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Steve DePalma, Ph.D. Seidman lab, HMS Genetics depalma@rascald.harvard 3/31/2005

Mapping human disease genes with Affymetrix 10K SNP chips and the HMS Orchestra Shared Research Cluster. Steve DePalma, Ph.D. Seidman lab, HMS Genetics depalma@rascal.med.harvard.edu 3/31/2005. Full genome scan, the old way family size of 20 people. Genotype: microsatellite marker.

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Steve DePalma, Ph.D. Seidman lab, HMS Genetics depalma@rascald.harvard 3/31/2005

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  1. Mapping human disease genes with Affymetrix 10K SNP chips and the HMS Orchestra Shared Research Cluster Steve DePalma, Ph.D. Seidman lab, HMS Genetics depalma@rascal.med.harvard.edu 3/31/2005

  2. Full genome scan, the old wayfamily size of 20 people

  3. Genotype: microsatellite marker = affected = unaffected 5 / 6 2 / 4 5 / 4 6 / 2 6 / 4 5 / 2 5 / 4 1 / 3 (dominant inheritance) Two-point Lod at 0% = +2.4 4 / 1 5 / 1 5 / 3

  4. Full genome scan, old vs. newfamily size of 20 people

  5. Genotype: SNP marker G / G T / T G / T G / T G / T G / T G / T G / G Two-point Lod at 0% = +0.90 T / G G / G G / G

  6. Haplotype: SNP markers G/G A/C G/C T/G T/T C/C G/G G/G G/T A/C G/G T/G G/T C/C C/G G/G G/T C/C C/G G/G G/T A/C G/G T/G G/T A/C G/G T/G G/G A/C G/G G/G Multipoint Lod = +2.0 T/G A/C G/G G/G G/G A/A G/G T/G G/G A/A G/G T/G

  7. Multipoint calculations,sliding window of 4 SNPs * 1 * 2 * 3 * 4 * 5 SNP 1 5 9 13 17 21

  8. Example of a result lod Family N1, chromosome 1, 6-snp window

  9. Calculations per chromosome Family N1, 6-snp window

  10. SNP multipoints: sliding window Lod Family N2, chromosome X

  11. Window size vs. CPU timeFamily N1, using Vitesse on Orchestra

  12. The Future • Affymetrix 100K SNP chip • Affymetrix 500K SNP chip?

  13. Thanks to: • Sumy Mathew • Okan Toka • Yami Nicolau • Meredith Moore • Jon and Kricket Seidman • Marcos Athanasoulis and the ORCHESTRA team

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