Genetics II: Molecular Basis for Genetic Diseases

Mutation and Protein Function

Mutations

Ultimate source of genetic variation

Loss of funtion

May alter coding, regulatory, or other regions
Can have range of effects if residual function is maintained

Gain of Function

Enhance one or more of the functions of the protein
Increase in amount of function or abundance of the protein

Novel Property mutations

Sickle Cell Anemia:
Hemoglobin chains aggregate.
E6V (AA Sub)

Heterotropic or ectopic gene expression

Review of Terms

Locus

Position on the chromosome:

Disease Locus & Marker Locus

Marker

A measurable unit on a chromosome
single nucleotide polymorphism (SNP)

Allele

One of several alternative forms of sequence at a locus
2 alleles per locus, one per chromosome

Genotype

Alleles present at that locus

Heterogeneity

Allelic Heterogeneity

The occurrence of more than one allele at a locus
Diff mutation at same gene

B-Thalassemia:
HBB: chromosome 11p15.4
over 200 disease causing mutations identified

Locus Heterogeneity

Assosiation of more than one locus with clinical phenotype

Ex: thalassemia. genes at diff loci (16 a-globin and 11 B-globin gene both causing thalassemia

Phenotypic Heterogeneity

Sickle cell disease and B-thalassemeia each result from distinct B-globin gene mutations.

Hemoglobin and Hemoglobinopathies

The Hemoglobins:

a, b, and y: Globin switching
changes in expression of global molecules during development

Temporal switches of globin synthesis are accompanied by changes in the principal site of erythropoiesis

Locus Control Region (LCR):
req for expression of all genes in B-globin cluster
areas of "open" DNA gives TF access to reg elements that mediate expression

Structural variants

Alters AA sequence of globin PP--> alter properties of the protein

Ex: Sickle Cell and Methemoglobin

Thalassemias

Diseases that result from decreased abundance of one or more of globin chains

Ex: B-thalassemias

Hereditary persistence of fetal hemoglobin

A group of clinically benign conditions that impair perinatal switch: y-globin --> B-globin synthesis

Ex: Hb F

Practical:

The most common forms of α-Thalassemia
are the result of gene deletions. Rationalize
the high frequency of deletions in mutational
carriers.

a- Thalassemia:
-Two identical a-globin genes on each chromosome (16)
Tandem homologous a-globin genes facilitates misalignment between domains

Population Genetics

Forces of Evolution

Random Mutation

New Traits arise via chance mutations in DNA

Genetic Drift

Mutations may change in frequency by chance events

Gene Flow

Mutations spread by migration

Mutations increase in freq if they increase in number of offspring

Calculating allele frequency

Number of Indi x allele count

Hardy-Weinberg Law

p2 + 2pq + q2=1

1=p+q

Assumes no evolution

Sexual Selection vs Assortative Mating

Sexual selection:
increases trait frequency

Assorative mating:
Increases homozygosity of variants, creates correlations across distant loci within complex traits
creates confounding across traits
overestimates heritability of traits

Genetic basis for mendelian disease

Objectives

-Demonstrate genetic mapping by following the co-
segregation of alleles within a family, i.e. linkage analysis

- Quantify the extent to which a genetic marker and disease
locus are linked, i.e. co-inherited

- Review successful examples of disease loci identified
through linkage analysis
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Steps for Disease Gene Identification

Linkage analysis

Posostionlal cloning

use fam with disease, identify regions that co-seg with phenotype

Why Linkage:

• In most cases little is known about the genomic location of
genes contributing to disease

• Thus, the study design usually consists of systematically
surveying the entire genome

• The extent of linkage is a function of the physical distance
between the loci on the chromosome

• Based on recombination between loci
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Recombination happens in prophase

Candidate gene

Genome wide association study (GWAS)

Characteristics for Mendelian Disease

Recognizable pattern of inheritance

single gene mutation

Allelic heterogeneity

Risk variants have high disease penetrance with strong genetic defects

Low frequency of variants and low risk disease prevalence

Linkage analysis

Goal:

