free Selection of Tagging SNPs for ...

SNPs and the Human Genome Prof. Sorin Istrail Single Nucleotide Polymorphism (SNP) GATTTAGATCGCGATAGAG GATTTAGATCTCGATAGAG A SNP is a position in a genome at which two or more different bases occur in the population, each with a frequency >1%. The two alleles at the site are G and T The most abundant type of polymorphism t tttctccatttgtcgtgacacctttgttgacaccttcatttctgcattctcaattctatttcactggtctatgg c g cagagaacacaaaatatggccagtggcctaaatccagcctactaccttttttttttttttgtaacattttacta a g

t t acatagccattcccatgtgtttccatgtgtctgggctgcttttgcactctaatggcagagttaagaaattgtag a c c cagagaccacaatgcctcaaatatttactctacagccctttataaaaacagtgtgccaactcctgatttatgaa cttatcattatgtcaataccatactgtctttattactgtagttttataagtcatgacatcagataatgtaaatc g ctccaactttgtttttaatcaaaagtgttttggccatcctagatatactttgtattgccacataaatttgaaga a g tcagcctgtcagtgtctacaaaatagcatgctaggattttgatagggattgtgtagaatctatagattaattag c t aggagaatgactatcttgacaatactgctgcccctctgtattcgtgggggattggttccacaacaacacccacc c ccccactcggcaacccctgaaacccccacatcccccagcttttttcccctgctaccaaaatccatggatgctca Human Genome contains ~ 3 G g agtccatataaaatgccatactatttgcatataacctctgcaatcctcccctatagtttagatcatctctagat a

basepairs arranged in t46 t t tacttataatactaataaaatctaaatgctatgtaaatagttgctatactgtgttgagggttttttgttttgtt c c c chromosomes. ttgttttatttgtttgtttgtttgtattttaagagatggtgtcttgctttgttgcccaggctggagtgcagtgg g tgagatcatagcttactgcagcctcaaactcctggactcaaacagtcctcccacctcagcctcccaaagtgctg a ggatacaggtgtgacccactgtgcccagttattattttttatttgtattattttactgttgtattatttttaat Two individuals are 99.9% the tattttttctgaatattttccatctatagttggttgaatcatggatgtggaacaggcaaatatggagggctaac same. I.e. differ in ~ 3 M g t g tgtattgcatcttccagttcatgagtatgcagtctctctgtttatttaaagttttagtttttctcaaccatgtt basepairs. c

a a tacttttcagtatacaagactttgacgttttttgttaaatgtatttgtaagtattttattatttgtgatgttat ttaaaaagaaattgttgactgggcacagtggctcacgcctgtaatcccagcactttgggaggctgaggcgggca t g gatcacgaggtcaggagatcaagaccatcctggctaacatggtaaaaccccgtctctactaaaaatagaaaaaa SNPs occur once every ~600 bp c a g attagccaggcgtggtggcgagtgcctgtagtcccagctactcgggaggctgaggcaggagaatggtgtgaacc c g tgggaggcggagcttgcagtgagctgagatcgtgccactgcattccagcctgcgtgacagagcgagactctgtc c g Average gene in the human aaaaaaataaataaaatttaaaaaaagaagaagaaattattttcttaatttcattttcaggttttttatttatt a g

t tctactatatggatacatgattgatttttgtatattgatcatgtatcctgcaaactagctaacatagtttatta genome spans ~27Kb a c tttctctttttttgtggattttaaaggattttctacatagataaataaacacacataaacagttttacttcttt cttttcaacctagactggatgcattttttgtttttgtttgtttgtttgctttttaacttgctgcagtgactaga g g g gaatgtattgaagaatatattgttgaacaaaagcagtgagagtggacatccctgctttccccctgattttaggg ~50 SNPs per gene a c a g ggaatgttttcagtctttcactatttaatatgattttagctataggtttatcctagatccctgttatcatgttg a aggaaattcccttctatttctagtttgttgagattttttaattcatgtgattgcgctatctggctttgctctca Haplotype

C A G T T G Haplotypes G C T C G A C A A C A G G T T C G T C A A C A G SNP Two individuals SNP SNP Mutations Infinite Sites Assumption: Each site mutates at most once Haplotype Pattern C T

C C A T A T G G T G T A G T 0 1 0 0

0 1 0 1 0 0 1 0 0 1 0 1 At each SNP site label the two alleles as 0 and 1. The choice which allele is 0 and which one is 1 is arbitrary. Recombination G T T C G A C A A C A T A C G T A T C T A T T A

G T T C G A C T A T T A Recombination The two alleles are linked, I.e., they are traveling together G T T C G A C A A C A T A C G T A T C T A T T A Recombination disrupts the linkage ? G T T C G A C T A T T A Linkage Disequilibrium (LD) Emergence of Variations Over Time Disease Mutation Common Ancestor

time present Variations in Chromosomes Within a Population Extent of Linkage Disequilibrium Disease-Causing Mutation 2,000 gens. ago 1,000 gens. ago Time = present

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