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Questions and Answers

What type of traits are governed by a single gene and often follow Mendelian inheritance patterns?

  • Polygenic Traits
  • Omnigenic Traits
  • Monogenic Traits (correct)
  • Oligogenic Traits

Which model suggests that nearly all genes in a genome can influence a trait indirectly through core genes?

  • Polygenic Model
  • Monogenic Model
  • Oligogenic Model
  • Omnigenic Model (correct)

Heritability values greater than what threshold are typically considered significant enough to pursue gene identification?

  • 0.8
  • 0.1
  • 0.5
  • 0.3 (correct)

What is the heritability formula used to calculate the genetic contribution to a quantitative trait?

<p>Heritability = 2 x (MZ - DZ) (A)</p> Signup and view all the answers

What type of model describes the accumulation of genetic and environmental risk factors leading to disease occurrence?

<p>Threshold Model (A)</p> Signup and view all the answers

Which of the following is NOT true about heritability?

<p>It applies to individuals. (A)</p> Signup and view all the answers

Which of the following traits is an example of a polygenic trait?

<p>Height (D)</p> Signup and view all the answers

What do endophenotypes represent in the context of genetics?

<p>Multiple measurable phenotypes (C)</p> Signup and view all the answers

What is the gold standard method to control false positive associations in genetic studies?

<p>Bonferroni correction (B)</p> Signup and view all the answers

What happens to statistical power when a stricter alpha level is chosen?

<p>Statistical power decreases (B)</p> Signup and view all the answers

Which of the following is a potential issue that could occur due to hidden population stratification?

<p>Different prevalence of disease across subsets (A)</p> Signup and view all the answers

What is indicated by an r-squared value of 1 in terms of linkage disequilibrium?

<p>Perfect linkage disequilibrium is observed (B)</p> Signup and view all the answers

Which factor can help mitigate confounding caused by family structure in genetic studies?

<p>Including unrelated individuals (A)</p> Signup and view all the answers

Why are rare variants challenging to detect in genetic studies?

<p>They require larger sample sizes for detection (D)</p> Signup and view all the answers

What characterizes linkage disequilibrium (LD)?

<p>Non-random association of alleles at two loci (A)</p> Signup and view all the answers

What is the role of Tag SNPs in genetic association studies?

<p>They indicate a likely causal variant linked with another significant variant (A)</p> Signup and view all the answers

What does Linkage Disequilibrium (LD) signify?

<p>Non-random association of alleles at different loci (B)</p> Signup and view all the answers

What is a haplotype?

<p>A group of alleles inherited together (A)</p> Signup and view all the answers

What is the primary purpose of imputation in genetics?

<p>To predict untyped genotypes based on known patterns (D)</p> Signup and view all the answers

What is indicated by an r-squared value of 1 in imputation?

<p>Perfectly imputed genotypes (A)</p> Signup and view all the answers

How does pharmacodynamics differ from pharmacokinetics?

<p>Pharmacodynamics refers to the effects of drugs on the body (C)</p> Signup and view all the answers

What is the goal of pharmacogenetics?

<p>To identify genetic variants affecting drug response (C)</p> Signup and view all the answers

Why is the VKORC1 gene variant significant in pharmacogenetics?

<p>It influences the metabolism of Warfarin (A)</p> Signup and view all the answers

What role do reference panels play in imputation?

<p>They provide information on haplotype frequencies (D)</p> Signup and view all the answers

What is the primary purpose of identifying genetic profiles in pharmacogenetics?

<p>To increase the efficacy and safety of pharmaceuticals (B)</p> Signup and view all the answers

Which type of study is best suited for analyzing very low variance with large effect sizes?

<p>Link Analysis or Clinic Exome Sequencing (B)</p> Signup and view all the answers

Which study is conducted to assess the adverse reactions to medications in pharmacogenetics?

<p>Genome-wide association study (GWAS) on adverse reactions (D)</p> Signup and view all the answers

What does a Weighted Genetic Risk Score (GRS) take into account?

<p>Each allele's effect size alongside its presence (B)</p> Signup and view all the answers

What coding scheme is used in the additive model for genetic variants?

<p>0, 1, or 2 copies of the coded allele (B)</p> Signup and view all the answers

Which statement accurately describes Genome-Wide Association Studies (GWAS)?

<p>All results from GWAS are reported, minimizing publication bias. (C)</p> Signup and view all the answers

In the pipeline using GWAS, what is the first step in identifying a causal gene for a disease?

