genotype-phenotype correlations 1 dr mohamed fakhry 2015

Genotype-Phenotype correlations

1 Dr MOHAMED FAKHRY 2015

ObjectivesObjectives

Polymorphisms Vs mutations

Detection and clinical applications

Polymorphisms at protein level Polymorphisms at DNA level

Genotype and phenotype

GenotypeGenotype The genetic constitution (genes on the pair of homologous

chromosomes).

The alleles present at one locus. e.g..

(a) TT or Tt or tt i.e genes for height.

Where T is the “tall” gene and t is the gene for “short” height

(b) A A, A S, or S S

Where A is for HbA and S for HbS.


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PhenotypePhenotypeThe observed biochemical, physiological and morphological characteristics of an individual as determined by his/her genotype and the environment in which it is expressed. e.g.

Genotype Phenotype TT or Tt Tall tt Short AA HbA (normal)

A S (Hetero ) HbAS (carrier) SS HbS (SCA)

( Homo = Identical , Hetero = different)

Dominant * Hetero

RecessiveDr MOHAMED FAKHRY 2015

Genotype – Phenotype Genotype – Phenotype relationshiprelationship

Genotype (i.e. genetic make up) determines phenotype (i.e. appearance etc.), though environmental factors may modify the phenotypic expression:

e.g.TT (Proper nutrition) → TallTT (Poor nutrition) → Stunted growth and

poor development.

- The Genotype determines the phenotype, but is affected by presence of Recessive or Dominant Gene, e.g. (Conti..)


e.g:(i) As T is dominant, it is expressed in Homozygotes and Heterozygotes, but t is recessive and is expressed only in Homozygotes.

TT and Tt → tall tt → short

(ii) s is recessive, it is expressed only in Homozygotes while Heterozygotes are carriers but normal:

A A ⇒ HbA (Normal) A S ⇒ HbAS (Normal but carrier) S S ⇒ HbS (Abnormal “Sickle cell anemia”)

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⇒The Genotype determines the phenotype, but is affected by presence of Recessive or Dominant Gene, e.g. (Conti..)

- Genotype differ in the degree of their expression of: Clinical severity, onset age, or both (Variable expressivity).

Variable expressivity refers to the range of signs and symptoms that can occur in different people with the same genetic condition. variable expressivity is probably caused by a combination of genetic, environmental, and lifestyle factors.

Expression of abnormal genotype maybe modified by: Other genetic loci, environmental factors or both

Reduced Penetrance: If some people with the mutation do not develop features of the disorder, the condition is said to have reduced (or incomplete) penetrance in some heterozygous individuals with a dominant disorder, the presence of the mutation is reduced.

“Pleiotropy”; single basic gene defect → multiple phenotypic effects on multiple organs (genetic heterogeneity) e.g Tuberous sclerosis (AD); rare genetic disease that causes noncancerous (benign) tumors to grow in many parts of the body) : learning disability, epilepsy, facial rash.

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- New Mutations: A sudden appearance of a dominant disorder in the offspring with normal parents.

- Codominance: With codominance, a cross between organisms with two different phenotypes produces offspring with a third phenotype in which both of the parental traits appear together . When two allelic traits are both expressed equally in a heterozygote e.g ABO blood groups.

↦ Genotype differ in the degree of their expression of: Clinical severity, onset age, or both (Variable expressivity)

Dr MOHAMED FAKHRY 2015

Genetic Genetic PolymorphismPolymorphism


PolymorphismPolymorphism is the natural variations in a gene, DNA sequence, or

chromosome that have no adverse effects on the individual and occur with fairly high frequency in the general population

Polymorphism is the inheritance of genes in different forms termed alleles

Is common (probably all genes show allelic variation)

Alleles have different DNA sequences

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Polymorphisms Vs Mutations

Genetic polymorphisms:Common alleles > 1%

Mutations:Rare alleles < 1%


Polymorphisms: Sites

Inter-genes or intronic:Detected by DNA sequence analysis

Gene coding sequences: Different protein variants →Distinct phenotypes (may be)

DNA regulatory regions: → may affect phenotypes

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Mutations Mutations

Genetic diversity among individuals Genetic diversity among individuals

Over generations, the influx of new nucleotide variations has ensured a high degree of genetic diversity and individuality.

Over generations, the influx of new nucleotide variations has ensured a high degree of genetic diversity and individuality.

