BYU BIO 465 - SNPs (22 pages)

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SNPs



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SNPs

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Pages:
22
School:
Brigham Young University
Course:
Bio 465 - Bioinformatics & Proteomics
Bioinformatics & Proteomics Documents

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SNPs DNA differs between humans by 0 1 1 in 1300 bases This means that you can map DNA variation to around 10 000 000 sites in the genome Almost all variation is ancient and 90 of SNP variation are constant across all populations These Single Nucleotide Polymorphisms SNPs can be correlated to human disease 1998 4 000 SNPs 1994 7 800 000 nearly all mapped Alzheimer s Disease Apolipoprotein E ApoE carries cholesterol and fat It comes in three variants with two SNPs APoE2 T T APoE3 T C ApoE4 C C In 1993 ApoE4 was correlated with 1 3 of the cases of Alzheimer s disease If you have the E4 variant you have a 60 70 lifetime risk of Alzheimer s Disease Current research is focused on drug development that takes advantage of this knowledge Haplotype Maps Although there are around 10 000 000 SNPs they group into a small number of groups of SNPs that are correlated with each other So there are around around 300 000 unique arrangements of the SNPS This is not that big of a number CS people can imagine an exhaustive search Imagine SNP 1 2 3 4 5 10 000 000 Alzheimers 0 1 0 1 0 0 0 Leukemia 1 0 0 0 0 0 1 Breast Cancer 0 0 1 1 0 0 1 1 0 0 0 0 0 0 Differences between individuals Pima Indians Anti depressants Coronary Artery Disease Basic Concepts Parent 2 Parent 1 A a B b A B a b A B a b X OR a b A B A B a b High LD No Recombination r2 1 SNP1 tags SNP2 A a B b A b A B a B A B A b a B A B A b etc Low LD Recombination Many possibilities HapMap Glossary LD linkage disequilibrium For a pair of SNP alleles it s a measure of deviation from random association i e no recombination Measured by D r2 LOD Phased haplotypes Estimated distribution of SNP alleles Alleles transmitted from Mom are in same chromosome haplotype while Dad s form the paternal haplotype Tag SNPs Minimum SNP set to identify a haplotype r2 1 indicates two SNPs are redundant so each one perfectly tags the other Questions help hapmap org HapMap Project Phase 1 Phase 2 Phase 3 Samples POP panels 269 samples 4 panels 270



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