Pedigree Analysis- Sep 24

Genetics and Humans

Introduction to Human Genetic Experiments

Human genetics applies classical genetic concepts to the study of inheritance and disease in humans. Due to ethical and practical limitations, experiments often rely on observational data, such as pedigrees, to map mutations and understand inheritance patterns.

• Pedigree analysis is a key method for mapping mutations and studying inheritance in families.

• Genetic studies in humans are based on associations and correlations rather than direct experimental crosses.

Pedigree Analysis

Mapping a Disease Locus Using Pedigrees

Pedigree analysis is used to trace the inheritance of traits and identify genetic markers linked to disease loci. This method is especially important for mapping autosomal dominant and recessive traits in families.

• Pedigree: A diagram showing the occurrence of phenotypes and genotypes in several generations of a family.

• Inheritance pattern: Determined by observing how a trait segregates in a pedigree (e.g., autosomal dominant, autosomal recessive).

• Polymorphic marker: A genetic marker (such as a microsatellite or SNP) with multiple alleles used to track inheritance.

Example: Polydactyly (Autosomal Dominant Disease)

Polydactyly, characterized by extra fingers, is used as an example of an autosomal dominant trait. Pedigree analysis can identify which marker allele is linked to the disease locus.

• Identify inheritance pattern: Autosomal dominant

• Identify the polymorphic marker linked to the disease trait: e.g., A2 allele

• Determine genotypes of family members using marker data

Calculating Genetic Distance Using Recombination Frequency

Geneticists use recombination frequency (RF) to estimate the distance between a mutation and a polymorphic marker. This is expressed in centimorgans (cM).

• Recombinant: An individual whose genotype shows evidence of crossing over between the marker and the disease locus.

• Informative meiotic event: A meiosis in which the parental origin of alleles can be determined.

• Formula:

$\text{RF} = \frac{\text{number of recombinant events}}{\text{total number of possible observable recombination events}}$

$\text{Genetic distance (cM)} = \text{RF} \times 100$

• Lower RF indicates closer linkage between marker and disease locus.

Case Study: Mapping LDL Cholesterol Genes

LDL Cholesterol and Cardiovascular Disease

High LDL cholesterol is a major risk factor for cardiovascular disease. Both genetic and environmental factors contribute to LDL levels.

• Classical genetic technique: Study families with extreme LDL levels (high or low).

• Linkage analysis: Used to map disease loci to specific chromosomal regions.

• Example: Families with hypercholesterolemia (high LDL) showed autosomal dominant inheritance.

• Known genes (LDLR, APOB) excluded; linkage mapped to chromosome 1: 1p34.1-p32.

Using Polymorphisms to Map Disease Alleles

Polymorphisms such as SNPs and microsatellites are used to track inheritance and identify candidate genes.

• Sequencing affected and unaffected family members can reveal mutations associated with disease.

• Example: Missense mutations in PCSK9 gene found in affected individuals.

• Missense mutation: A point mutation resulting in a single amino acid change in the protein.

• Nonsense mutation: A mutation that introduces a premature stop codon, truncating the protein.

Association vs. Proof

Finding a mutation in affected individuals is an association, not definitive proof of causation. Additional evidence is needed:

• Sequence all affected and unaffected family members.

• Sequence other families with similar phenotypes.

• Consider population frequency of the variant.

• Many genes may remain unsequenced.

Modern Approaches: Haplotypes and Sequencing

Haplotypes in Disease Mapping

Haplotypes are groups of linked SNPs/alleles inherited together. They are useful for identifying genetic regions associated with disease.

• Unrelated disease families may share haplotypes if the same mutation is present.

• Sequencing technologies allow rapid identification of shared haplotypes and rare variants.

Example Table: Haplotypes and SNPs

Chromosome	SNP1	SNP2	SNP3	SNP4	SNP5
Control 1	T	G	A	C	C
Case 1	T	G	T	C	A
Case 2	T	G	T	C	A

Additional info: Table inferred from slide showing haplotypes and SNPs.

PCSK9 and LDL Cholesterol

Genetic Variants in PCSK9

Mutations in the PCSK9 gene affect LDL cholesterol levels:

• Missense mutation in PCSK9: Leads to high LDL levels.

• Nonsense mutation in PCSK9: Leads to low LDL levels.

Mechanism of PCSK9 Action

• PCSK9 regulates LDL receptor levels, affecting cholesterol clearance from blood.

• Inhibition of PCSK9 increases LDL receptor activity, lowering LDL cholesterol.

Example Table: PCSK9 Mutation Effects

Mutation Type	Effect on LDL
Missense	High LDL
Nonsense	Low LDL

Applications: Therapeutics Targeting PCSK9

Monoclonal Antibodies to PCSK9

Therapeutic antibodies targeting PCSK9 can significantly lower LDL cholesterol in patients, as shown in clinical trials.

• Example: Repatha (evolocumab) is a monoclonal antibody that inhibits PCSK9.

• Clinical studies show up to 90% reduction in LDL cholesterol when combined with statins.

Summary Table: Steps in Pedigree-Based Disease Mapping

Step	Description
1. Identify inheritance pattern	Determine if trait is autosomal dominant, recessive, etc.
2. Identify linked marker	Find polymorphic marker allele segregating with trait
3. Calculate recombination frequency	Count recombinants and informative meioses
4. Convert RF to cM	Use $\text{cM} = \text{RF} \times 100$

Key Terms and Definitions

• Pedigree: Family tree diagram showing inheritance of traits.

• Polymorphic marker: Genetic marker with multiple alleles used for mapping.

• Recombination frequency (RF): Proportion of recombinant offspring, used to estimate genetic distance.

• Centimorgan (cM): Unit of genetic distance; 1 cM ≈ 1% recombination frequency.

• Missense mutation: DNA change resulting in a different amino acid.

• Nonsense mutation: DNA change introducing a stop codon.

• Haplotype: Group of alleles inherited together from a single parent.

Example Application

• Mapping a disease locus in a pedigree can identify candidate genes for further study.

• Genetic mapping is foundational for understanding inherited diseases and developing targeted therapies.

Additional info: Some explanations and tables expanded for clarity and completeness.