Presentation on theme: "Genetic Approaches to Thinking, Moving and Feeling"— Presentation transcript:
1Genetic Approaches to Thinking, Moving and Feeling Richard B. Lipton, M.DProfessor and Vice Chair, NeurologyProfessor of Epidemiology and Population HealthAlbert Einstein College of Medicine
2Why consider genetic approaches? Genetic factors play a crucial role in disease that affect thinking, feeling and movingGenetic factors are relevant to potential shared mechanisms: vascular disease, inflammation, recovery from injuryMethod for parsing the heterogeneityEnvironmental risk factors interactIdentify molecular targets and treatments with pleiotropic effects
3The best of times Human Genome Project -Identify the 30,000 genes in the human genome-Sequenced 3 billion base pairs(2003)-<2% of the genome codes for protein-3 million loci with single base pair differencesHapMap Project-Systematic genotyping of 3 million SNPsAvailable of high throughput technologies
4The genome, the transcriptome and the proteome The genome is staticThe transcriptome is dynamic and tissue and cell specific. SNPs in a coding region may alter protein structure; SNPs in a promoter region may alter mRNA levels. Non-coding RNA can activate arrays of related genes.The proteome reflects post-transcriptional processes including RNA spicing, post-translational modification
5Mendelian vs. Complex Diseases and Traits 1. Mendelian (single gene)a. Autosomal dominant (Huntington’s disease)b. Autosomal recessive (Cystic fibrosis)c. X-linked2. Complex diseases and traits are multifactoriala. Oligogenic or polygenic susceptibility genes(No one gene is necessary or sufficient)b. Locus heterogeneity (different genescan cause same trait)c. Pleiotropic effectsd. Environmental factors contribute
6Causes of Complex Cognitive, Emotional and Motor TraitsGenes+EnvironmentGenesEnvironment
7Defining the phenotypes Define the phenotype of interest-Diseases-heterogeneity is the rule-Single domain phenotypes: declarative memory, depression, walking speed-Multiple domain phenotypes: executive function and walking speed-Covariance shared by traits-Use biological markers or endophenotypesOnce genes are identified contrast carriers and non-carriers to refine the phenotypesChallenge: pleiotropy and polygenicity
8Can a single gene influence thinking, feeling and moving Yes for Huntington’s, TDP-43Relevant genes might influence transmitters, ion channels, recovery from insults, plasticity, dendritic complexity, etc.A gene may influence an area of the brain that has distal secondary affectsA gene may influence several areas of the brain each of which influences a distinct cognitive, emotional or motor processA gene may influence several brain regions or processes each of which affects more than one domain (Kovas and Plomin, Trends in Cog Sci, 2006)
9Approach to Complex Diseases Assess the influence of genetic factors (heritability)-Family studies-Twin studiesIdentify specific genetic factors-Linkage analysis-Allele sharing methods-Case-control studies
10Determining the Genetic Component Familial aggregation-Measure family relative risk.-Suggests but does not prove genetic mechanism-Look for aggregation of one domain (thinking) in relativesof probands selected for another domain (moving)Twin studies-If concordance rate for MZ twins > DZ twinssome genetic influence-Look for aggregation of one domain in MZ and DZ twinswith issues in another domainHeritability: the proportion of the variance in a diseaseor trait accounted for by genetic factors
11Higher Concordance Rates for MZ vs. DZ Twins Shows a Significant Genetic ComponentConcordanceTrait MZ DZSchizophreniaInsulin-dependent diabetes mellitusPD < age 50*PD ≥ age 50*Survival** to 90 (females)*Tanner, 1999** Hjelmborg et al, 2006
12Identification of Genetic Factors in Complex DiseasesLinkage analysis: Identify extended familieswhere disease or an endophenotype appearsMendelian (usually early-onset)Allele sharing methods, genome wide screening inaffected sibling pairs (Identity by descent)Association studies in human populations
13Identification of Genetic Factors in Complex Diseases: Linkage AnalysisIdentify large families where the trait appears Mendelian(Are there high density families with relevant phenotypes?)Look for genes or DNA segments which segregate with the disease or trait.Genes and DNA segments close to each other on a chromosome tend to be inherited together.Look for coinheritance of polymorphic markers and disease.
