Lecture 1 Genetic Aetiology PDF

Remember the Genetics and Immunology Module? Go to Nearpod.com Join lesson code: MI2VK You’ve got 30seconds to answer each of the questions… Genetic Aetiology of Human Disease Dr Keeley Brookes Module Learning Outcome K1. Understand variations in human genomes Gene Structure The Triplet Code...

Remember the Genetics and Immunology Module? Go to Nearpod.com Join lesson code: MI2VK You’ve got 30seconds to answer each of the questions… Genetic Aetiology of Human Disease Dr Keeley Brookes Module Learning Outcome K1. Understand variations in human genomes Gene Structure The Triplet Code Otherwise known as a codon TTT Phe TCT Ser TAT Tyr TGT Cys TTC Phe TCC Ser TAC Tyr TGC Cys TTA Leu TCA Ser TAA STOP TGA STOP TTG Leu TCG Ser TAG STOP TGG Trp CTT Leu CCT Pro CAT His CGT Arg CTC Leu CCC Pro CAC His CGC Arg CTA Leu CCA Pro CAA Gln CGA Arg CTG Leu CCG Pro CAG Gln CGG Arg ATT Ile ACT Thr AAT Asn AGT Ser ATC Ile ACC Thr AAC Asn AGC Ser ATA Ile ACA Thr AAA Lys AGA Arg ATG Met* ACG Thr AAG Lys AGG Arg GTT Val GCT Ala GAT Asp GGT Gly GTC Val GCC Ala GAC Asp GGC Gly GTA Val GCA Ala GAA Glu GGA Gly GTG Val GCG Ala GAG Glu GGG Gly The genetic code DNA to Protein DNA Sequence TAC ATG CAC GTG GTG CAC GAC CTG TGA ACT GGA CCT CTC GAG CTC GAG ACT TGA mRNA Sequence AUG GUG CAC CUG ACU CCU GAG GAG UGA AminoAcid Sequence Met Val His Leu Thr Pro Glu Glu Stop From The Genomics & Comparative Genomics website: https://www.integratedbreeding.net/courses/genomics-and-comparativegenomics/www.generationcp.org/genomics/index2ab1.html?page=1156 The International Union of Pure and Applied Chemistry (IUPAC) Mutations are the original source of genetic variation. Image source: “The causes of mutations” Understanding Evolution. University of California Museum of Paleontology. 22 August 2008. http://evolution.berkeley.edu/evolibrar y/article/evo_20. https://germguy.wordpress.com/ Somatic versus Germline Mutations 11 Somatic mutation 12 Dominant Mutations Where only one mutated allele is required to exhibit the disease phenotype Gain-of-Function: Mutation increases gene product Loss-of-Function/Haploinsufficiency: 50% of gene product Dominant-Negative No, or very little gene product 15 Recessive Mutations Where both alleles have to carry the mutation to exhibit the disease phenotype Loss-of-function: 50% of normal protein in carriers None in homozygous So why don’t we get a phenotype in the carriers??? Kacser & Burns (1973) • Hyperbolic Curve • Possible subtle phenotypes exist Wilkie, Andrew OM (April 2018) Dominance and Recessivity. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0005475.pub2 18 Mendelian versus Complex Mendelian Complex • Single mutation/gene • Rare • Mutation=disease phenotype • Easily track through families • Dichotomy or discontinuous presentation of phenotype • Rarely does environment play a role…PKU? • Multiple variations across many genes • Alternative alleles are common • Affects the risk/likelihood of phenotype • No clear pattern of inheritance • Continuous & discontinuous presentation of phenotype • Environmental factors involved too Discontinuous Continuous • One or a few genes/variations • Distinct categories of phenotype • Environment rarely plays a role • Multiple variations across many genes • Variable is quantifiable • Normal distribution • Environment can play a role Mutations versus Polymorphisms Mutation • Creates a distinct phenotype • Rare (not always e.g SCA/CF) • Large effect size • Identified by sequencing • Pedigrees/family studies Polymorphism • Contributes to normal variation within population • Neither necessary nor sufficient for phenotype • Common • Multi-allelic • Small effect size • Sequencing or genotyping • Population based studies https://biodifferences.com/difference-between-mutation-and-variation.html Different types of variation Type Frequency # alleles Location Detection RFLPs >105 Bi-allelic Genome-wide PCR/Enzymes SNPs >106 Bi-allelic Genome-wide Minisatellites (14-100bp) >105 Multi-allelic >104 Multi-allelic aka VNTRs Microsatellites (1-6bp) aka STRs End-point quantitative PCR Centromere/telomeres PCR Genome wide Genome-wide Capillary-based Downstream affects of genetic variation Single base pair substitution (Point mutation) Single Nucleotide Polymorphism (SNP – complex disease) 26 Effect on transcript Effect on gene product Missense mutation Single amino acid substitution Protein with potentially altered function Nonsense mutation Formation of a termination codon Truncated protein RNA splicing mutation Lack of an exon Abnormal protein Point mutations Changes in coding region Changes in non coding region 22 May 2023 27 Effect on transcript Effect on gene product Mutations in regulatory sequences Alteration of transcription level Increase/decrease gene product Mutations in RNA processing/translation Altered stability of transcript Increase/decrease gene product Point mutations 22 May 2023 28 Deletion mutations • • • • • A number of deletions occur in the Dystrophin gene Often shows a X-linked recessive pattern of inheritance A genetic disorder of the muscles Duchenne’s muscular dystrophy (DMD) is the most common form Usually affects only males • one out of 3,500 live male births 22 May 2023 29 Trinucleotide repeat disorders • Caused by the expansion of trinucleotide repeats CAG; CTG; CGG; GAA. • The number of these repeats is unstable and can vary. • Affected individuals have a sudden increase in the number of copies of the trinucleotide repeats. • The expansion can alter expression/structure of a protein 22 May 2023 30 Huntingdon’s Disease • autosomal dominant disease • CAG repeats diseases 5’ end of Huntingtin gene • stretch of glutamines (Gln) at the amino terminal end • Leads to late onset neuronal loss How does Gln expansion lead to neurological disorder? Poly-Gln interacts with G3PD* causing metabolic stress in neuron. • Repeats biased towards increasing in number • Anticipation Formation of intranuclear and intracytoplasmic inclusions (hallmarks of the disease) • Increase repeats through generations – Symptoms get more severe – Earlier onset *glyceraldehyde -3 phosphate dehydrogenase (function in glycolysis) 22 May 2023 31 Plenty of other examples Sickle Cell Anaemia Fragile X Syndrome Cystic Fibrosis β-thalassemia Phenylketonuria (PKU) Rett Syndrome Complex Disease is a different story There is still plenty of work to do Still looking for genetic causes • Associated polymorphisms • Mostly in non-coding regions • Likely to have subtle effects on gene function • Most are unknown • Large scale studies Genome-wide association studies Sequencing Finding out what they do • Determine the effects of the polymorphism • Confirm role in disease aetiology • Increase our knowledge of how the genome is regulated • Aid in drug development or therapeutic treatments These have monogenic/mendelian forms too What to do next? ➢ Make sure you understand the differences between the different types of genetic aetiology ➢ Make sure you know a couple of disease examples IN-DEPTH ➢ QUESTION FOR NEXT WEEK: ➢ Do you think studying monogenic forms of complex disease can help determine the genetic aetiology of the complex version?