<p>Performing gene silencing in relevant cell lines (B)</p> Signup and view all the answers

What is the significance of assessing pleiotropic effects in drug targets?

<p>To ascertain whether variants affect other phenotypes (C)</p> Signup and view all the answers

Why is it important for GWAS to have large sample sizes?

<p>To ensure sufficient power for detecting associations. (B)</p> Signup and view all the answers

Which method is primarily utilized for gene replacement in gene therapy?

<p>CRISPR-Cas9 (C)</p> Signup and view all the answers

What is the appropriate genome-wide significance threshold for GWAS?

<p>&lt; 5 x 10 ^ -8 (A)</p> Signup and view all the answers

What is a major weakness of Candidate Gene Studies?

<p>They are prone to publication bias and may miss new biology. (B)</p> Signup and view all the answers

What does the genetic risk score (GRS) represent?

<p>The cumulative burden of risk alleles for a disease (B)</p> Signup and view all the answers

What plays a more critical role in determining power in GWAS compared to other epidemiological studies?

<p>The number of cases rather than controls. (A)</p> Signup and view all the answers

Which of the following is NOT a step in the process of identifying drug targets via GWAS?

<p>Conducting a market analysis of pharmaceuticals (C)</p> Signup and view all the answers

Which factor may lead to genomic inflation in GWAS results?

<p>Population stratification. (B)</p> Signup and view all the answers

Which statement best reflects the outcomes expected from replicating findings in GWAS?

<p>Replication drastically reduces the false positive rate. (D)</p> Signup and view all the answers

What is one limitation of GWAS mentioned in relation to statistical correction?

<p>It cannot use Bonferroni correction effectively. (B)</p> Signup and view all the answers

What characterizes cancer as a set of disorders?

<p>It is marked by abnormal cell proliferation. (B)</p> Signup and view all the answers

What does the Multiple-Hit Theory in cancer genetics describe?

<p>The accumulation of mutations in oncogenes and tumor suppressor genes. (B)</p> Signup and view all the answers

How do oncogenes typically promote cancer?

<p>Through gain of function mutations that aid in cell growth. (A)</p> Signup and view all the answers

What role do tumor suppressor genes play in normal cell function?

<p>They control the progression of the cell through the cell cycle. (B)</p> Signup and view all the answers

Which type of mutation commonly contributes to the activation of oncogenes?

<p>Missense mutations that lead to aberrant protein functions. (D)</p> Signup and view all the answers

What is the consequence of a loss of function in DNA repair genes?

<p>The development of tumors through increased mutation rates. (C)</p> Signup and view all the answers

How do mutations in tumor suppressor genes typically affect cancer progression?

<p>They act dominantly at the cellular level and are recessive for individuals. (D)</p> Signup and view all the answers

What gene mutation can lead to an increased risk of developing cancer in individuals?

<p>Promoter mutations in tumor suppressor genes. (C)</p> Signup and view all the answers

Flashcards

Monogenic Trait

A trait controlled by a single gene, often following Mendelian inheritance patterns.

Polygenic Trait

A trait influenced by multiple genes with additive effects. Often involves environmental factors.

Omnigenic Model

A model where nearly all genes in a genome can influence a trait indirectly through core genes in relevant pathways.

Threshold Model

A model that suggests disease risk is a quantitative trait, where exceeding a certain threshold leads to disease.

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Endophenotype

A measurable quantitative phenotype that contributes to the genetic architecture of a complex trait.

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Heritability

The proportion of variance in a quantitative trait attributable to genetic variation within a population.

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Additive Genetic Variance

Variation in a trait due to the additive effects of alleles.

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Environmental Variance

Variation in a trait attributable to environmental factors.

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Low variance, low effect size

This scenario is challenging for genetic association studies as it requires large sample sizes to detect small effects.

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Very low variance, large effect size

Genetic association studies are easier in this case, as strong effects are easier to identify in smaller samples.

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Very high variance, low effect size

This scenario is where association studies are most commonly employed. They require large samples due to the widespread variability present.

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Additive model in genetic coding

This involves assigning a numerical score to each variant based on the number of copies of the coded allele an individual carries: 0, 1, or 2.

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Candidate Gene Studies

These studies specifically target genes believed to be relevant to a trait, testing for associations with disease.

