APA 2005 Strategies for Genetics

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Information about APA 2005 Strategies for Genetics

Published on September 18, 2007

Author: Malbern

Source: authorstream.com

Slide1:  Strategies for investigating the genetics of psychiatric disorders Margit Burmeister, Ph.D. Molecular andamp; Behavioral Neuroscience Institute (formerly Mental Health Research Institute) Department of Psychiatry Department of Human Genetics Neuroscience Program Bioinformatics Program University of Michigan, USA Overview:  Overview Heritability Terminology Linkage analysis Association studies – candidate genes Whole genome association studies Phenotypes Gene x environment interaction Familiality is not heritability:  Familiality is not heritability Bipolar Disorder, Depression, Schizophrenia and Alcoholism run in families But: Going to Medical School, being Catholic and speaking Mandarin also run in families. Heritable due to genes? Familial due to environment? Adoption: risk of child more influenced by biological parents (genetic) or adoptive (environment) parents? Twins: Monozygotic (MZ, identical) twins share 100% of genes, dizygotic (DZ, fraternal) twins share 50% of genes. Twin concordance rates:  Twin concordance rates (From: Plomin et al. 1994, Science 264: 1733-9) Locus (plural: Loci):  Locus (plural: Loci) The position on a chromosome of a gene or a genetic marker or a SNP From Latin: Place Allele one of several forms of a locus We inherit one allele from each parent A locus that comes in several forms is called polymorphic Genetic marker:  Genetic marker DNA segment with known location on a chromosome whose inheritance can be followed DNA segments near each other on a chromosome tend to be inherited together so markers are an indirect way to track inheritance of an unknown gene Eye color and bristle length are used as easily recognizable genetic marker in Drosophila crosses Molecular markers are now used in human genetics Restriction fragment length polymorphisms (RFLPs). minisatellites, often also called VNTR markers microsatellite or STRP markers, e.g. CA/GT repeats SNPs: Single nucleotide polymorphism Linkage analysis:  Linkage analysis Hypothetical marker with alleles A, B, C and D is is linked to the disease. In the first pedigree, allele A segregates with the disease, but in the second pedigree, allele B segregates with the disease. The indicated recombination event leads to allele C segregating with the disorder in the right branch. What is linkage?:  What is linkage? Linkage is caused by loci (e.g. the risk gene and a genetic marker) being close to each other on a chromosome. The recombination fraction θ is the probability that, in any meiosis, there will be a recombination between them. θ=0.5 Mendelian segregation – no linkage θ=0.0 very tight linkage – no recombination. How sure are we of linkage?:  How sure are we of linkage? LOD score! Logarithm of Odds (Probability of a particular family constellation if the marker and disease locus are linked, with 10% recombination between them) LOD (q=0.1) = log ----------------------------------------------- (Probability of the same family constellation of markers and disease if the marker is unlinked to the disease locus) When is linkage significant?How many families are needed?:  When is linkage significant? How many families are needed? LOD score of 3.0 - odds of 1000:1 are equivalent to p= 0.05 With pedigree at hand, the best possible and a likely LOD score can be calculated. For a Mendelian disease, only 10 informative meioses are needed to get a LOD score of 3.03 – single families can be enough to find linkage Slide11:  In this single family with a rare recessive disorder, we found linkage to 1p36 with a LOD score of 3.28 Unaffected; Affected; * DNA available * * * * * * +* * * * * * + * Family with recessive ataxia: SCASI Complex Disorders:  Complex Disorders Psychiatric disorders are complex - unlike Mendelian disorders, where a single mutation is both necessary and sufficient to bring about the disorder. Complexity can be due to genetic heterogeneity: many different risk genes small effect of each genetic factor: risk allele only increases risk by a small fraction diagnostic uncertainty: is a depressed or alcoholic subject in a Bipolar pedigree affected or not? What about a BP II subject? interaction with the environment LOD score for complex traits – in multipoint analysis:  LOD score for complex traits – in multipoint analysis (Probability of this particular data constellation if a locus that increases risk for the disorder is in a particular chromosomal region) LOD = log ----------------------------------------------- (Probability of this particular data constellation if there is no locus that increases disease risk in this particular chromosomal region) Slide14:  COGA Genome Linkage Scan (Max. Drinks) Saccone et al. (2000) Am J Med Genet 96:632-7. Summary linkage/LOD score:  Summary linkage/LOD score looks at chromosomal location, with the help of informative genetic markers powerful for simple Mendelian inheritance – no need for large samples assumes you know the genetic model no assumptions about the biology involved Assumes one or just a few genes are involved Families easily combined – add LOD scores More powerful if less heterogeneous subtypes can be defined (e.g. Bipolar Disorder with psychosis, antisocial alcoholism; early onset MDD) Slide16:  How do I follow up my positive linkage finding that showed 3 great POSITIONAL candidate genes in the region linked to the disease? How do I test whether a new BIOLOGICAL candidate gene is involved in alcoholism? Association:  Association Cases with Alcoholism Control sample ALDH2*2 allele significantly protects against alcoholism in this sample from China (Chen et al., Am J Hum Genet. 