Genetics Day 1

Case Overview

• 35-year-old investment banker with routine health examination, presenting no significant health issues.
• Lifestyle factors: cigar smoking, 15 lbs overweight, infrequent exercise.
• Engaged in genetic testing through a saliva sample for predictive analysis.

Consumer Predictive Genetic Testing

• Identified increased risk for several conditions:
  • Emphysema
  • Coronary artery disease
  • Allergy to penicillin-type antibiotics
  • Colon cancer
  • Early onset Alzheimer's
• Patient expresses concern about sharing genetic information with wife and seeks guidance.

Importance of Patient’s Genome

• Patient's genome reveals ancestry and potential health risks.
• Mutations may indicate possible diseases and responses to treatments, diet, and medications.
• The genome acts as a guide for disease prevention and healthcare customization.

Human Nuclear Genome

• Composed of approximately 3.1 billion DNA letters across 2 sets of 23 chromosomes from each parent.
• Encodes about 25,000 genes responsible for cellular functioning.
• Protein-coding sequences constitute only 1.5% of the entire genome.

Mitochondrial Genome

• Contains 16.5 kb of DNA, encoding essential components for oxidative phosphorylation and protein synthesis.
• Inherited exclusively from the mother and linked to ~1% of genetic diseases, affecting high-energy-use organs.

Gene Counting and Expression

• Estimated 25,000 genes contribute to human traits.
• Various mechanisms such as epigenetics and alternative splicing enable diverse protein production.
• Promoters and regulatory elements influence gene expression in specific tissues.

Genetic Diversity

• Unrelated humans exhibit 99.9% shared DNA.
• Human diversity includes approximately 10 to 15 million single nucleotide polymorphisms (SNPs) arising from evolution.

Single Nucleotide Polymorphisms (SNPs)

• Polymorphic variations in DNA sequences potentially affecting protein function.
• Two categories:
  • Tolerated SNPs: typically do not alter function.
  • Deleterious SNPs: can disrupt protein function, impacting health.

Genome Sequencing Costs and Accessibility

• Cost of sequencing the human genome has drastically decreased from 2.3billion(2001)toapproximately2.3 billion (2001) to approximately 2.3billion(2001)toapproximately500 (2024).
• Advances in technology have reduced the time for sequencing to 1-3 days and increased coverage.

Copy Number Variations (CNVs)

• Submicroscopic genetic variations that can influence gene expression and phenotypic outcomes.
• CNVs include deletions, insertions, duplications, and other complex changes.

Genetic Variation and Disease Risk

• Genetic disorders can be monogenic or complex, involving multiple genes.
• Common monogenic disorders include cystic fibrosis and hereditary hemochromatosis.

Modifier Genes

• Genes that influence the relationship between other genes and their expression, contributing to phenotype variations.

Complex, Multigenic Disorders

• Disorders like cardiovascular diseases, diabetes, and certain cancers arise from the interaction of multiple genes.

Genetic Alleles in Complex Disorders

• Low prevalence, high penetrance alleles like BRCA1/2 and HNPCC increase the risk of specific cancers.
• High prevalence, low penetrance alleles such as APC and Factor V Leiden can elevate risks for certain health conditions.

Alzheimer’s Disease

• Involves both high and low prevalence genetic factors in its manifestation and progression.

Cystic Fibrosis Carrier Probability

• Cystic fibrosis (CF) is an autosomal recessive disorder; both parents must carry the mutation for a child to be affected.
• Probability of being a carrier for a woman with a niece affected by CF is 1 in 4, or 25%, assuming the affected niece's parents are both carriers.

Phenylketonuria (PKU) Overview

• Phenylketonuria is an autosomal recessive condition characterized by metabolism errors in phenylalanine, leading to severe intellectual disabilities if untreated.
• A known heterozygous carrier mother has a probability of 25% for each child to inherit the PKU disorder.

