Download Origin and Nature of Genetic Variation

M1 – Genetics
Origin and Nature of Genetic
Variation
Dr. Pandya
10/3/2008
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OBJECTIVES
1. Origin of genetic variation at protein
and DNA level.
2. Concept of mutation/polymorphism.
3. Molecular basis for different types of
mutation.
4. Methods used to detect genetic
variation/mutations.
II. CLASSIFICATION
I. MUTATION: Ultimate source of genetic
variation.
DEFINITION: Any permanent change in the
genetic material.
FREQUENCY: Mutation rate (μ) is the
frequency of such change and is usually
expressed as the number of
mutations/locus/gamete/generation.
1.
Mutations associated with base pair
changes in single genes (e.g., insertions,
deletion, substitution)
2.
Others:
a. Chromosomal rearrangements which
may include several genes (deletion,
duplication, translocation, etc.)
b. Chromosomal mis-segregation resulting
in aneuploidy involving the entire chromosome
e.g. trisomy 21. These are the most common
human mutations.
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III. FREQUENCY
IV. TYPES OF MUTATIONS
1. Gene mutations: 10-6 – 10-8 /locus/generation.
1. Germline Mutations:
• These can be transmitted
• Occur during spermatogenesis/oogenesis
• Implication for counseling of recurrence risk.
2. Chromosomal: 10-2 – 10-4/cell division
ORIGIN
1. Errors occurring during DNA replication.
2. Somatic Mutations:
2. Changes induced by mutagens e.g. radiation,
chemicals.
• Antibody diversity
• Relevance to cancer
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MOLECULAR BASIS OF MUTATIONS
SIGNIFICANCE
The characterization of specific mutations permits screening for
genetic disorders in families at risk as well as in the general
population for certain diseases.
1. EVOLUTION – Mutation is the ultimate source of
genetic variation that is required for evolutionary
change. (Each zygote has approximately 100 new base
pair combinations not present in the genome of either
parent.)
A. Nucleotide substitutions (point mutations) in
a DNA sequence can have a variable effect
depending on the location and nature of the mutation.
2. HEALTH RISK – Most recognized mutations are
harmful (teratogenesis, carcinogenesis), but some
may be advantageous. Mutations can be viewed
as the price a species must pay for the privilege
of evolving.
B. Deletions and Insertions of one or more
base pairs, or involving a substantial segment
of a gene or an entire gene.
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MISSENSE SUBSTITUTIONS
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NONSENSE MUTATIONS
• A single base pair substitution
• Amino acid substitutions due to a single base pair change
• Introduction of a premature “stop” codon
• e.g. Sickle cell disease which is caused by single nucleotide
change from AÜT in the beta globin gene.
• A form of beta thalassemia is caused by a premature
“stop” codon at position 39.
GAG to GTG
• This mutation causes a hereditary anemia common in
patients of Mediterranean (especially Sardinian)
origin.
• Results in substitution of glutamic acid to valine at the sixth
position of the polypeptide denoted as
E6V
codon 39
gln Ü stop
CAG Ü UAG
• Not all mis-sense mutations are deleterious.
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RNA SPLICING MUTATIONS
Splice Site mutation
• A single bp change involving intron /exon
splice sites or cryptic sites.
• Beta-Thalassemia syndromes have mutations that
alter the normal splice acceptor or donor
sites
• Activate cryptic splice sites that compete with the
correct site.
• A splicing mutation can also occur secondary
to deletion or insertion of one or more than
one base pair.
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“Synonymous” Substitutions
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Substitutions in the non coding sequence.
Ordinarily, base pair substitution
within intron or outside the 5' or 3' end
of the gene would be expected to have
no effect unless they alter splice site, a
regulatory sequence or mRNA
processing site.
Some base pair substitutions may change
the codon for an amino acid but do
not alter the polypeptide sequence.
AGG to AGA (arginine)
Such a mutation can have phenotypic
effects by activating cryptic splice
sites that compete with the correct site.
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Frameshift mutations
• Number of bases involved is not a multiple of 3
•The resulting protein could either be shorter or longer
than normal
MUTATIONS INVOLVING
MORE THAN A SINGLE
BASE
•e.g., beta thalassemia, Hb Tak, Tay Sachs disease.
