Genetics: Terminology and Study Design

1. Genetics: Terminology and Study Design Henry R. Kranzler, M.D. Alcohol Research Center University of CT School of Medicine

2. Organization of the Talk • Primer in genetics • How to identify genes that contribute to a specific phenotype (including some potential pitfalls) • What’s the payoff?

3. DNA Encodes Genetic Information • Long, coiled, double-stranded chain of interlocking base-pairs • 4 types of bases : A (adenine), T (thymine), G (guanine), and C (cytosine) • Sequence of the bases encodes information • One copy of the human genome: 3,000,000,000 bases long

4. DNA Is Packaged in Chromosomes • 46 chromosomes, which are strands of DNA bundled together by proteins (histones). • A typical human cell has 22 pair of autosomes and a pair of sex chromosomes (i.e., X and Y). • Each parent contributes 23 chromosomes (22 autosomes and a sex chromosome) to each cell.

5. Genes • Sections of DNA that carry instructions for a specific function (e.g., transcription of a message that is ultimately translated into protein). Proteins (e.g., neurotransmitter receptors) can have behavioral effects. • Humans have about 25,000 different genes, many of which interact in complex ways. • While by and large all humans have the same genes, the different forms of many genes, called alleles, are a major source of genetic diversity.

6. Polymorphisms • Alternate forms of a gene, with the minor allele having a frequency >1% (cf. mutation) • Single nucleotide polymorphisms (SNPs) occur throughout the genome at a frequency of about 1/1,000 bp • Most polymorphisms are not functional (i.e., they don’t directly affect protein structure), but they may be in linkage disequilibrium with a functional polymorphism • Other kinds of polymorphisms (e.g., STRs) are often more informative than SNPs

7. Central Dogma

8. Molecule to Malady • What are you looking for? • Genetic association to phenotype (e.g., diagnosis or trait) • How do you get there? • Genomewide methods • Gene-based methods • Why is it important? • Screening • Prevention • Treatment

10. Heritability Proportion of the variability in phenotype that is attributable to additive genetic effects

11. Heritability of Psychiatric and Medical Disorders

12. Nearly All Psychiatric Phenotypes Are Complex Genetic Traits • They do not follow Mendelian inheritance • Many genes are involved • Phenotypes are difficult to define

13. “Malady” or “Phenotype” • Diagnosis or behavior • Categorical diagnosis (e.g., Alcohol Dependence) • Single characteristics related to diagnosis (e.g., “MAXDRINKS”) • “Endophenotypes” or “Intermediate phenotypes” • Neuroimaging measures • EEG measures

14. Progress in Mapping Mendelian and Complex Traits From: Glazier et al., Science, 2002

16. Molecule to Malady • What are you looking for? • Genetic association to phenotype (e.g., diagnosis or trait) • How do you get there? • Genomewide methods (i.e., linkage) • Gene-based methods (i.e., association) • Why is it important? • Screening • Prevention • Treatment

17. Two Basic Approaches to Gene Mapping or Identification • Genetic Linkage • Interrogate the entire genome by genotyping 300-400 highly polymorphic markers at regular intervals (e.g., 10 cM) • Genetic Association • Start with a candidate gene and genotype polymorphisms within that gene • Genomewide association studies (GWAS) currently use 1 million or more SNPs to interrogate the genome

18. Observation of cotransmission of trait and genetic marker alleles within families Can’t be confounded by population stratification (which is the bane of association studies A positive study gives a map location, not a specific gene Expensive to collect specialized pedigree materials Power is compromised by genetic heterogeneity and other kinds of complexity Genetic Linkage

19. Affected Unaffected 12 23 22 13 13 13 12 23 1 D 2 d 2 d 3 d 12 Identity-by-descent (i.b.d.) linkage

20. 12 23 22 13 13 13 12 23 1 D 2 d 2 d 3 d 12

21. 12 23 22 13 13 13 12 23 1 D 2 d 2 d 3 d 12 i.e., the marker (allele 1) and the disease (inferred locus D) are co-inherited Usual test statistic is the lod score

22. 1 D 2 d Smaller region, Fewer genes { perhaps 20-30 centiMorgans 300 genes Linkage region must be narrowed for gene identification using other methods

23. Observation of increased or decreased allele or haplotype frequency in cases compared to a control sample Can be confounded by population stratification A positive study gives something close to or in a specific gene With GWAS, there is not an a priori hypothesis, so the issue becomes dealing with the high rate of false positive findings. Genetic Association

24. CONTROLS * * * * * * * * * * Genetic Association Study CASES * * * * * * * * * * * * * * Can reflect either a direct functional effect, or linkage disequilibrium with a functional variant

25. Population Stratification • Confounding of population or subpopulation differences in allele frequencies with phenotype • Key issue for case-control association designs

26. Obvious Global Genetic Diversity Source: NY Times Magazine 5-6-01 via Milunsky A: Your Genetic Diversity, Perseus Publishing, 2001

27. Non-Obvious Global Genetic DiversityTwo exon 1 polymorphisms at the m-opioid receptor locus Gelernter et al., 1999

28. Molecule to Malady • What are you looking for? • Genetic association to phenotype (e.g., diagnosis or trait) • How do you get there? • Genomewide methods • Gene-based methods • Why is it important to identify the genetic basis of a disorder? • Screening • Prevention • Treatment

29. More Specifically Identifying the genetic contribution to a disorder helps to: Screen for those at risk of developing the disorder Intervene to prevent the disorder (e.g., diet) Develop treatments (e.g., medications) to treat the disorder Select individuals most likely to benefit from specific treatments