The Biology and Genetic The Biology and Genetic

Base of Cancer. Base of Cancer.

22(Mutation)(Mutation)

Gene

Chemical bases

DNA Molecule

Chromosome

From cellular to molecular biology

Mutation the effect from chromosome to ProteinMutation the effect from chromosome to Protein

Mutation …Mutation …Bad ….GoodBad ….Good

It is good, it is bad also!!It is good, it is bad also!! Mutation in the long term it is essential to our Mutation in the long term it is essential to our

existance. existance. Without mutation there Could be no change and Without mutation there Could be no change and

without change life cannot evolve.without change life cannot evolve.

Ex. Adaptive mutation Ex. Adaptive mutation

Definition of mutationDefinition of mutation

A change in DNAA change in DNA

1.1. Arrangement.Arrangement.

2.2. Context. Context.

3.3. Dosage.Dosage.

4.4. Sequence.Sequence.

Causes of mutationsCauses of mutations

Size of mutationSize of mutationPoint mutation.Point mutation.Submicroscopic mutation.Submicroscopic mutation.Microscopically visible Microscopically visible

mutation.mutation.Loss of a whole chromosome.Loss of a whole chromosome.

Somatic or germinal?Types of mutationsTypes of mutations

Del(5)(p15)

Germinal mutation Germinal mutation

Normal 1st event 2nd event

Born with mutation 2nd event

Familiar.Familiar. Sporadic.Sporadic.

Type of MutationsType of Mutations

MutationMutationChromosomal levelChromosomal level

Aneuploidy, robertsonian translocationAneuploidy, robertsonian translocation

Change in DNA sequence arrangementChange in DNA sequence arrangementGenomic regional level – e.g. translocation, inversion,Genomic regional level – e.g. translocation, inversion,

Retrotransposition.Retrotransposition.

Change in sequence contextChange in sequence contextWhWhole gene level – e.g. whole gene deletion or duplicationole gene level – e.g. whole gene deletion or duplication

Change in gene dosageChange in gene dosageNucleotide level – e.g. change, deletion, duplication of oneNucleotide level – e.g. change, deletion, duplication of one

or a few bases Change of nucleotide sequenceor a few bases Change of nucleotide sequence

Acquired Acquired mutationsmutations

HereditaryHereditary mutationsmutations

Methods detect mutations

Three common methodsThree common methods

For acquired mutation

MutationMutationChromosomal levelChromosomal level

Aneuploidy, robertsonian translocationAneuploidy, robertsonian translocation

Change in DNA sequence arrangementChange in DNA sequence arrangementGenomic regional level – e.g. translocation, inversion,Genomic regional level – e.g. translocation, inversion,

Retrotransposition.Retrotransposition.

Change in sequence contextChange in sequence contextWhWhole gene level – e.g. whole gene deletion or duplicationole gene level – e.g. whole gene deletion or duplication

Change in gene dosageChange in gene dosageNucleotide level – e.g. change, deletion, duplication of oneNucleotide level – e.g. change, deletion, duplication of one

or a few basesor a few bases

Change of nucleotide sequenceChange of nucleotide sequence

Mutation reflects the event, not Mutation reflects the event, not its consequencesits consequences

Does a mutation need to relate to an effect Does a mutation need to relate to an effect (gain, loss or alteration) on gene function?(gain, loss or alteration) on gene function?

Is a new sequence change with no effect on the Is a new sequence change with no effect on the individual a mutation?individual a mutation?

Context may be important e.g. “polymorphism” Context may be important e.g. “polymorphism” that leads to disease susceptibilitythat leads to disease susceptibility

e.g. new recessive mutatione.g. new recessive mutation

e.g. point mutation with no effect on the protein e.g. point mutation with no effect on the protein sequencesequence

Mutation may be viewed as the Mutation may be viewed as the engine that drives evolutionengine that drives evolution

Is mutation rate determined (selected) by evolution?Is mutation rate determined (selected) by evolution?mutation rate as a balance between benefit and liabilitymutation rate as a balance between benefit and liability

too low leads to a species that is not adaptive.too low leads to a species that is not adaptive. too high leads to a species in which there is disease and too high leads to a species in which there is disease and

decreased fitness.decreased fitness.

Mutation rate reflects:Mutation rate reflects: Replication error: the major contributor.Replication error: the major contributor. Copying, proofreading, repair tuned to the optimum error rateCopying, proofreading, repair tuned to the optimum error rate Damage and repair: may be primarily somatic.Damage and repair: may be primarily somatic. Other biological processes with built-in error rates (e.g. Other biological processes with built-in error rates (e.g.

recombination)recombination)

Types of mutationsTypes of mutations Point mutations: Change of the normal base Point mutations: Change of the normal base

to anotherto another Possible consequences:Possible consequences:

Silent mutation: No consequenceSilent mutation: No consequenceMissense mutation: changes the codon to one Missense mutation: changes the codon to one

encoding a different amino acidencoding a different amino acidNonsense mutation: Changes codon from one Nonsense mutation: Changes codon from one

encoding an amino acid to a stop codonencoding an amino acid to a stop codonSplice site alteration: can abolish or create a splice siteSplice site alteration: can abolish or create a splice siteRegulatory region mutation: Can result in net increased Regulatory region mutation: Can result in net increased

or decreased gene expressionor decreased gene expression

DeletionDeletion DuplicationDuplication InversionInversion

What is the mutation rateWhat is the mutation rateOverall rates consider the fidelity of DNA replicationOverall rates consider the fidelity of DNA replication - - in vitro in vitro fidelity, studies in model organismsfidelity, studies in model organisms - 10 -9 – 10 –11 per bp per replication (10 -6 – 10 –8 per gene per division)- 10 -9 – 10 –11 per bp per replication (10 -6 – 10 –8 per gene per division) - Deleterious mutation rate (# per zygote) is difficult to accurately determine- Deleterious mutation rate (# per zygote) is difficult to accurately determine - Disease-based estimate: extrapolate from incidence of one disease- Disease-based estimate: extrapolate from incidence of one disease - individual genes may not be representative- individual genes may not be representative - Population-based estimate: molecular clock based on species divergence- Population-based estimate: molecular clock based on species divergence - estimate the “neutral” mutation rate in non-coding vs. coding- estimate the “neutral” mutation rate in non-coding vs. coding - infer the lost, presumably deleterious, mutations lost- infer the lost, presumably deleterious, mutations lost - extrapolate over the whole genome- extrapolate over the whole genome - use time since split, generation time, gene number estimates- use time since split, generation time, gene number estimates - estimated 3 deleterious mutations/zygote- estimated 3 deleterious mutations/zygote

6. In the face of the deleterious mutation rate, how can a species persist?6. In the face of the deleterious mutation rate, how can a species persist? - The rate of accumulation of deleterious mutations must be balanced by loss- The rate of accumulation of deleterious mutations must be balanced by loss - Highly deleterious mutations are purged individually (Haldane)- Highly deleterious mutations are purged individually (Haldane) - Mildly deleterious mutations persist initially and are then lost by selection, drift- Mildly deleterious mutations persist initially and are then lost by selection, drift - Crow: quasi truncation selection model:- Crow: quasi truncation selection model: - assume 3 new deleterious mutations per generation- assume 3 new deleterious mutations per generation - assume mutations persist for 100 generations- assume mutations persist for 100 generations - question: what level of loss (genetic death) is needed to balance the load?- question: what level of loss (genetic death) is needed to balance the load? - average of 16% reproduction failure- average of 16% reproduction failure - as the load increases, a point is reached at which fitness decreases- as the load increases, a point is reached at which fitness decreases - a probabilistic model relating load to fitness (reproduction)- a probabilistic model relating load to fitness (reproduction) - variables that could affect the result- variables that could affect the result - number of mutations, persistence- number of mutations, persistence - environmental improvements lead to increased tolerance- environmental improvements lead to increased tolerance - medical intervention leads to increase tolerance- medical intervention leads to increase tolerance

Types of mutationTypes of mutation

Point mutations: single nucleotide changes synonymous Point mutations: single nucleotide changes synonymous (silent), nonsynonymous (missense, nonsense)(silent), nonsynonymous (missense, nonsense)

- microdeletions/duplications – one or a few nucleotides- microdeletions/duplications – one or a few nucleotides - may be mediated by short repeated sequences- may be mediated by short repeated sequences - larger deletions/duplications – large portions of a gene - larger deletions/duplications – large portions of a gene

or genesor genes - single gene or contiguous gene disorders- single gene or contiguous gene disorders - often mediated by larger repeat elements: e.g. LINE1, - often mediated by larger repeat elements: e.g. LINE1,

AluAlu - microsatellite repeat deletion/expansion – CA or - microsatellite repeat deletion/expansion – CA or

trinucleotide repeatstrinucleotide repeats

Major mutation typesMajor mutation types Single base substitutions that cause premature termination of Single base substitutions that cause premature termination of

protein synthesis, change of amino acid, suppress termination protein synthesis, change of amino acid, suppress termination of protein translation, alter level of gene expression, or alter of protein translation, alter level of gene expression, or alter patterns of mRNA splicingpatterns of mRNA splicing

Translocations, that bring disparate genes or chromosome Translocations, that bring disparate genes or chromosome segments togethersegments together

Deletions of a few nucleotides up to long stretches of DNADeletions of a few nucleotides up to long stretches of DNA Insertions and duplications of nucleotides up to long stretches Insertions and duplications of nucleotides up to long stretches

of DNAof DNA Many different mutations can occur within a given gene, Many different mutations can occur within a given gene,

although it appears that genes have different degrees of although it appears that genes have different degrees of mutabilitymutability

Different mutations affecting a gene can result in distinct clinical Different mutations affecting a gene can result in distinct clinical syndromessyndromes

Types of mutationsTypes of mutations Translocations:Translocations:

Fusion of one chromosomal segment or gene Fusion of one chromosomal segment or gene fragment with anotherfragment with another

May result in disruption of gene(s)May result in disruption of gene(s)May result in a hybrid gene with novel function or May result in a hybrid gene with novel function or

combination of the functions of both genescombination of the functions of both genes

Location, location, locationLocation, location, location