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Gene Duplications & Deletions
Codon deletions and insertions
Hb Lepore: Some patients with moderate to severe β-thalassemia have an
unusual product with a δβ fusion gene which occurs by a process of
non- homologous / unequal crossing over.
• Number of bases involved is a multiple of 3
• e.g. Cystic Fibrosis.
• A 3-base pair deletion at amino acid position 508,
deletes the codon for phenylalanine
• The ΔF508 mutation accounts for 70% of all mutant CF
alleles.
• This mutations results in synthesis of an abnormal gene
CFTR gene product
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The alpha thalassemias are a group of hereditary anemias
which can be due to deletion of one or more tandemly
duplicated -globin loci on chromosome16
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UNSTABLE PREMUTATIONS
• AKA as unstable dynamic mutations
• A class of trinucleotide repeats
• Variation within a restricted range is found in the general
population as a normal polymorphism.
• When the number of repeats exceeds a threshold the gene
may become unstable & exhibit phenotypic effects
CCG CCG CCG… x 4-50 repeats
CAG CAG CAG… x 2-12 repeats
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POLYMORPHISM
EXAMPLES OF POLYMORPHISM
DEFINITION: Genetic polymorphism is defined as
the occurrence of multiple alleles at a locus in the
population where no allele occurs with a frequency of
greater than 0.99.
1. Phenotype: e.g. eye color
1. Average frequency of loci heterozygous for alleles
which determine structurally different polypeptides
is 12% - 18%.
2. Protein polymorphisms
3. DNA polymorphism
2. Average frequency of base pairs that are
heterozygous in a diploid individual is 1 in 270.
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BLOOD GROUP POLYMORPHISM
PROTEIN POLYMORPHISM
a. Blood groups e.g. ABO, Rh and MNS blood
group systems
b. Galactosemia locus
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Red blood cell antigens are useful genetic
markers in family population studies and in
linkage analysis.
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These are the first example of genetically
determined protein variation.
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Relevance in clinical medicine.
c. Alpha, antitrypsin locus
d. HLA system (Human Leukocyte Antigen)
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GENETICS OF ABO AND RH SYSTEMS
GENE PRODUCT
ANTIGEN
GENE PRODUCT
ANTIGEN
H and A
A-transferase
H-transferase
PRECURSOR
H
B-transferase
O
No transferase
GENOTYPE
PHENOTYPE
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ABO blood groups determined by a locus
on chromosome 9.
AA
OA
A
AB
AB
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A, B, and O alleles / examples of multiallelism.
BB
B
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The three alleles determine four phenotypes;
A, B, AB and O.
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Molecular differences in the glycosyltransferase gene
responsible for the A, B and O alleles:
H and B
OB
Unchanged H
OO
O
Diagram of the pathways of biosynthesis
Of the H, A, and B antigens. Alleles h and
O have no detectable effect.
- four nucleotide sequence difference between A and B
alleles.
Pathways of Biosynthesis of
The H, A, and B Antigens
- O allele has a single base pair deletion in the ABO gene
coding region i.e. frame shift mutation.
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• • Discovery of Rh system and its role in hemolytic disease of the newborn is
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a major contribution of genetics to medicine.
DNA POLYMORPHISMS
a. Base pair substitution
(1)
RFLP
(2)
others (detected by denaturing
gel electrophoresis)
b. Variable number tandem repeats (VNTR)
c. Minisatellites/microsatellites (di- tri- and
tetranucleotide repeats)
d. Single nucleotide polymorphism (SNP)
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Comparison between the two categories of markers
VNTR
MICROSATELLITE
Each repeat unit 20 to several hundred
bp in length
Each repeat units 2,3,4,5 bp in length
No. of repeats range from 2 to 20
No. of repeats variable
Detection by Southern analysis due to
large size
Detection by polymerase chain reaction
due to small size
Uneven distribution; clustered near
chromosome ends
Even distribution in the genome
Less polymorphic
More polymorphic
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Applications of Polymorphisms
Single Nucleotide Polymorphism
• A variation of a single nucleotide in the
genome
• Frequency of at least 1% in the population
• Occur every 1000 bp
• Do not alter a restriction site unlike RFLP
• Bi-allelic, but compensated by the numbers
• Dense SNP maps of genome available
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Mapping genes by linkage analysis
Forensic applications i.e. paternity testing
Organ transplantation for HLA matching
Hapmap allows association studies for
complex disorders
• Pharmacogenetics
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