Deleterious= harmfull mutations

not deleterious mutation

Disease May effect phenotype

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Genetic Variation (polymorphism or muation)* Genetic Variation (polymorphism or muation)*

I. Some mutations in the gene (coding

sequence)

Variant protein

Altered structure and

Altered properties

I. Some mutations in the gene (coding

sequence)

Variant protein ,but not critical for the function

II. Some mutations in DNA (non-coding regions)

Normal properties

No effect on proteins structure

*Polymorphisms are common, particularly in non-coding regions of DNA

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Genetic Polymorphism* Genetic Polymorphism*

Many genetic loci are characterized by a number of relatively common alleles, thus producing many phenotypes in normal

population

Alleles that occur at a frequency of > 1% are said

to be polymorphic variants

Alleles that occur at a frequency of < 1% are said

to be rare variants

If there are two or more alleles (several forms of the same genes occupy the same locus) and

the rarest occurs at a frequency of more than 1%

then this loci will be considered polymorphic.15

Gene polymorphismGene polymorphisme.g. Gene for hair coloure.g. Gene for hair colour

Wild type Alleles

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Types of Polymorphisms (Defined by the method of detection)


DNA Polymorphism

- Restriction Fragment Length Polymorphism (RFLPs):- Inherited variations in DNA sequence, - Results in gain or loss of a site recognized by restriction endonuclease

- Variable number of tandem repeats (VNTRs): - Variations in the number of short, repeated nucleotide sequences (eg GC) between restriction sites - VNTRs are extremely polymorphic - Valuable in forensic medicine

Detected by altered DNA sequences

Protein Polymorphism

Altered physical features

Chromosome heteromorphisms

Contd…..

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↦Polymorphisms: Detection At DNA level

DNA sequence analysis

Restriction fragment length polymorphisms (RFLPs)

PCR-based Methods:Conventional PCRReal-time PCR



Contd…


Contd…

- Enzyme variant: altered enzyme activity, electrophoretic mobility, thermostability or other physical properties e.g.G-6-PD deficiency.

- Antigenic variants: altered antigenic properties e.g. ABO blood groups.

Protein Polymorphism Altered physical features


Contd…..Detected by:

ElectrophoresisAltered activity,

Altered physical properties

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↦Polymorphisms: Detection At protein level

ABO System:A, B & O alleles: Chromosome 9A & B: 4 nucleotide differencesO: One base deletion and frame-shiftPhenotypes: O, A, B & AB

This blood group may be the most complex genetically of all blood type systems since it involves 45 different antigens on the surface of red cells that are controlled by 2 closely linked genes on chromosome 1.

Rh System:

Rh-D: RH gene located on short arm of Chromosome 1. There are two alleles, D and d. Individuals who are homozygous dominant (DD) or heterozygous (Dd) are Rh+. Those who are homozygous recessive (dd) are Rh- (i.e., they do not have the key Rh antigens).

Phenotypes: Rh-positive and Rh-negativeIncompatibility:Hemolytic disease of newborn

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Several proteins exist in two or more relatively common:

genetically distinct , structurally different & functionally identical.

The causes of polymorphic forms: Mutation in or around gene

- Examples :

ABO Blood groups, Transferrin, Hb, 1 antitrypsin.

Protein Polymorphism


Not all variant proteins have clinical consequences

Not all variant proteins have clinical consequences



Contd…


Contd…

Altered physical features e.g. polydactyly, gigantism, dwarfs, hair on

ears, baldness.

Altered physical features


Detected by:Physical appearance

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Contd…


Contd…

Heritable differences in chromosomal appearances from one person to another, e.g.

Variations in the size of the Y chromosome long arm. Variation in the size of the centromere . Variation in satellite size and structure. The occurrence of fragile sites.

Chromosome heteromorphisms Detected by:Cytogenetic studies

FISH (Fluorescence in situ hybridization)

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Genetic diversity among individuals Genetic diversity among individuals


• Generally, the karyotype of normal persons of the same sex are quite similar.

•Occasional variants are seen on staining. These are called

heteromorphisms.

•These reflect difference in amount or type of DNA sequence at a particular location along a chromosome.

• Almost 25% are silent mutation with no effect on protein structure.

• Most mutations alter amino acid sequence but do not have phenotypic effect (e.g. ABO blood groups).

•Rare mutations produce severe phenotype effect or influence survival (e.g. phenylketonuria)

• In long arm of chromosome.• In chromosomes 1, 9, 16.• In short arm of acrocentric chromosomes

Protein variations

e.g

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As genetic “Markers” To distinguish inherited forms of a gene in a family.

Presymptomatic and prenatal diagnosis of genetic disease.

Evaluation of high and low – risk persons.

Paternity testing and forensic applications.

Matching of donor-recipient pairs of tissue and organ transplantation.

Uses of PolymorphismUses of Polymorphism

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Summary

Polymorphisms is : ⇒High degree of biochemical individuality (Every individual is unique)

Due to Different responses of individuals to environment, diet and drugs

Used as genetic markers; powerful tools in clinical genetics

genotype-phenotype correlations 1 dr mohamed fakhry 2015

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