14Common Useful Genetic Markers Simple Sequence RepeatsTens of thousands in genomeTypically di-, tri- or tetra- nucleotide repeats(GT)nunique flanking DNA sequenceSingle Nucleotide Polymorphisms (SNPs)Millions distributed throughout genomeSingle base pair substitutionsATunique flanking DNA sequence
15Association StudiesComparison of allele frequencies between unrelated affected and unaffected individuals.Case – ControlUnaffectedcontrolsAffected casesDisease-marker association exists when alleles at the marker locus occur with different relative frequencies in affected and unaffected individuals.Most important: Use unaffected individuals from the same population!
16Association Study Approaches Genome-wide scanDense set of markers throughout genome:Candidate gene searchfunctional variants (if possible) in gene with biological relevance:Single marker associationDefine common haplotypesAssess haplotypes for association
17Gene Identification in Complex Traits using Candidate Gene Approaches Select candidate genes based on biology and the availability of functional SNPs or SNP haplotypesSelect candidates for thinking, feeling and moving from the genes-Expressed in brain-Related to a specific domain-Identified based on biology (brain recovery-ApOE, inflammation-CRP, vascular risk genes-lipid related, intracellular signal transduction genes, longevity, energy metabolism)Options limited by current hypotheses
18What is the Significance of a Population Association Between a Disease and a Particular Allele (Genetic Variant)?Allele is directly involved in the pathogenesis of the diseaseThe result is a false positive due to statistical errorThe result is a false positive due to inadequate matching of cases and controls (population stratification)4) Linkage disequilibrium
19Whole Genome Association (WGA): In WGA, high density chip arrays containing hundreds of thousands of SNPs are used to screen the entire genome on a single array.Using cases and controls, WGA association results in the generation of thousands of genotypes. Identify SNPs and SNP haplotypes associated with disease.Then need to determine the disease causing SNPs among these, either coding sequence changes or possible promoter/enhancer etc variations.
20Affymetrix Genotyping Technology 250 ng Genomic DNANspRE DigestionAdaptorLigationPCR: One Primer AmplificationComplexityReduction250,000 GenotypesFragmentationand LabelingAA BB ABHyb & Wash
21Genetic approaches to thinking, feeling and moving: Centenarian studies Only ~1/10,000 individuals is 100 years oldExceptional longevity occurs with greater frequency in the siblings and offspring of CentenariansLongevity genes may contribute to successful cognitive, motor and emotional agingLonGenity PPG PI: Nir Barzilai focus on Ashkenazi Jews as a founder population
2210490 years before989295Barzilai et al, PLoS Biology 2006
23A Major Barrier to Genetic Studies in Centenarians What is the appropriate control group?
24A Major Barrier to Genetic Studies in Centenarians What is the appropriate control group?Age mates of centenarians?
25A Major Barrier to Genetic Studies in Centenarians What is the appropriate control group?Age mates of centenarians?AlternativeStudy centenarians their offspring and ages mates of their offspringHypothesis: Longevity gene frequencyCentenarian > Offspring > Controls
26Offspring of Centenarians are Less Likely to Have Age-Related Diseases 40CntnrnP35**OffspringOCControl3025Prevalence in population2015** p<0.0110****5**HTN (%)DM (%)MI (%)Stroke (%)JAGS 2004; 52:274
27Modeling Changes in the Frequency of a Genotype as a Function of Age Aging or “killing” genes0.7Longevity genes0.6Genes not contributing to life-span0.5Genotypic Frequency0.40.30.20.16065707580859095100Age
28Favorable genotype in population (%) Favorable Longevity-Associated Genotypes in Unrelated Year-Old Ashkenazi Individuals35ADIPOQ del/del30APOC3 CC25CETP VVFavorable genotype in population (%)201510565758595105Age (Year)
29Of the three longevity genes identified to date All are associated with large lipoprotein particle sizeThe favorable form of CETP is associated with high HDL levels and large lipoprotein particle sizes and with successful cognitive agingThe favorable form of adiponectin is associated with succesful motor aging
30“Longevity Genotypes” are associated with HDL and LDL particle size **1020304050607080*Large LDL (%)--VVI/VCCC/AA/-*p<0.05CETPAPOC3ADIPOQ(ug/mL)(mg/dL)(ug/mL)
31CETP VV Genotype and Cognitive Function Barzilai et al, Neurology 2007 CETP VV frequency (%)20304010MMSE<25MMSE ≥ 25*Centenarians*p<0.0491015205Dementia(n=31)Non-demented(n=129)*EASBarzilai et al, Neurology 2007
32Is Size of Lipoproteins Associated with Cognitive Function? ***P<0.003
33ADIPOQ: A Longevity Genotype with a Successful Motor Aging Phenotype The ADIPOQ del/del genotype is associated with longevity and a reduced risk of insulin resistance.The less favorable forms of ADIPOQ genotype has links with insulin resistance and metabolic syndrome, pathways which may influence motor function.Verghese et al. therefore examined the relationship between ADIPOQ del/del and gait performance in 322 subjects (mean age 78, 27% AJ, 63% women) who received quantitative gait measures.
