1. Polysubstance Abuse–Vulnerability Genes: Genome Scans for Association, Using 1,004 Subjects and 1,494 Single-Nucleotide Polymorphisms Uhl, Liu, Walther, Hess, Naiman Presented by Brian O’Leary

2. Why This Article? Talkin’ about substance abuse Talkin’ about substance abuse The goal is similar to TrAPSS The goal is similar to TrAPSS UI is interested in using this method UI is interested in using this method Cheep: 11,500 SNP Chip for $500 Cheep: 11,500 SNP Chip for $500 Possible computing projects for sophomores who need something better to do than drink and play UT. Possible computing projects for sophomores who need something better to do than drink and play UT.

3. Key Definitions SNP SNP Microarray Microarray Association genome scanning Association genome scanning Pooled analysis Pooled analysis

4. SNP Stands for: Single Nucleotide Polymorphism Stands for: Single Nucleotide Polymorphism Which means: Single Nucleotide Polymorphism Which means: Single Nucleotide Polymorphism For example: AAGGCTAA  ATGGCTAA. For example: AAGGCTAA  ATGGCTAA. “For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome. “ http://www.ornl.gov/TechResources/Human_Genome/faq/snps.html “For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome. “ http://www.ornl.gov/TechResources/Human_Genome/faq/snps.html

5. Microarray Technology A technique that utilizes hybridization to evaluate expression levels of thousands of genes in a single experiment A technique that utilizes hybridization to evaluate expression levels of thousands of genes in a single experiment A microarray consists of a chip with oligonucleotides designed to hybridize to different parts of the genome A microarray consists of a chip with oligonucleotides designed to hybridize to different parts of the genome

7. Association Genome Scanning Technique that uses co-segregation to determine a marker/locus associated with a specific phenotype Technique that uses co-segregation to determine a marker/locus associated with a specific phenotype Makes use of higher genomic marker densities Makes use of higher genomic marker densities Does not require the participation of family members which increases the size of the sample Does not require the participation of family members which increases the size of the sample Downside: Downside: Founder effect – multiple founders of same phenotype Founder effect – multiple founders of same phenotype

8. Pooled Analysis Performing an analysis on one set of people vs. another set (as opposed to one individual vs. another) Performing an analysis on one set of people vs. another set (as opposed to one individual vs. another) This analysis technique loses individuality but gains a large amount of data at reduced cost. This analysis technique loses individuality but gains a large amount of data at reduced cost.

9. Snapshot of Article Few chromosomal locations confirmed for drug-abuse vulnerability alleles Few chromosomal locations confirmed for drug-abuse vulnerability alleles Used pooled-sample SNP microarray analysis to define markers and identify chromosomal regions containing allelic variants related to drug- abuse vulnerability Used pooled-sample SNP microarray analysis to define markers and identify chromosomal regions containing allelic variants related to drug- abuse vulnerability

10. Motivation Improve understanding of human addictions Improve understanding of human addictions Assist efforts to prevent and/or treat individuals with vulnerability to addictions Assist efforts to prevent and/or treat individuals with vulnerability to addictions

11. Methods – who Research volunteers provided ethnicity and drug history Research volunteers provided ethnicity and drug history European American pools: European American pools: 239 control individuals 239 control individuals 415 abusers 415 abusers African American pools: African American pools: 99 control individuals 99 control individuals 252 abusers 252 abusers

12. Methods – data technique Washed pooled DNA over an Affymetrix HuSNP GeneChip microarray Washed pooled DNA over an Affymetrix HuSNP GeneChip microarray Assessed total of 1,494 SNP markers Assessed total of 1,494 SNP markers Genotype calls were made using Affymetrix GeneChip software Genotype calls were made using Affymetrix GeneChip software A/B SNP ratios were computed A/B SNP ratios were computed Experiment replicated twice Experiment replicated twice

13. Methods – analysis Top and bottom 5% of the distributions for European American abuser/control hybridization ratios considered “candidate positive” SNPs Top and bottom 5% of the distributions for European American abuser/control hybridization ratios considered “candidate positive” SNPs Reproducibility sought by finding SNPs in top and bottom 7.5% of the African American abuser/control hybridization ratios Reproducibility sought by finding SNPs in top and bottom 7.5% of the African American abuser/control hybridization ratios

14. Methods – analysis Mapviewer used to determine SNPs close to markers linked to alcohol or nicotine dependence Mapviewer used to determine SNPs close to markers linked to alcohol or nicotine dependence Pooled results compared to individual DNA samples Pooled results compared to individual DNA samples Monte Carlo simulations used to compare results with results expected by chance Monte Carlo simulations used to compare results with results expected by chance

15. Results “ “Pooled SNP genotyping was performed with acceptable reproducibility and evidence for validity.” Of 150 candidate positive SNPs in European Americans, 42 were also in the candidate list for African Americans. By chance, 22 markers would have appeared in both sets

16. Results Three pairs of markers close to each other in genome Three pairs of markers close to each other in genome Monte Carlo simulation indicated a 0.042 probability that this would occur by chance Monte Carlo simulation indicated a 0.042 probability that this would occur by chance

17. We Know What We’re Doing So There. “ “Features of the SNP-analysis method used here also indicate sufficient reliability and validity to test our working hypotheses.” 1. 1. Test-retest, sense/antisense, and pooled and individual genotypes correlations 2. 2. Reproducible positive results 3. 3. Location of markers not likely due to chance

18. That’s It