1999,795-807). ALDH2: 1/1: 304 (56%) 1/2: 218 (40%) 2/2: 23 ( 4%) ALDH2: 1/1: 283 (83%) 1/2: 57 (17%) 2/2: 0 Slide18:  Blood Flow to Face Blood Flow to Body Feel Itchy Feel Dizzy Feel Tired Feel Anxious Pounding Head Have Sweats Increased Heart Rate Feel Nauseous These symptoms are experienced by those heterozygote for the ALDH2*2 allele, and are severe in homozygotes FLUSHING SYMPTOMS IN RESPONSE TO DRINKING ALCOHOL Pharmacogenetic association:  Pharmacogenetic association Within a disease population, pharmacogenetic studies ask about drug side effects and/or response: drop outs versus drug continuation 'responders' versus non-responders Greer and Schatzberg, 2003 Am J Psychiatry 160:1830-5. Zanardi et al., 2001 Biol. Psych. 50: 323-30. Confounding of association by ethnicity (stratification):  Confounding of association by ethnicity (stratification) Example: alcoholics in San Francisco. Asians (stripes) will be underrepresented among cases. ANY genetic marker more common among Asians will also be overrepresented in the controls – e.g. HLA. cases controls Slide21:  Linkage disequilibrium (LD) Linkage disequilibrium shows the history of the mutation. starting chromosomes that exist in population at one point A,a B,b C,c and D,d are different alleles at four different nearby loci: A b c D A b C d a b C d New mutation arises on one particular chromosome: a B C d Haplotype:  Haplotype Combination of specific SNPs on chromosome A c D A C d a C d I: A,c,D II: A,C,d III: a,C,d We might find association of a disorder with haplotype III because of linkage disequilibrium with the (untyped) allele B! a B C d b b b Applying the data::  Applying the data: There are andgt;10 Million SNPs in the human genome. Because of LD (linkage disequilibrium), typing 300,000-500,000 SNPs may give us some information about all the andgt;10 Million SNPs Single SNPs as well as haplotypes can be tested for association with disease Slide24:  COGA Genome Linkage Scan (Max. Drinks) Saccone et al. (2000) Am J Med Genet 96:632-7. Slide25:  cM/Mb bp Drawn by Jeffrey Long from Edenberg HJ, et al. (2004) Am J Hum Genet 74:705-14 SNPs haplotypes Linkage - versus - Association:  Linkage - versus - Association Needs families (e.g. sibpairs) in which the disease segregates powerful when there are just a few predisposing genes Works well even when many different mutations or alleles in those few genes increase risk for the disease Requires no hypothesis about the nature of the defect in the disorder usually requires a model of the pattern of inheritance Needs unrelated cases and unrelated controls Assumes that only one or few common variants in each gene are risk factors Powerful even when there are many different genes, each with a small effect, as long as the variant in each gene is common Until recently, required having a limited number of genes in mind 2005 and beyond:Whole Genome Association Studies:  2005 and beyond: Whole Genome Association Studies 500-1000 cases 500-1000 controls Extract DNA – hybridize to whole genome chip Construct haplotypes Calculate which of 300-500,000 SNPs and ??? haplotypes is more frequent in cases than controls Currently: $1,000 per individual – planned: $100 Slide28:  Evidence from Twin Studiesfor involvement of genes in depression:  Evidence from Twin Studies for involvement of genes in depression Redrawn from Kendler et al., 1995 Am. J. Psychiatry 152: 833 MZ Co-Twin Aff MZ Co-twin Unaff Risk of Major Depression Onset by Genotype and Severe Life Event Probability of Onset of Major Depression Absence Presence DZ Co-Twin Aff DZ Co-twin Unaff of severe life event Genes, Stress and Depression:  Genes, Stress and Depression Genetic Vulnerabilities (Personality, Physiology, …?) Early experiences (stress, rearing,..?) Vulnerable Phenotype Depression Daily stress Traumatic event Life event Exercise, antidepressants psychotherapy High Neuroticism score is a risk factor for depression:  High Neuroticism score is a risk factor for depression Endophenotypes or intermediate traits mark the genetic predisposition to a disorder, less dependent on the additional external triggers or vulnerabilities. Neuroticism is a psychological domain, measured with the established NEO-PI. Sample questions: I often feel tense and jittery (anxiety facet) Sometimes I feel completely worthless (depression) When I’m under a great deal of stress, sometimes I feel like I’m going to pieces (vulnerability) Twin and high risk studies suggest that a high Neuroticism score is a trait marker for depression At least in women, about 55% of the genetic liability to depression is shared with Neuroticism Serotonin Transporter Promoter Variant 5-HTTLPR:  Serotonin Transporter Promoter Variant 5-HTTLPR 5-HTT target of SSRIs S-short and L- long form of promoter: The L form has higher promoter activity Both are quite common in Caucasians 5-HTTLPR is associated with Neuroticism:  5-HTTLPR is associated with Neuroticism p=0.015 Total variance explained: 1.8% From: Sen et al. 2004, Biol Psychiatry. 55:244-9. Genes, Stress and Depression:  Genes, Stress and Depression Genetic Vulnerabilities (Personality, Physiology, …?) Early experiences (stress, rearing,..?) Vulnerable Phenotype Depression Daily stress Traumatic event Life event Exercise, antidepressants psychotherapy Is there an effect of childhood maltreatment on depression risk? :  Is there an effect of childhood maltreatment on depression risk? Caspi et al., Science 2003 Genotype x life events interact with respect to 5-HTTLPR genotype and depression (Caspi et al., 2003: Science 301:386-9) :  Genotype x life events interact with respect to 5-HTTLPR genotype and depression (Caspi et al., 2003: Science 301:386-9) symptoms MDD episode suicidality MDD per informant Conclusions:  Conclusions Twin and adoption studies suggest genes are involved in nearly all psychiatric disorders Psychiatric disorders are complex Linkage studies are a powerful means to find where genes are located Subtypes of psychiatric disorders that decrease heterogeneity will increase power of linkage analysis Association studies can help identify common genetic risk factors even with very small effect size Association studies are now feasible for the whole genome, not just candidate genes Research into intermediate traits/endophenotypes can help identify genetic risk variants Genes and environment interact

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