34Relationship between genotype and measures of gait In linear regression analysis, adjusted for age and sex, the favorable form of the ADIPOQ gene (del/del) was associated with better performance on stance, swing, and double support phases.These variables generally reflect balance and rhythm (Verghese et al. JNNP,2007).
36SummaryDefine the phenotypes of interest with care considering the spatiotemporal expressionConsider family aggregation and twin studies to look at distribution within families of domains of interest.Consider searching for genes that account for the covariance among traits
37Summary Bank DNA (and other tissue?) Consider candidate gene and WGAS in cross sectional and longitudinal studies (LonGenity focuses on AJs, EAS on the Bronx population)Begin studies in midlife or early adult life to reduce influence of phenocopiesUse genes to refine phenotypes
39Genetic Research Methods: Advantages and Disadvantages Study theAdvantagesIdentify single genes with large effectsSurvey the whole genomeDisadvantagesMust be family-basedLimited power for complex disordersLow resolutionLinkageMore power for complex diseasesLarge samples for genes with small effectAssociationCustomize choicesFind selected associationsCandidate genes ( SNPs)Survey the genomeExpensiveBioinformatic challengeFalse positivesWhole genome ( SNPs)
40Pair Wise Concordance in Survival to Age 90+ Among Swedish, Danish and Finnish Twins MZConcordant TotalPairs Pairs ConcordanceMale %Female %Total %DZConcordant TotalPairs Pairs ConcordanceMale %Female %Total %Concordance = C/C+DHjelmborg et al, Human Genetics, 2006
41Can Plasma HDL Levels Predict Longevity? Females80SpouseOffspringProband*7060HDL (mg/dl)n=147n=1575040n=122*p< vs. Others
42These results support an association between specific genes and motor function.
44Lipoprotein particle size as function of age Heritability (h) of lipoprotein particle size9.820.620.821.021.221.42188.8.131.52HDL Particle Size (nm)LDL Particle Size (nm)Control9.2OffspringProbands9.08.88.620.46065707580859095100<6065707580859095100<AgeAgeBarzilai et al JAMA 290:2030, 2003
45Are lipoprotein sizes associated with protection from age-related diseases? (in offspring of centenarians)**P<0.003Barzilai et al JAMA 290:2030, 2003
46Lipoprotein and their size in healthy or subjects with the Metabolic Syndrome (MS) ***P<0.001Barzilai et al JAMA 290:2030, 2003
48Are “Longevity Genotypes” Associated with Clinically-Significant Phenotypes? 246810121416(ug/mL)--A/-**p<0.05APOC3(mg/dL)CCC/A*Levels*VVI/VCETPADIPOQ(ug/mL)
49Cross Sectional HDL Levels (Data from the Framingham study) HDL (mg/dl)5050Age
50Genetic Research Methods: Advantages and Disadvantages Study theAdvantagesIdentify single genes with large effectsSurvey the whole genomeDisadvantagesMust be family-basedLimited power for complex disordersLow resolutionLinkageMore power for complex diseasesLarge samples for genes with small effectAssociation
51Genetic Research Methods: Advantages and Disadvantages Study theAdvantagesIdentify single genes with large effectsSurvey the whole genomeDisadvantagesMust be family-basedLimited power for complex disordersLow resolutionLinkage
52Levels of analysisGenetics- study of single genes and their effects. Focus on the disease.Genomics-study of the functions and interactions many genes, their transcription and regulationProteomics-Study of proteinsMetabolomics-Study of small molecules (physiologic indicators) in plasma, tissues or cells including peptides, lipids, carbs, drugs