Goal: Identify a chromosomal region linked to a
disease within families that exceeds the null
expectation, which enable localization of disease
gene in the genome

Two point linkage analysis

Test if a genetic marker & disease locus are linked
• Genotypes at disease locus are unknown but
phenotype (affection status) is known

LOD

Log Likelihood ratio

Z(theta) = log 10 (L(theta)/L(theta=0.5))

Likelihood:
probability of data given the prarmetiers

theta: Pr (recombination

1-theta=Pr (no recom)

Problems:

Mendelian diseases are not really “simple”
• Reduced penetrance
• Heterogeneity (allelic, phenotypic)

• Genotyping errors leads to spurious
recombinants → loss of power
• The multi-locus map helps to detect this error by checking
for unusual double recombinants

Phase concept

Specific alleles that a person has/ that are inherited

Biochemical and genetic basis for disease

Protein Classes

Housekeeping proteins

Specialty Proteins

Disease based on Mutation in diff class of proteins

Enzymes

PKU and Tay-Sachs

PKU:
mutation in PAH--> neg impact on degre of phenylalanine
PAH expressed in liver, damage CNS
First genetic defect to cause intellectual disability
normal at birth, microcephaly, hyperactivity, seizures, and learning disability
Phenyalaline--> Tyrosine, with help from BH4 (cofactor) and PAH

Example of allelic Heterogeneity:
Over 1557 mutations world wide found in patients with PKU
Variant and non-variant PKU

Tay-Sachs:
Lysosomal storage disease
Pseudodeficiency Alleles: clinically benign allele that has a reduction in function activity detected by in vitro assays but has suffiecnt activity

Defects in receptor proteins

Familial Hypercholesterolemia

Group of metabolic disorders
chracterized by elevated plasma lipids carried by apolipoprotein B

LDLR mutations are auto semidom trait
Both homo and heterogeneity phenotypes

Gene dosage: earlier manifestation and sev.

Transport defects

Cystic Fibrosis

Principal effects in lungs and exocrine pancreas
increase in sweat sodium and Cl concentration

Genocopy: Similar phenotypes show varying genotypes
on different loci

CFTR only gene assoc with CF

Structural Proteins

DMD

Duchenne Muscular Dystrophy

Muscle weakness at 3-5 yoa, heart and resp are also affected

X linked rec, mutation rate 10^-4

Multifactorial Disorders

Qualitative and Quantitative traits

Qualitative: trait that the person either does or does not have

Qunatiative:Measurable physiological or biochem quantity that differs among diff indivs, usually follows normal dis.

Familial Aggregation and Correlation

Siblings share 50% of alleles

More close the fam member, share more allele

Fam Ag: greater than expected number of affected relatives
compared to that of the freq of general pop.

Measures: RR and Fam hx case-control

Larger rrr, greater fam ag (greater than 1)

Quantitative: Correlation and Heritability

Coefficient of Correlation (r)

(higher heritability, greater contribution of genetic diff.
0= no genetic contrib
1=genotype is responsible (totally)

Distinguish Genetic and environmental

Use fam Studies:
Use twin studies- MZ and DZ

DNA finger printing

MZ/DZ graph

Estimate Heritability of twins:
H2= 2 x (rmz-rdz)

Identifying genetic basis for complex disease

Objectives:

Understand the fundamentals of study design for a genome-wide association study (GWAS).

Become familiar with analytical approaches to extend the capabilities of GWAS, e.g. LD and imputation.

Acknowledge the strengths and limitations of the GWAS approach

Genetics to Phenotype

Mendelian traits:
Ex. Sickle cell Anemia and CF

Complex traits: height, Type 2 diabetes
mix of genetic and environment

Genomic association studies

Good for high heritability

Mendelian disorders

Large study pop (case/control unrelated)

Dense genotyping

GWAS

Examination of genetic variation across a given genome

Many SNPs

Designed to identify genetic associations with observable triats

Qualitative: Obesity, T2D, Asthma, CVD

Quantitative: BMI, Fasting glucose

Agnostic (genome scan) approach