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Genome-Wide Association Studies (GWAS)

GWAS assess millions of genetic variants across the entire genome for their association with specific traits.

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GWAS Correction for Multiple Testing

Instead of using Bonferroni correction, GWAS uses a more lenient threshold of < 5 x 10 ^ -8, correcting for 1 million independent tests.

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Replication in GWAS

Repeating the study in an independent sample helps to validate findings and minimize false positives.

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Importance of Sample Size in GWAS

Larger sample sizes are crucial for GWAS power, making the number of cases more important than the number of controls.

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Genomic Inflation Factor

Measures how much the results from GWAS are inflated due to factors like population structure. A value close to 1 suggests a lack of true associations.

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Unacceptable Inflation

An inflation rate greater than 1.1%. This rate is considered too high and can negatively impact the economy.

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Statistical Power

The ability of a study to detect a statistically significant difference or association. In genetic studies, it's influenced by effect size, allele frequency, and sample size.

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Bonferroni Correction

A method to adjust the significance level (alpha) for multiple hypothesis testing. It reduces the chance of false positives by dividing the original alpha by the number of tests.

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Population Stratification

A confounding factor in genetic studies where a population is divided into subpopulations with different disease prevalences and allele frequencies.

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Linkage Disequilibrium (LD)

Non-random association of alleles at two loci. Alleles are found together more often than expected by chance.

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Haplotype

A combination of alleles at closely linked loci on a chromosome. It's inherited as a unit.

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Tag SNP

A single nucleotide polymorphism (SNP) that is in strong linkage disequilibrium with other SNPs in a region. It can be used to represent a group of SNPs.

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Causal Variant

A genetic variant that directly influences a trait or disease.

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Imputation

Predicting missing or unmeasured genotype values based on known linkage disequilibrium patterns.

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Reference Panel

A database of whole genome sequences used to inform imputation. Provides information on haplotype frequencies.

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Pharmacodynamics

How a drug affects the body. Focuses on the drug's interactions with biological targets like enzymes, receptors, ion channels, and transporters.

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Pharmacokinetics

What the body does to a drug. Involves how the drug is absorbed, distributed, metabolized, and eliminated.

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Pharmacogenetics

The study of how genetic variations influence drug response. Aims to personalize drug prescriptions based on individual genetic profiles.

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Warfarin Example

Warfarin is a blood thinner that can be affected by genetic variation in the VKORC1 gene, impacting how the body metabolizes the drug.

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GWAS for Drug Response

Genome-wide association studies (GWAS) can be used to identify genetic variants associated with drug efficacy, toxicity, and drug metabolism.

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GWIS

Genome-wide interaction study (GWIS) investigates how genetic variants interact with medications to influence drug efficacy.

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Loss-of-Function vs Gain-of-Function

Describes how genetic variants affect gene activity. Loss-of-function reduces gene function, while gain-of-function increases function.

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Pleiotropy

When a gene affects multiple traits in the body.

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Genetic Risk Scores (GRS)

A measure of an individual's overall genetic risk for a disease, taking into account multiple genetic variants.

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Gene Therapy for Mendelian Disorders

Replacing faulty genes with functional copies to treat inherited diseases.

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CRISPR-Cas9 for Gene Therapy

A gene editing technology used to precisely target and correct genetic mutations, mainly for Mendelian disorders.

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Cancer: What's it all about?

Cancer isn't a single disease, but a group of conditions caused by abnormal cell growth. This growth is often uncontrolled, leading to the formation of tumors.

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What causes cancer?

Cancer arises from mutations in genes that control cell growth and division. These can be oncogenes, which promote growth, or tumor suppressor genes, which prevent uncontrolled growth.

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Role of Proto-oncogenes

Proto-oncogenes are normal genes that promote cell growth. Mutations in these genes can create oncogenes that trigger uncontrolled cell growth, like a broken throttle in a car.

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What are Tumor Suppressor Genes?

Tumor suppressor genes act like brakes, controlling cell growth and stopping it from becoming uncontrolled. Mutations in these genes lead to uncontrolled cell division.

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DNA Repair Genes

DNA repair genes act like repairmen, fixing DNA damage to prevent errors from accumulating. A loss of function in these genes increases the risk of cancer.

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Multiple-Hit Theory

This theory proposes that cancer doesn't arise from a single mutation, but from a series of accumulated mutations in key genes. It's like a domino effect leading to cancer.

