Human Genetic Experiments: Sep 29

Human Genetic Experiments

Overview

Human genetics employs a variety of experimental approaches to understand the inheritance and molecular basis of traits and diseases. Key methods include pedigree analysis, twin studies, identification of de novo mutations, linkage analysis, and genome-wide association studies (GWAS). These approaches help elucidate both monogenic and polygenic disease mechanisms.

Pedigree Analysis

Pedigree analysis is a classical genetic method used to track inheritance patterns of traits or diseases within families across generations.

• Monogenic Diseases: Typically caused by mutations in a single gene with a large effect size.

• Requirements: Generational data, including DNA sequence information, is necessary to identify inheritance patterns.

• Limitations: Only a small percentage of genetic diseases are identified through pedigrees because many diseases are polygenic or involve de novo mutations.

• Example: Familial recessive inheritance, where both parents carry a recessive allele leading to affected offspring.

Twin Studies

Twin studies compare monozygotic (identical) and dizygotic (fraternal) twins to distinguish the effects of genetics and environment on traits.

• Monozygotic Twins: Share nearly identical genomes; differences are attributed to environmental factors.

• Dizygotic Twins: Share about 50% of their genetic material; differences can be due to both genetic and environmental factors.

De Novo Mutations

De novo mutations are genetic changes that arise spontaneously during gametogenesis or early embryonic development, rather than being inherited from parents.

• Replication Errors: Occur at a rate of approximately $1 \times 10^{-10}$ nucleotides per cell division, even with proofreading mechanisms.

• High Cell Division: The large number of cell divisions during development increases the chance for mutations.

• Types: Homogeneous de novo mutations (all cells affected) and mosaic de novo mutations (only some cells affected).

• Dominance: De novo mutations must be dominant to manifest a phenotype unless loss-of-heterozygosity (LOH) occurs.

Diagram: Types of Mutation Inheritance

Type	Description
Normal	No mutation present
Familial Recessive	Inherited from carrier parents
Homogeneous De Novo	Mutation occurs at 1-cell stage, all cells affected
Mosaic De Novo	Mutation occurs after several divisions, subset of cells affected
Loss-of-Heterozygosity (LOH)	De novo mutation causes loss of heterozygosity, leading to phenotype

Trio Studies

Trio studies involve sequencing the genomes of a child and both parents to identify de novo mutations.

• Purpose: To discover mutations present in the child but absent in both parents.

• Variables to Isolate: Mutations unique to the child, excluding inherited variants.

• Applications: Useful for identifying genetic causes of rare diseases.

Polygenic Traits and Diseases

Most human traits and diseases are polygenic, meaning they are influenced by multiple genes, each contributing a small effect.

• No Trait is Monogenic: Traits are rarely determined by a single gene.

• Redundancy: Genetic networks often have duplications and redundancies.

• Example: Grain color in wheat is determined by additive alleles at multiple loci.

Example: Grain Color in Wheat

Genotype	Phenotype	Frequency (F2)
AABB	Red	1/16
AABb, AaBB	Intermediate	2/16 each
Aabb, aaBB, AaBb	Intermediate	4/16
aabb	White	1/16
Additional info: Other combinations produce gradations of color

Genome-Wide Association Studies (GWAS)

GWAS is a powerful method for identifying genetic variants associated with complex diseases by comparing the genomes of large numbers of unrelated individuals.

• Method: Compare cases (with disease) to controls (without disease) to find variants more common in cases.

• Linkage Disequilibrium: Non-random association of alleles at different loci; marker alleles appear together more often than expected.

• Interpretation: GWAS identifies associations, not causation; further studies are needed to determine functional effects.

• Example: GWAS for myopia genes identifies candidate regions but does not specify how genes are affected.

GWAS Process Table

Step	Description
Sample Collection	Collect DNA from cases and controls
Genotyping	Identify genetic variants (SNPs)
Statistical Analysis	Test for association between variants and disease
Interpretation	Identify candidate genes/regions

Linkage Disequilibrium

Linkage disequilibrium (LD) refers to the non-random association of alleles at different loci. In GWAS, LD allows researchers to identify regions of the genome associated with disease, even if the causal variant is not directly genotyped.

• Marker Alleles: Alleles that appear together in disease populations more than expected by chance.

• LD Blocks: Regions where genetic variants are inherited together.

GWAS Pitfalls and Population Effects

GWAS studies can be confounded by population structure, leading to false associations.

• Population Stratification: If a disease is more prevalent in one population, alleles specific to that population may appear associated with the disease.

• False Positives: Mistakenly concluding that population-specific loci are causative for disease.

Comparison: Pedigree Analysis vs GWAS

Feature	Pedigree Analysis	GWAS
Sample Type	Families	Unrelated individuals
Effect Size	Large	Small
Number of Genes	Few	Many
Inheritance Pattern	Concrete	Complex
Population Frequency	Rare	Common

DNA Polymorphisms

DNA polymorphisms, such as single nucleotide polymorphisms (SNPs), are variations in DNA sequence that serve as markers for genetic studies. They are essential for both pedigree and association analyses.

Application Example: GWAS and Cholesterol

A GWAS study identifies allele rs1767474A as associated with high cholesterol. If an individual is found to have this allele, it suggests increased risk but does not guarantee disease. Clinical decisions, such as starting statins, should consider additional factors beyond genetic association.

Summary Table: Key Concepts in Human Genetic Analysis

Concept	Definition	Example/Application
Pedigree Analysis	Tracking inheritance in families	Identifying monogenic diseases
De Novo Mutation	New mutation in gamete or embryo	Trio studies for rare diseases
Polygenic Trait	Trait influenced by many genes	Height, grain color in wheat
GWAS	Association study in populations	Identifying risk alleles for myopia
Linkage Disequilibrium	Non-random allele association	GWAS marker identification

Additional info:

• Polygenic traits often show continuous variation and are influenced by environmental factors.

• GWAS results require careful interpretation due to possible confounding by population structure.

• Loss-of-heterozygosity (LOH) is a mechanism by which recessive mutations can manifest in the presence of a heterozygous parent.