Gene 271 Outline PDF

GENE 271 OUTLINE September 23, 2024 Mutation: a permanent change in the DNA sequence, which may result in functional and phenotypic changes ○ Preferred terminology is variant → impartial, classified Somatic changes: acquired over a lifetime in single cells, not inherit...

GENE 271 OUTLINE September 23, 2024 Mutation: a permanent change in the DNA sequence, which may result in functional and phenotypic changes ○ Preferred terminology is variant → impartial, classified Somatic changes: acquired over a lifetime in single cells, not inherited Germline changes: present in every cell of the body including egg and sperm Different mechanisms of mutation ○ Point mutation: substitution of one nucleotide by another nucleotide ○ Insertion: addition of one or multiple nucleotides ○ Deletion: loss of one or multiple nucleotides Different effects of mutation ○ Silent: substitution does not cause an amino acid change Change in DNA base → leads to the same AA sequence Aka synonymous mutations Due to redundancy in amino acid codons Usually doesn't cause health issues → except when regulatory elements are disrupted ○ Missense: substitution does cause an amino acid change Impact on protein structure and function can be difficult to predict Example: achondroplasia is a short-limbed skeletal dysplasia (dwarfism) Caused by missense mutations G>A or G>C Thanatophoric dysplasia is a skeletal dysplasia that is lethal before birth, caused by other missense mutations ○ Nonsense: substitution which results in a premature stop codon It may produce a truncated protein with abnormal function Or mRNA may be targeted for degradation by nonsense-mediated decay and no protein is expressed Example: Hurler Syndrome aka mucopolysaccharidosis type 1 (MPS 1) is a lysosomal storage disorder 70-80% caused by nonsense mutations in the IUDA gene Some drug therapies aim to treat nonsense mutation disorders by promoting readthrough after the premature stop codon (nonsense suppression) ○ Frameshift: insertion or deletion of bases, not in a multiple of 3, which disrupts the reading frame Multiple of three = in-frame insertion or deletion Insertion of deletion of 1+ not in frame = frameshift mutation Changes to codon reading frame and changes all AA after Example: Duchenne muscular dystrophy: frameshift mutation in DMD gene No functional protein is produced, and more severe  Example: Becker muscular dystrophy (BMD): caused by in-frame deletions in DMD Dystrophin protein has some residual function, a milder clinical phenotype ○ Splicing: any mutation which disrupts proper mRNA splicing mRNAs are processed before translation into protein Splicing: removal of introns and splicing together exons Genes normally contain splice donor and acceptor sites, which mutations can disrupt thus introducing a new site or interrupting an existent one September 25, 2024: Population Genetics for Genetic Counseling genetic variant: a specific region of the genome that differs between two genomes How is variation produced? ○ Mutation ○ Migration ○ Recombination What happens to variation ○ Genetic drift, bottleneck, and founder effects ○ Natural selection ○ Sexual selection Assortative mating (similar genotype/phenotype) disassortative mating (different genotype/phenotype) Allele frequency: the number of individual alleles of a certain type at a locus, divided byt he total number of alleles of all types at that locus in a population Pathogenicity: a probabilistic assertion of the likelihood that the variant is cuasally related to a heritable disease – not a clinical diagnosis Penetrance: the proportion of individuals in a population who carry a specific variant and express the related phenotype  Effect size: the percentage of the phenotypic variants in a population attributable to the variant: i.e how much of the phenotype is due to the variant Populations are continuous, hard to define Population can affect variant interpretation; differing populations How can common variants' effects be measured ○ GWAS: genome-wide association study ○ eQTL: expression quantitative trait locus ○ Chromatin QTL, cQTL: chromatin quantitative trait locux October 2, 2024: DNA Sequencing Technologies - Sanger Sequencing - Uses modified PCR to amplify DNA - Uses chain terminators – ddNTPs which halt the elongation of DNA – labeled with fluorescent dye - ddNTPS (dideoxynucleotides) – do not have free 3' OH group usually present on DNA and needed for synthesis to continue - Reaction components: DNA fragments, DNA primer, DNA polymerase, 99% regular dNTPs, fluorescent ddNPTs 1% - Process: Annealing and chain extension, ddNTP binding and chain termination, fluorescently labelled DNA sample, capillary electrophoresis, sequence analysis and reconstruction → resulting in a chromatograph - DNA fragments are separated by gel/capillary electrophoresis and identified by fluorescent labels - Stats: - Up to 384 samples of up to 700 base size and 1 million bases per day  - Error rate: 11kb and share >90% of sequnce identity, accounts for 5% of genome – when located close together, can predispose to structural rearrangements - Mutation rates for CNVs much higher than for point mutations  - 1000s genomes: discover genotype and haplotype in more people - gnomAD: expanded to include a broader representation of humans from across the globe - International Hap Map: The goal is to develop a haplotype map of the human genome to compare (GWAS). - Human Pangenome reference - Clingen: effort to categorize the clinical consequences of variants in the human genome - EVE: evolutionary conservation analysis: a high degree of conservation at a specific amino acid position across many species suggests the necessity of that specific residue for normal protein structure or function - Pangolin and SpliceAI: predict splicing from pre-mRNA sequence - All of Us program October 9th, 2024: Genetic Disease Mechanisms - Haploinsufficiency: mutation in one copy of the gene results in a loss-of-function of the allele - Types of mutations: nonsense, frameshift - Leads to nonsense-mediated decay - Unable to function at full capacity → leads to disease - Dominant Negative Effect: mutation in one copy of the gene causes the defective copy to produce a protein that has a negative or 'toxic' effect on the cell - Missense mutations - More common in proteins that form complexes (multimers) - Misfolded proteins can accumulate → cell death - Gain-of-function: mutation in one copy of the gene causes the defective copy to produce a protein that has an increased or unregulated function - Missense mutations - Mutant 'toxic' protein has excessive or new protein function that could have a selective advantage, could be expressed at the wrong time - Clinical heterogeneity: mutations in one gene can cause many genetic disorders - Diff mutations, different protein domains - Genetic heterogeneity: genetic disorder caused by mutations in one of many genes - Same heteromeric protein or complex - Steps of same regulatory/signal transduction pathway October 14th, 2024 Population Genetics cont. - GWAS: Genome-wide association studies: ~ 500,000 variants tested for association with a given phenotype - eQTL studies: ~ 500,000 variants tested for each phenotype (~20,000 genes) - Chromatin eQTL studies: ~ 500,000 variants tested for each phenotype (ex 60,000 acetylations) Workshop - Why is the mechanism of disease important? - To explain the biology of the condition - To determine what kind of testing to consider and order - Pedigree risk evaluation - Terms to know - Incomplete penetrance - Genomic imprinting - Mosaicism - Dynamic mutations - Clinical heterogeneity - Genetic heterogeneity (locus heterogeneity): - Allelic heterogeneity: different mutations in the same gene can cause similar or the same phenotypes - Case example: - CDKN1C gene can cause multiple conditions: BWS, IMAGe, RSS - Imprinting disorder: only the maternal allele is expressed