Genetic Probability Calculations

• The formula for genetic inheritance probability in autosomal recessive conditions:
  • For a mother's heterozygosity (P): 1 (mother) x 1/4 (child probability) = 1/4 chance of child being affected.
• Further calculations for different scenarios can yield probabilities such as 1 in 256 for certain offspring combinations.

Pedigree Analysis and Inheritance

• Pedigree must be assessed to determine inheritance modes: dominant, recessive, or linked traits.
• Affected individuals can be represented; homozygous normal individuals can be assumed based on pedigree notation (e.g., II-1 and II-5).
• Example calculations for III-1 and III-2 mating:
  • Both heterozygous (1/2 x 1/2) yield a 1/4 chance for affected children, contextualizing genetic ratio implications.

Probability of Offspring Affected

• If both III-1 and III-2 are heterozygous carriers, the offspring have a calculated probability of being affected:
  • Using the formula 1/4 (affected children probability) x 1/3 (heterozygous probability) results in 1/36 chance for an affected offspring.

Conclusion

• Understanding probabilities in genetic counseling is crucial for assessing risks and guiding patients in potential genetic outcomes for their children.

Base Pairing and DNA Structure

• Base pairing follows Watson-Crick rules: A pairs with T (2 hydrogen bonds) and G pairs with C (3 hydrogen bonds).
• A constant width in DNA is maintained by pairing a purine (A, G) with a pyrimidine (T, C).
• Chargaff's rule states that the amount of adenine (A) plus guanine (G) equals thymine (T) plus cytosine (C).
• DNA was structurally modeled by James Watson and Francis Crick in 1953.
• Methylation of guanine can be reversed by the enzyme MGMT, critical for DNA repair.

DNA Repair Mechanisms

• Excision repair types include Base Excision Repair (BER), Nucleotide Excision Repair (NER), and Mismatch Repair (MMR).
• BER addresses damage from endogenously occurring events, such as oxidative damage and deaminations.
• Key steps in BER include damage recognition, incision, removal, gap filling, and ligation.
• BER is energetically inexpensive but requires specificity provided by DNA glycosylases.

Nucleotide Excision Repair (NER)

• NER is used for repairing bulky DNA adducts that distort the helix, offering flexibility in response to environmental damage.
• In prokaryotes, NER is carried out by the Uvr excinuclease system.

Central Dogma of Molecular Biology

• Central dogma describes the flow of genetic information from DNA to RNA to protein.
• RNA, differing from DNA by containing ribose sugar and uracil (U) instead of thymine (T), exists as a single strand.
• Transcription involves synthesizing mRNA from DNA, while translation converts mRNA to peptides in the cytoplasm.

Transcription and Translation

• Transcription occurs in the nucleus, resulting in the formation of mRNA.
• Translation involves the decoding of mRNA into polypeptides, utilizing tRNA and ribosomes.
• Co-transcriptional translation is observed where translation occurs simultaneously with transcription.

Variability in Translation

• Some viruses utilize leaky scanning, tRNA slippage, and other mechanisms to generate multiple peptides from one mRNA strand.
• Proofreading during translation is maintained by elongation factors which ensure accuracy by driving the process and hydrolyzing GTP.

Ribosome Function and Antibiotic Interaction

• Multiple ribosomes can simultaneously translate a single mRNA (polyribosome) for efficient protein synthesis.
• Common antibiotics and toxins target prokaryotic ribosomes, inhibiting processes such as tRNA-mRNA interactions and peptide bond formation:
  • Aminoglycosides (e.g., streptomycin) bind to small ribosomal subunits.
  • Chloramphenicol inhibits peptide bond formation at the peptidyl transferase center.
  • Tetracycline blocks tRNA-mRNA interactions.
  • Macrolides bind the large subunit, preventing peptide bond formation.
  • Ribosome inactivating proteins like Shigella toxin and ricin disrupt rRNA GTPase interactions.