Common Disease Intro 2

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  • Created by: Hpgrice
  • Created on: 21-10-19 09:40

Human Genome Project

Large number of inter-individual genetic variations in our genome 

Novel sequences technologies and analytical tools

Cost was originally $100 million dollars but no approx $1000

Development of genomics research

Application of high-throughput technologies

Large biological data sets

Personalised medicine is a emerging field

Discover aetiology, novel therapeutic targets, identification of biomarkers

Candidate SNP approach

Aim: discovery of new functional genetic associations (or absence of association) between functional SNPs within pre-specified genes of interest and disease

Approach: based on prior knowledge about the genes and SNPs in relation to disease = hypothesis driven, study small number of SNPs (1-20), genotyping of theses SNPs in a population (e.g case-control study) and compare genotype frequency between cases and controls at each locus

Advantages: relatively cheap, small to medium size study population (100s-1000s) - cheap, look at functional impact of the SNPs, can account for SNP x SNP or SNP x Environment interaction 

Limits: need prior knowledge, small to medium size study population - is this representative of all the population

Pathway approach and GWAS

SNP - known or unknown functionality

Large number of SNPs studied:

  • multiple statistical test - risk of false positives
  • requires corrections for multiple testing e.g if significant p-value threshold p<0.05 for 1 test then for n-tests i.e n SNPS p<( 0.05/ n)
  • increase statistical power so need to use a very large study population and reduce the number of SNPs to genetype: use of Tag SNPS

A Tag SNP is a representative SNP in a genome region with high LD that represents a group of SNPs (haplotype). Means you don't have to genotype all the SNPs reducing cost and number of tests required

Pathway Analysis

Aim: discover new genetic SNPs, disease associations within a given metabolic pathway, identify genes invovled in the disease mechanism within this pathway

Approach: based on prior knowledge about the role…

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