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Positional Cloning Genetics Sib pairs Chromosome Region Association Study Genomics Physical Mapping/ Sequencing Candidate Gene Selection/ Polymorphism Detection Mutation Characterization/ Functional Annotation Netherton Syndrome Linkage Chavanas et al., Am J Hum Genet, 66:914-921, 2000 Netherton Syndrome Haplotypes Chavanas et al., Am J Hum Genet, 66:914-921, 2000 Chavanas et al. 2000, Nature Genetics Inflammatory Bowel Disease Genome Screen Hampe et al., Am J Hum Genet, 64:808-816, 1999 Inflammatory Bowel Disease Genome Screen Hampe et al., Am J Hum Genet, 64:808-816, 1999 Allelic Association A Special Type of Linkage 3/5 3/6 2/6 5/6 3/5 3/2 2/6 5/2 Both families are ‘linked’ with the marker, but a different allele is involved. This is Linkage but no Association Allelic Association A Special Type of Linkage 3/5 3/6 2/6 5/6 3/6 3/2 2/4 6/2 4/6 6/6 All families are ‘linked’ with the marker Allele 6 is ‘associated’ with disease Linkage is just association within families 2/6 6/6 Allelic Association A Special Type of Linkage Controls Cases 6/6 6/2 3/5 3/4 3/6 2/4 3/2 5/6 3/6 4/6 6/6 2/6 5/2 Allele 6 is ‘associated’ with disease 2/6 Association study: Uses Pharmacogenetics genotyping clinically relevant samples (toxicity vs efficacy) Insurance purposes contentious, but likely at some point Candidate genes for specific diseases common practice in medicine/genetics Positional cloning the most frequent source of new loci at present Genome-wide association with 2-3 million SNPs, can search whole genome exhaustively