MESA Candidate Gene Project

1. MESA Candidate Gene Project MESA Steering Committee Meeting September 2005

2. Specific Aim • Conduct an association study of 2,880 MESA participants (parent study) • 720 randomly selected from each ethnic group of Caucasian-, African-, Mexican-, and Chinese-Americans • Include the well-phenotyped “MESA 1000” • Genotype 1536 SNPs in candidate genes proposed by MESA Investigators

3. Candidate Gene Selection • MESA investigators were asked to propose candidate genes at Fall 2004 meeting. • List collated by DCC and resent to MESA investigators for ranking (267 genes) • Ranking conducted by DCC. Semi-final list ready by Spring 2005 meeting. • Further refinements • More genes added & some priorities altered • More discussion with MESA Eye • More coordination with the laboratory tests

4. (Candidate Gene Selection, con’t) • List grew from 267 to 294 genes • Initial analysis of number of “tagSNPs” per gene in order to give idea of the possible number of genes that could be studied • HapMap data analyzed using “Tagger” • PGRN data (Seattle SNPs) / LD Select output • Check of what would be missing and what was included (keep current with known gene associations)

5. Selection of tagSNPs • List of 294 genes sent to Illumina, list of 60,293 SNPs returned with info • Illumina validated, 95% predicted success • Double-hit and designable, 80-85% • Non-validated and designable, 30-50% • Non-designable • tagSNPs selected with goal of 80-85% or greater

6. Selection of tagSNPs • HapMap genotyping information for one ethnic group was downloaded • Minor allele frequency set at 0.05 or greater • Merge Illumina designability info with tagSNPs • Use “Tagger” to select tagSNPs AND Illumina predicted high success rate, reiterate if necessary • Dump final tagSNP list to SNPLIST database • Repeat for other ethnic groups & combine in SNPLIST database • Add any cSNPs with Illumina predicted high success rate, add to SNPLIST • Go to next gene on gene list

7. Selection of tagSNPs • HapMap genotyping information for one ethnic group was downloaded

8. Selection of tagSNPs

9. Selection of tagSNPs • Obtain HapMap info for gene & ethnic group Example: ABCC1

10. Selection of tagSNPs

11. Selection of tagSNPs Add Margin of 10kb on promoter end and 3 kb to 3’-utr end

12. Selection of tagSNPs Add Margin of 10kb on promoter end and 3 kb to 3’-utr end Isoforms must be checked for cSNPs

13. Selection of tagSNPs Dump SNP data

14. Selection of tagSNPs Dump SNP data

15. Selection of tagSNPs Import into Haploview Program

16. Selection of tagSNPs Import into Haploview Program

17. Selection of tagSNPs List of HapMap SNPs for Caucasian population in HapMap database

18. Selection of tagSNPs • HapMap genotyping information for one ethnic group was downloaded • Minor allele frequency set at 0.05 or greater

19. Selection of tagSNPs Change MAF to 0.05 Dump SNP list

20. Selection of tagSNPs • HapMap genotyping information for one ethnic group was downloaded • Minor allele frequency set at 0.05 or greater • Merge Illumina designability info with tagSNPs (uses relational database technology).

21. Selection of tagSNPs List of SNPs from HapMap now merged with Illumina designability info

22. Selection of tagSNPs • HapMap genotyping information for one ethnic group was downloaded • Minor allele frequency set at 0.05 or greater • Merge Illumina designability info with tagSNPs • Use “Tagger” to select tagSNPs AND SNPs with an Illumina-predicted high success rate, reiterate if necessary

23. Note, for example, that SNP #11 has low designability. This SNP is excluded from Tagger Use Tagger List of SNPs from HapMap now merged with Illumina designability info

24. Use aggressive tagging, including 2 and 3 marker haplotypes Use Tagger

25. Use aggressive tagging, including 2 and 3 marker haplotypes r2 ≥ 0.8 Use Tagger

26. Thus far, I have 32 SNP’s to genotype Use Tagger

27. Use Tagger But a few SNPs are “untaggable”

28. Remember that I excluded the “Non-validated but designable” class. Go back and add some of these back in. Use Tagger

29. Final list gives 41 SNPs required to tag 51 alleles of caucasian SNPs in the 200kb span of the ABCC1 gene Dump to SNPLIST Use Tagger

30. Selection of tagSNPs • HapMap genotyping information for one ethnic group was downloaded • Minor allele frequency set at 0.05 or greater • Merge Illumina designability info with tagSNPs • Use “Tagger” to select tagSNPs AND Illumina predicted high success rate, reiterate if necessary • Dump final tagSNP list to SNPLIST database • REPEAT for other ethnic groups & combine in SNPLIST database (combined for ABCC1 is 50 SNPs) • REPEAT for all genes

31. AND: Add cSNPs • Add any cSNP from dbSNP with frequency information and high designability • (none for ABCC1 example) Add Investigator-proposed SNPs • Some investigators submitted cSNPs or tagSNPs, these were checked for designability in the Illumina system and also added to SNPLIST

32. Add ethnic-specific SNPs • ~110 ethnic-specific SNPs were added • (SNPs showing a MAF > 0.3 in one population and no MAF in the other populations) • Will be available if analysis of population stratification becomes important in the subsequent analysis

33. Result:

34. Result • List of 1536 SNPs has been sent to Illumina and has been input into the pipeline for oligo synthesis • Mike Tsai’s group has sent the DNAs to Illumina for the genotyping pipeline

35. caveats • To reduce the total number of SNPs for some genes, the MAF was increased to > 0.20, and/or the SNPS were limited to Caucasians • So not all “eggs in one basket” • Some genes are represented by a few SNPs that were proposed by investigators only • cSNPs tended to fail Illumina designability • This program will not look at APOE very well because the most important SNPs failed designability