Gene Mapping and Complex Traits Notes

Mendel and Modes of Inheritance

• Revision of Mendel's laws and modes of inheritance.
• Understanding when these principles break down.

Mendel's Peas

• Classic example of dominant and recessive traits.
• P generation: Round peas (RR) and wrinkled peas (rr).
• F1 generation: All offspring are round (Rr).
• F2 generation: 3 round : 1 wrinkled phenotypic ratio.

Modes of Inheritance

• X-linked recessive: Affected males do not have affected sons.
• Autosomal recessive: Trait skips generations.
• Autosomal dominant: Trait does not skip generations; both males and females are affected.
• Elimination strategy:
  • Does the trait skip a generation? (Yes = recessive; No = dominant)
  • Are both males and females affected? (Yes = autosomal; No = sex chromosome-linked)
  • Do affected males have affected sons? (No = X-linked)
• Y-linkage and X-linked dominant disorders are rare.

Punnett Square

• Used to predict the probability of offspring genotypes.
• Example: Mother (XaX) x Father (XAY) yields XaY and X Xa Xa X products.

Hardy-Weinberg Equilibrium

• Used to calculate carrier frequencies in a population.
• Given: Frequency of cc (affected individuals) is 1/2500 = 0.0004.
• Therefore: $c^2 = 0.0004$, $c = \sqrt{0.0004} = 0.02$
• Frequency of C: $1 – 0.02 = 0.98$
• Frequency of carriers (Cc + cC): $(0.98 * 0.02) + (0.02 * 0.98) ≈ 0.04 = 1/25$

When Things Break Down

Incomplete Penetrance

• Penetrance: The proportion of individuals with the disease-causing allele that develop clinical symptoms.
• Example: Polydactyly.

Variable Expressivity

• Expressivity: The severity and type of symptoms shown in an individual with the disease-causing allele.
• Example: Osteogenesis imperfecta.

Penetrance vs. Expressivity

• Penetrance: Proportion of individuals affected.
• Expressivity: Individual symptoms.
• Suggests trait is complex, not single-gene.

Complex Traits

• Determined by:
  • Genes: additive, dominance, epistasis
  • Environment: diet/exercise, smoking, etc.
• Genes and environment contribute to total phenotypic variance.
• Heritability depends on genes.

Broad Heritability ($H^2$)

• Definition: Proportion of phenotypic variance due to genetic effects.
• Most commonly quoted measure for humans.
• Estimated using twin studies:
  • Monozygotic (MZ) twins: same genes.
  • Dizygotic (DZ) twins: share half their genes.
• Concordance in MZ twins estimates heritability.

Heritability Estimates

• Psoriasis: ~90%
• Diabetes: ~70%
• Major depression: ~50%
• Schizophrenia: ~50%
• IQ: ~50%
• Neurotic/extravert: ~40%
• Asthma: ~30%
• Sexual preference: ~30%
• Cardiac conditions: ~30%
• Many cancers: ~20%
• Multiple sclerosis: ~10%
  *Figures vary slightly from study to study

The Human Genome

• 3 billion base pairs
• 23 chromosomes
• ~15,000 genes

Gene Maps

• Physical maps
• Linkage maps

Methods of Mapping

• Segregation analysis (pedigrees, recombination)
• Association analysis (linkage disequilibrium)

Modern Genome Maps

• Interactive maps with click and zoom functionality.
• Provide extensive information.

Mapping Disease

Approaches for Genetic Mapping

• Linkage mapping
• Association mapping
• Sequencing

Gene Mapping

• Achieved using DNA markers.
• If a marker is often inherited with a disease, it may be close to the disease locus.
• Need to establish the involved DNA sequence.

DNA Markers

• Requirements:
  • Clean Mendelian inheritance
  • Sufficiently polymorphic
  • Easy to type
  • High density, spread across the genome

Types of DNA Markers

• Blood groups
• Electrophoretic mobility variants of serum proteins
• HLA tissue types
• DNA RFLPs
• DNA VNTRs (minisatellites)
• DNA VNTRs (microsatellites)
• DNA SNPs

Examples of DNA markers

• Microsatellites: Short tandem repeats (e.g., CT, CA).
• Single nucleotide polymorphisms (SNPs): Single base variations.

Linkage Revision

• Assessed by observing how often disease and marker are inherited together.
• Marker and disease locus may be close together on the same chromosome (linked).

Meiosis and Linkage

• Crossing over during prophase I of meiosis can separate linked alleles.

Linkage Principles

• The closer two loci are, the more likely they are to be inherited together.
• Different chromosomes = independent assortment (50% chance of co-segregating).
• Same chromosome = linked.
• Linked alleles can be separated by recombination (crossing over).

Punnett Square for Testcross

• Predicted ratio with independent assortment: 1:1:1:1.
• Observed ratio suggests linkage if it deviates significantly.

Linkage Scenarios

• Independent assortment: vg+ vg, b+ b, vg b+, vg+ b+ = 25% each.
• If linked (0% recombination): vg+ vg = 50%, b+ b = 50%, others = 0%.
• If linked (25% recombination): Parental types = 37.5% each, recombinant types = 12.5% each.
• 50% recombination is the same as independent assortment.

Using Linkage in Families (Pedigrees)

• Recombination frequency indicates distance between loci on a chromosome.
• Used to determine the most likely position of a disease gene (i.e., the closest marker).
• Probability of linkage is calculated by determining log of odds (LOD) scores.

Summary: Linkage in Families

• Examines co-segregation of markers and disorder phenotype.
• Genotyping for microsatellites and/or SNPs.
• Calculation of LOD scores.
• Study of candidate genes.
• Limitations: poor pedigree data, difficult for polygenic traits.

Linkage in Populations

Linkage Disequilibrium (LD)

• The non-random association of alleles within a genome.
• Based on population information, not pedigree.

Assessing LD

• Assume two loci A and B are linked.
• Allele A1, freq = 0.1; allele B1, freq = 0.1.
• Assess frequency of haplotype A1B1.
• freq (A1B1) = freq(A1) * freq(B1) = 0.1 x 0.1 = 0.01.
• Compare to observed frequency.
• If frequency of A1B1 is significantly different from 0.01, there is linkage disequilibrium.

Assumptions for Linkage Disequilibrium (LD) Mapping

• Disease caused by single mutation event – Identity by Descent.
• Large patient cohort carrying the new allele.
• Disease mutation was recent enough to avoid randomisation of allele association due to recombination.
• The closer the linked allele is to the disease:
  • The less opportunity for recombination.
  • The stronger the linkage disequilibrium.
• Pattern can be used to locate disease gene in affected Haplotypes.

Cystic Fibrosis Example

• X and K markers near CF.
• 2 alleles each.
• One haplotype common in CF.
• Haplotypes: X1K1, X1K2, X2K1, X2K2.

Genome-Wide Association Study

• Graph showing -log10(P) values for different chromosomes.

Difficulties in Mapping Diseases

• Complex disease
• Multigenic trait
• Heterogeneity
• Phenocopies
• Reduced Penetrance
• Mistyping

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