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What is Germline Mutation?

A germline mutation occurs in a sperm or egg cell, meaning that it can be inherited by offspring. These mutations are rare but can have significant impact on cancer risk.

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How can mutations cause cancer?

Mutations can lead to cancer through several ways: over-expression of a normal protein, creation of an abnormal protein, or changes in how a gene is regulated. These disruptions disrupt the delicate balance of cell growth.

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Study Notes

Genetic Architectures

  • Monogenic traits are controlled by a single gene, often following Mendelian patterns. Examples include cystic fibrosis.
  • Polygenic traits are controlled by multiple genes with additive effects. Examples include height.
  • Oligogenic models involve a small number of genes influencing a trait or disease.
  • Omnigenic models suggest nearly all genes in a genome can influence a trait indirectly via core genes in relevant pathways.

Dichotomous Phenotypes

  • Threshold models describe disease risk as a hypothetical quantitative trait. Disease occurs when liability crosses a threshold.
  • Burden of both genetic and environmental risk factors contribute to disease occurrence, as seen in schizophrenia.
  • Endophenotypes are multiple measurable quantitative phenotypes with distinct genetic architectures.
  • Liability is a cumulative effect of unfavorable phenotypes.

Heritability and Variance Explained

  • Heritability represents the proportion of variance in a quantitative trait attributable to genetic variation.
  • Heritability above 0.3 is considered high enough to warrant gene searches. Heritability values apply to populations, not individuals.
  • Heritability is not probability of inheritance; it describes proportion of variance explained by genetics.
  • Heritability increases as environmental variance decreases.

Genetic Association Studies

  • Studies design various approaches for complex disorders, including low variance, high effect size studies, association studies, and GWAS.
  • Candidate gene studies examine specific genes based on existing hypotheses, whereas genome-wide studies evaluate all measured genetic variants.
  • GWAS are hypothesis-free, analyze millions of variants, and are valuable for large sample sizes, but need larger samples compared to candidate gene studies.
  • Replication of GWAS results in independent samples is critical for minimizing false positives.

Confounding in Genetic Studies

  • Chance associations can occur even in the absence of causality. Correction strategies, like Bonferroni corrections, can mitigate these random chance positives.
  • Hidden population stratification (genetic and phenotypic differences between populations within a group) can introduce spurious associations.
  • Alleles and disease prevalence may vary between population groups, which can confound results if not accounted for.
  • Linkage disequilibirum and haplotypes can be investigated through imputation. (Variants correlated in a population).

Pharmacodynamics and Pharmacogenetics

  • Pharmacodynamics examines how a drug impacts the body (e.g., receptors, enzymes, transporters).
  • Pharmacogenetics refers to how genetic variation affects a drug response to determine optimal treatment.
  • Pharmacogenetics aims to match drugs with individuals to maximize effectiveness and minimize side effects.

From Genetic Associations to Drugs

  • Genetic association studies can be used to identify genes linked to diseases.
  • Functional studies clarify the direction of the association (gain or loss of function effects).
  • Pleotropic effects are investigated; if genes affect multiple characteristics, this may impact treatment approaches.
  • Clinical trial progression proceeds from preclinical trials to FDA approval.

Genetic Risk Scores

  • Genetic risk scores (GRS) are single variables summing risk allele counts for a disease, potentially weighted according to effect size.
  • GRS can predict disease risk and determine treatment strategies.

Gene Therapy

  • Gene therapy focuses on replacing or correcting harmful mutations.
  • Various approaches exist (CRISPR-Cas9), and gene therapy currently mainly targets Mendelian conditions.

Cancer Genetics

  • Cancer results from abnormal cell proliferation, inhibited apoptosis, loss of differentiation, invasiveness, or metastasis.
  • Multiple-hit theories propose accumulation of mutations in oncogenes and tumor suppressor genes as a major causal factor for cancer.
  • Proto-oncogenes promote cell growth.
  • Tumor suppressor genes regulate cell cycle progression and cell death, acting as brakes on cell proliferation and cancer development.
  • DNA repair genes are crucial for detecting and repairing DNA damage.

Precision Medicine

  • Precision medicine aims to tailor treatments based on a patient's specific genetic profile, improving treatments for complex diseases and cancer.
  • Targeted therapies act on specific cancer-causing mutations.
  • Personalized medicine is a tailored approach to disease and treatment, considering the genetic make-up of the individual.

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