CS2220 Introduction to Computational Biology
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1 CS2220 Introduction to Computational Biology WEEK 7: SINGLE (SIMPLE) NUCLEOTIDE POLYMORPHISMS (SNPS) 1 Dr. Mengling FENG Institute for Infocomm Research Massachusetts Institute of Technology mfeng@mit.edu
2 PLANS FOR WEEK 7 AND WEEK 8! Week 7, 1 st Oct 2015! 2 hours class: Single (Simple) Nucleotide Polymorphism! 1 hour briefing on project and forming of project teams! Week 8, 7 th Oct 2015! 2 hours class: Genome-wide Association Study (GWAS)! 1 hour Q&A on the lectures and project 2
3 WEEK 7 S LEARNING OBEJECTIVES! After the class, students should be able to! Define the concept of SNP! Elaborate various types of SNPs and their functions! Explain the applications of SNPs! Know the major initiatives and projects related to SNP! Use online resources to find out information about SNPs 3
4 SINGLE (SIMPLE) NUCLEOTIDE POLYMORPHISM THE DEFINITION! SNP is a DNA sequence variation occurring commonly within a population! A single nucleotide A, T, C &G, mutation! Must be common! Minor Allele Frequency (MAF) >1% 4
5 5
6 SINGLE (SIMPLE) NUCLEOTIDE POLYMORPHISM! ~15 million possible SNP sites in human genome, ~10 million common SNPs (MAF >5%)! ~12 million SNPs have been identified (dbsnp 2012 release 137)! Each individual may carry 3~5 million common SNPs (inherited) and ~120 new mutations! SNPs VS Individual Mutations! Natural Selection! Founder Effect 6
7 SNPS AS AN EVIDENCE FOR NATURE SELECTION! Many Africans carry SNPs around gene G6PD and CD40 ligand, which may lead to resistance to malaria 7
8 FOUNDER EFFECT! Examples:! The Amish group National Cancer Institute! Ashkennazi Jews after the Holocaust 8
9 TYPES OF SNPS! Non-coding SNPs! 5 Un-Translated Regions (UTR)! 3 Un-Translated Regions (UTR)! Introns! Integenic Regions (IGR)! Psuedogenes! Coding SNPs! Synonymous substitution! Non-synonymous substitution! Missense! Nonsense 9
10 ! Take home message: FUNCTIONS OF SNPS! We still know very little about it! Genome-wide Association and other studies to identify associations and causations! Majority of SNPs are believed to be silent! Non-coding SNPs: regulatory functions! Splicing! Transcriptional regulation (promoter & TF binding sites)! Translational regulation (initiation or termination)! Regulate mrna target sites 10
11 FUNCTIONS OF SNPS SYNONYMOUS SUBSTITUTIONS! Do not trigger amino acid change in protein sequence! Were believed to be silent mutations! Recent studies shown that they can affect! Messenger RNA (mrna) splicing, stability, structure and protein folding => protein functions 11
12 FUNCTIONS OF SNPS NON-SYNONYMOUS SUBSTITUTIONS! Missense: change in amino acid of protein sequence! Nonsense: change in amino acid that lead to premature stop codon 12
13 APPLICATIONS OF SNPS! General Applications! Forensics! Paternity tests! Ancestry trace: immigration to the United Kingdom! Follow ethnic migrations 13
14 APPLICATIONS OF SNPS! Genetic marker for distinguishing traits! Predisposition for disease 14
15 APPLICATIONS OF SNPS! Genetic marker for distinguishing traits! Predisposition for disease! Drug efficacy! Drug adverse effect 15
16 APPLICATIONS OF SNPS! Genetic marker for distinguishing traits! Predisposition for disease! Drug efficacy! Drug adverse effect! Other traits 16
17 APPLICATIONS OF SNPS! Genetic marker for distinguishing traits! Predisposition for disease! Drug efficacy! Drug adverse effect! Other traits! Preventive medicine! Personalized and targeted medicine! Profession selection! etc 17
18 POPULATION GENETICS OF SNPS FOR FORENSIC AN INDIVIDUAL IDENTIFICATION PANEL 18
19 SNP PANEL SELECTION! SNPs data from 44 populations! Selection criteria! A small panel is preferred! Incomplete or damaged DNA samples! Reduce cost! For individual SNP! Average Heterozygosity > 0.4! Average Fixation Index Fst < 0.06! Linkage Disequilibrium ~
20 HETEROZYGOSITY! Human beings are diploid organism! We carry two copies of a gene! For a gene having two alleles: A & a! Homozygote: AA and aa! Heterozygote: Aa! Heterozygosity! Percentage of heterozygot in the population! SNP selection criterion:! Average heterozygosity > 0.4! High genetic variations among individuals are preferred 20
21 ESTIMATION OF HETEROZYGOSITY THE HARDY-WEIBERG THEOREM 2 i=1 H E = 2 pq = 1 p 2 q 2 = 1 p i 2 k i=1 H E = 1 p i 2 21
22 FIXATION INDEX FST! A measure of differentiation of subpopulations σ s 2 p F st = σ s 2 p(1 p) is the variance of allele frequencies among different subpopulations is the average allele frequency across the population! Selection Criterion:! Fst < 0.06! Similar genetic profiles among subpopulations are preferred 22
23 LINKAGE DISEQUILIBRIUM (LD)! Measures the non-random association of alleles at different loci! In the study, r2 measure was used! Selection criterion:! LD ~ 0.01! Avoid picking up highly linked SNPs! Minimize redundancy 23
24 AN INDIVIDUAL IDENTIFICATION SNP PANEL THE RESULTS! Identified two sets of SNPs! Set I: 45 SNPs! Estimated average matching probability < 10-15! An two random individuals to have the same genotype will be very unlikely! Set II: 89 SNPs! Estimated average matching probability <
25 SNP AS A DISEASE BIO-MAKER CYSTIC FIBROSIS! A genetic disorder that affects mostly the lungs! Inherited in an autosomal recessive manner! Most common among people of Northern European ancestry 25
26 SNP AS A DISEASE BIO-MAKER GAUCHER DISEASE! A genetic disease in which fatty substances accumulate in cells and certain organs! Inherited in an autosomal recessive manner 26
27 BREAKTHROUGH OF THE YEAR 2007 HUMAN GENOME VARIATION 27
28 THE HAPMAP PROJECT 28
29 1000 GENOME PROJECT 29
30 ONLINE RESOUCES: SNPEDIA 30
31 ONLINE RESOUCES: DBSNP 31
32 WEEK 7 S LEARNING OBEJECTIVES! After the class, students should be able to! Define the concept of SNP! Elaborate various types of SNPs and their functions! Explain the applications of SNPs! Know the major initiatives and projects related to SNP! Use online resources to find out information about SNPs! Understand the concept of haplotype and linkage disequilibrium 32
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