Siracusa Human Genes Nuclear genome: 1.

.1% - protein-coding genes 4% - RNA genes 6% - heterochromatin 45% - transposon repeats 44% - other Mitochondrial genome: 66% - protein-coding genes 32% - RNA genes 2% - other Between two individuals, sequences are 99.9% identical One change in every 1000bp Genetic Variation includes polymorphisms and mutations 1. Single nucleotide polymorphisms (SNPs) 2. Microsatellites (repeating unit 1-3bp) 3. Minisatellites (repeating unit 20-100bp) 4. Deletions/duplications/insertions at non-repeat loci Categories of Genetic Disease: 1. Chromosome disorders 2. Mendelian disorders (inherited) 3. Multifactorials disorders (inherited) 4. Somatic disorders 5. Mitochondrial disorders 22 Pairs of autosomes plus X and Y Some genetic diseases involve alterations in the number and/or shape of chromosomes Down Syndrome: extra chromosome 21 Kleinfelter: 2Xs and a Y; males have sexual problems Gross chromosome abnormalities: Abnormalities in chromosome number trisomy Trisomy 21 Down's Syndrome Trisomy 13, 18 Cause mental retardation and heart defects Other trisomies are lethal Abnormalities in chromosome structure Inappropriate exchange of genetic material between chromosomes Translocations, inversions, large rearrangements Inherited Disease

Simple: Caused by mutations in a single gene Inherited in families Recognizable inheritance patterns (AD, AR, X-linked dominant, Xlinked recessive, Y-linked) Complex: Caused by mutations in more than one gene Environmental influences May run in families Autosomal Dominant (AD): Heterozygotes are affected Over 3700 AD traits Huntington's, Osteogenesis imperfecta Pedigree characteristics: 1. Vertical pattern of inheritance 2. Recurrence risk is 50% if an affected marries an unaffected 3. Gender risk equal 4. Complications abound.. Complications: 1. Variable expressivity variation in age of onset, phenotypic severity, or any other measurable parameter 2. Incomplete or non-penetrance mutant genotype does not always cause a mutant phenotype; may also refer to agerelated penetrance 3. Phenocopy disease phenotype is not cause by an inherited mutant genotype 4. Anticipation tendency of some dominant conditions to become more severe in successive generations; usually due to expansion of trinucleotide repeats 5. Imprinting although certain genetic disease genes can be transmitted by parents of either sex, the phenotype is evident only when the mutation is transmitted from a particular parent 6. Mosaicism presence of mutant allele in only a subset of tissues Non-penetrance Genetic Modifier Loci are also known as epistatic factors, gene products that influence the phenotype of a disease state, but are not themselves the cause of the disease Environmental factors such as radiation and exposure to toxic agents and life-style factors such as diet and exercise can influence disease phenotypes Autosomal Recessive (AR): Homozygotes are affected (although sometimes heterozygotes manifest minor phenotypes

Examples: cystic fibrosis, Tay-Sachs Parents of affected children are often asymptomatic carriers Pedigree characteristics: 1. Horizontal pattern of inheritance 2. Frequently seen in consanguineous unions 3. Both sexes equally affected 4. If both parents are carriers, risk of affected child Sex-linked Inheritance May be either X- or Y-linked Y-linked disorder: Swyer Syndrome Leads to XY females with gonadal dysgenesis Translocation of Y to X at ARY causes XX male syndrome X-linked dominant (rare) X-linked hypophosphatemic rickets Child of an affected female, regardless of gender has 50% chance of being affected Inheritance pattern looks like AD, except all daughters of affected males are affected X-linked recessive disorders (common) pedigree features: Males affected (hemophilia A, Duchenne's musc. dystrophy) Disease transmitted by carrier women who are asymptomatic Disease can affect women if a carrier female mates with affected male (very rare) Finding Disease Genes: Input: Ascertainment of disease Family DNA collection Cytogenetic analyses Collection of unrelated patients and controls Direct gene tracking: Candidate gene analysis Screen/sequence candidate genes Compare to unaffected controls Confirm that all affected family members have the mutation Indirect gene tracking: Linkage analysis Used when there is no obvious candidate gene Uses polymorphic markers to track disease locus Variable among individuals Inherited from parent to child Location in genome is precisely known SNPs and CNVs now used on chip arrays Markers define disease interval Sequence genes in interval for mutations

Parametric genetic linkage analysis Determine genotypes of family members at many marker loci Observe occurrence of recombinants vs nonrecombinants Mode of inheritance is known LOD score calculations are performed over a range of recombination fractions LOD +3.3 = 1000:1 odds of linkage Sequence analysis Sequence whole transcriptome or genome Compare mutations in affected vs. non-affected people Cystic Fibrosis Over 100 mutations documented Homozygotes for common mutation F508 show full spectrum of disease Same genotype, variable phenotype: Modifier Genes Multifactorial Threshold Model for Complex Genetic Diseases Threshold marks the point at which a given genetic and environmental liability is expressed in the form of a disease (e.g. top 10% of liability) Susceptibility genes: genes whose variants may increase liability May be neither necessary nor sufficient for the development of disease of an individual Determining Genetic Basis of a Disease Familial clustering Concordance greater risk of disease in monozygotic vs dizygotic twins C / (C + D), C=total number of concordant twins, D = discordant Monozygotic study 11 con. : 11 dis. | Concordance = 50% Dizygotic study 3 con. : 30 dis. | Concordance = 9% Clustering in populations that share common ancestry GWAS Genome Wide Association Studies Goal 1 Test a large portion of common SNPs for association with a disease Goal 2 Identify disease-related variants without prior hypothesis of function Population level, not family level Based on identification of haplotype structure of human genome We share blocks of SNPs that identify haplotypes Screens for co-occurrence of SNPs witha disease in large populations GWAS vs Classical Mapping

More powerful for common, low penetrance variants Better resolution No need for candidate genes Procedure: 1. Collect cases and controls (1000s 10000s) 2. Test each person for expression of one or more traits 3. DNA microarrays to get whole-genome profile 4. Compute relationship of SNPs to phenotypes 5. Small number of SNPs will show association 6. Interrogate candidate region further