1. Population Pathway ? Genes SNPs Analysis Phenotypes Haplotypes/coding SNPs SNP discovery Sequencing/genotyping technology Polymorphism function Replication

2. Polymorphism Base pair substitutions Synonymous - Do not result in a new amino acid in the protein sequence. GCA (Alanine) to GCG (Alanine) (Silent mutation) Non-synonymous - Result in a new amino acid in the protein sequence. GAG (Glutamate) to GTG (Valine) (Missense mutation) - codon 6 substitution in the beta-globin protein chain causes sickle-cell anemia Nonsense mutations - Result in a termination codon. CAG (Glutamine) to TAG (stop)

3. Polymorphism Insertions - Deletions GAG TTT TCT CGG AAT GGT GGT GCT AAT GLU PHE SER ARG ASN GLY GLY ALA ASN GAG TTT CGG AAT GGT GGT GCT AAT GLU PHE ARG ASN GLY GLY ALA ASN - Fragile X Syndrome (X-linked retardation) Tandem CCG repeats - severity of disease depends on number of repeats - Huntington’s Disease Tandem CAG repeats adding Glutamine to encoded Huntingtin protein. Increasing number of proteins destabilizes the protein and interferes with synaptic transmission and leads to apoptosis of brain cells. GAG TTT TCT CGG AAT GGT GGT GCT AAT GLU PHE SER ARG ASN GLY GLY ALA ASN GAG TTT TCG GAA TGG TGG TGC TAA GLU PHE SER GLU TRP TRP CYS STOP (Often result in new stop codons and truncated proteins)

4. O6-MGMT Ile143Val Leu84Phe Lys178Arg 145Cys

5. DNA Repair Metabolism Inflammation Immunity

6. Vitamin D Metabolism 25-Hydroxylase (P450C25): Hydroxylates Vitamin D 3 producing 25(OH)D. 1-a-Hydroxylase (CYP27B1): Activates 25(OH)D to 1,25(OH) 2 D. 24-Hydroxylase (P450C24): Removes excess 25(OH)D from circulation and excess 1,25(OH) 2 D from the kidney. VDR: Mediates effects of 1,25(OH)2D. (1-a-Hydroxylase) (24-Hydroxylase) (25-Hydroxylase) VDR Ohmdahl et al. Ann. Rev. Nutr. 2002.

7. Pathways ‘Dynamic’ graphic models of molecular and biochemical pathways. WARNING: THIS IS A COMMERCIAL SITE! BioCarta http://www.biocarta.com/index.asp

8. Calorie restriction SIRTUIN NAD + Dependence Glucose Homeostasis G6Pase PEPCK PGC1  HNF4  LPK GCK ATP-synthase Cyt-C Glycolysis Glugoneogenesis Mitochondria Fat Mobilization NCOR1 SMRTRXR PPAR  ANT1 GDH IDE nDNA - Mitochondria NMNAT1 PBEF1 NNMT

9. Haplotypes

10. 7q21 Haplotype Blocks & Recombination Hotspots

12. Tags: SNP 1 SNP 3 SNP 6 3 in total Test for association: SNP 1 SNP 3 SNP 6 A/T 1 G/A 2 G/C 3 T/C 4 G/C 5 A/C 6 high r 2 AAAA TTTT G C C G G C C G T CCCCCC A CCCCCC G C C G T CCCCCC GGGG AAAA GGGG AAAA Pairwise Tagging

13. Vitamin D Receptor Sequenced 94/164 kb. 245 SNPs discovered 916 GB individuals genotyped 68 SNPs > 10% MAF Nejetsev et al. 2004. Human Molecular Genetics. Fok I Apa I, Taq I, Bsm I

14. Vitamin D Receptor 55 SNPs common in Britons, Norwegians, Gambians, Finns, Romanians TagSNPs (r 2 ≥ 0.8): Europeans: 26 TagSNPs Gambians: 42 TagSNPs Nejetsev et al. 2004. Human Molecular Genetics.

15. HapMap The International HapMap Project is analyzing DNA from a total of 270 people from populations with African, Asian, and European ancestry. Nigeria - 30 trio samples (two parents and an adult child) from Yoruba Japan - 45 unrelated individuals from Tokyo China - 45 unrelated individuals from Beijing U.S. – 30 trio samples with northern and western European ancestry. Genotyping all individuals for a SNP ~ 1,000 – 2,000 base-pairs. www.hapmap.org http://www.broad.mit.edu/mpg/haploview/

16. Resequencing

17. Resequencing Resources Systematic identification and genotyping of single nucleotide polymorphisms (SNPs) in environmental response, inflammation, immunity genes. Candidate genes are sequenced across a panel of individuals (~90) of known ethniticies to identify common sequence variation for functional analysis and population-based studies. Websites provide tools for haplotype determination and TagSNP selection. Environmental Genome Project http://egp.gs.washington.edu/ Seattle SNPs http://pga.gs.washington.edu/ Innate Immunity http://innateimmunity.net/

18. SNP databases

19. SNP Databases Warehouses of SNP information. WARNING: NOT ALL SNPs ARE VALIDATED! NCBI http://www.ncbi.nlm.nih.gov/ Utah SNPs http://www.genome.utah.edu/genesnps/ Children’s Hospital Informatics Program http://snpper.chip.org/

20. Evolution

21. VISTA Tools VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. VISTA Tools http://genome.lbl.gov/vista/index.shtml