The Discovery of Human Disease Genes PDF

The Discovery of Human Disease Genes Michael Simpson  Learning Objectives I The Discovery of Human Disease Genes An appreciation of the genetic contribution to disease An understanding of inheritance patterns in Monogenic disease An insight into evaluating se...

The Discovery of Human Disease Genes Michael Simpson  Learning Objectives I The Discovery of Human Disease Genes An appreciation of the genetic contribution to disease An understanding of inheritance patterns in Monogenic disease An insight into evaluating segregation of genomic regions How this segregation can be used to map disease genes with linkage How to find the disease causing mutation once a genomic region is mapped How contemporary DNA sequencing is enabling new approaches to disease gene discovery  The Spectrum of Genetic Disease Most disease states and traits result from a combination of genetic and environmental factors Crohn’s Disease Hitting your head on a door frame Cystic Fibrosis Chicken Pox Psoriasis T1 Diabetes Achondroplasia T2 Diabetes Genes Environment  Monogenic Diseases Monogenic diseases … Are caused by mutations in a single gene The mutation(s) in the single gene are both necessary to produce the clinical phenotype sufficient to produce the clinical phenotype Demonstrate transmission in pedigrees Transmission may follow dominant or recessive inheritance patterns  Human Monogenic Diseases Human phenotypes in ‘Mendelian Inheritance in Man’ 8000 6000 Molecular basis unknown 4000 Molecular basis known 2000 0 1970 1980 1990 2000 2010  Why Do We Want to Identify Disease Causing Genes? Molecular confirmation of clinical diagnosis Accurate carrier testing for individuals or couples Presymptomatic testing for adult onset conditions (e.g. Huntington’s disease, familial breast cancer) Prenatal diagnosis for pregnancies at high risk of severe disorder It provides an insight into the pathological mechanisms underlying the disease  Positional Cloning Identification of multigenerational Systematic evaluation of inheritance Mutational search within genomic affected pedigree patterns across the genome regions cosegregating with the disease  Inheritance Patterns Autosomal Dominant Inheritance Mutations in one copy of the gene is necessary to cause the disease Transmission is vertical Equal number of affected males to females Male to male transmission is observed Unaffected individuals have unaffected offspring but… may arise as new mutation  Inheritance Patterns Autosomal Recessive Inheritance Mutations in both copies of a gene are necessary to cause the disease Both parents are carriers, generally clinically normal Equal number of affected males and females Consanguinity may be present  Inheritance Patterns X-linked Recessive Mutations in one copy of a gene are necessary to cause the disease in males, females would need mutations in both copies of the gene Females with one mutated copy of the gene are normal Incidence is much higher in males than females No male to male transmission  Mapping the Location of a Disease Gene During meiosis… the precursor cells of the sperm or ova must multiply and at the same time reduce the number of chromosomes to one full set two chromosomes of a homologous pair exchange segments in a process known as recombination  Linkage Because recombination can (essentially) occur at any location along chromosome, the frequency of recombination between two locations depends on their distance As a consequence DNA regions that are located in close proximity are more likely to be co-inherited than DNA regions originating from further apart This phenomenon is called genetic linkage It can be observed experimentally by assessing genomic loci (specific sites) that vary and evaluating their co inheritance  Linkage Consider three variant loci A, B and C 11 informative miosies A 11 recombination events observed B C 8 recombination events between A and B 3 recombination events between A B and C B C Therefore B is closer to C than A is closer to B A B C  Measuring Variation to Evaluate Linkage Same scenario but with genotypes 11 informative miosies A1A2 A3A4 B1B2 B3B4 11 recombination events observed C1C2 C3C4 8 recombination events between A and B A2A4 ANAN A1A4 ANAN A1A4 ANAN 3 recombination events between B1B3 BNBN B2B4 BNBN B2B3 BNBN B and C C1C3 CNCN C2C3 CNCN C2C3 CNCN Therefore B is closer to C than A is closer to B A2AN A2AN A1AN A4AN A4AN B3BN B3BN B2BN B4BN B2BN C3CN C3CN C3CN C2CN C2CN  Linkage How does this help us map genes We can reconstruct the mutation M m m m genotype without actually knowing where the mutation locus is M m m m M m m m m m m m m m M m M m m m m m  Linkage How does this help us map genes? We can then consider a series of M m m m variable loci across the genome and see if they are linked to the mutation locus M m m m M m m m m m m m m m M m M m m m m m  Linkage How does this help us map genes? Considering cosegreagation with M m m m variant locus A A1A2 A3A4 We observe inheritance of the mutation once with allele A2 Once with allele A1 M m m m M m m m m m m m And twice where we cannot be A2A4 ANAN A1A4 ANAN A1A4 ANAN sure if it has been inherited with A1 or A2 Therefore the mutation locus is not linked to the locus A m m M m M m m m m m A2AN A2AN A1AN A4AN A4AN  Linkage How does this help us map genes? Considering cosegreagation with M m m m variant locus B B1B2 B3B4 We observe inheritance of the mutation three times with allele B1 Once with allele B3 M m m m M m m m m m m m B1B3 BNBN B1B4 BNBN B2B3 BNBN Therefore the mutation locus is nearly linked to the locus B m m M m M m m m m m B3BN B3BN B1BN B4BN B2BN  Linkage How does this help us map genes? Considering cosegreagation with M m m m variant locus C C1C2 C3C4 We observe inheritance of the mutation with allele C1 every time the disease is transmitted And never when the disease is not M m m m M m m m m m m m transmitted C1C3 CNCN C1C4 CNCN C2C3 CNCN Therefore the mutation locus is linked to the locus C Therefore the mutation is located m m M m M m m m m m close to variant locus C C3CN C1CN C1CN C4CN C2CN  Linkage The linkage approach is typically used to asses segregation of gnomic regions using ~400 multialelic loci or ~5000 biallelic loci This approach enables systematic evaluation of cosegreagation of genomic regions with the disease locus A statistical test, known as the LOD score is used to detect the presence of linkage L(linkage ) LOD = log10 L(no linkage ) A LOD score >3 is consistent with linkage whereas a LOD score