Class 22 DNA Polymorphisms Based on Chapter 10 Recombinant DNA Technology

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1. Questions you should be able to answer from today’s lecture.

1. How do polymorphisms arise in the genome?2. What types of DNA polymorphisms are present in the genome? 3. How can DNA polymorphisms be used in genetic analysis and in

disease diagnosis? 4. What is DNA fingerprinting (DNA typing) and how can it be used?

3. Mutations rate vs frequency

• Mutations are quantified in two different ways:– Mutation rate is the probability of a particular kind of mutation

as a function of time (e.g., number per gene per generation).– Mutation frequency is the number of times a particular

mutation occurs in proportion to the number of cells or individuals in a population (e.g., number per 100,000 organisms).

4a. Types of Point Mutations

• There are two general categories of point mutations: base-pair substitutions and base-pair deletions or insertions.

• A base-pair substitution replaces one base pair with another. There are two types (Figure 7.3):

• Base-pair substitutions in ORFs are also defined by their effect on the protein sequence. Effects vary from none to severe.

4b. Types of Point Mutations

• Deletions and insertions can change the reading frame of the mRNA downstream of the mutation, resulting in a frameshift mutation.

4d. Types of Point Mutation.

2. Uses of DNA Polymorphisms in Genetic Analysis

• Genes have historically been used as markers for genetic mapping experiments.

• A DNA polymorphism is two or more alleles at a locus that vary in nucleotide sequence or number of repeated nucleotide units (indels).

• DNA markers are polymorphisms suitable for mapping, used in association with gene markers for genetic and physical mapping of chromosomes.

3. Single Nucleotide Polymorphism (SNPs, “Snips”):Southern Blot

4. Single Nucleotide Polymorphism (SNPs, “Snips”): PCR

5. Detection of All SNPs

6. Short Tandem Repeats (STRs) & Variable Number Tandem Repeats

(VNTRs)

7. DNA Molecular Testing for Human Genetic Disease Mutations

• DNA testing is increasingly available for genetic diseases, including:– Huntington disease.– Hemophilia.– Cystic fibrosis.– Tay–Sachs disease.– Sickle-cell anemia.

8. Purposes of Human Genetic TestingHuman genetic testing serves three main purposes:• Prenatal diagnosis - uses amniocentesis or chorionic

villus sampling to assess risk to the fetus of a genetic disorder

• Newborn screening .- examples of tests for specific mutations using blood from newborns include:– Phenylketonuria (PKU).– Sickle-cell anemia.– Tay–Sachs disease.

• Carrier (heterozygote) detection - Carrier testing is now available for many genetic diseases, including:– Huntington disease.– Duchenne muscular dystrophy.– Cystic fibrosis.

9. Examples of DNA Molecular Testing: Testing by Restriction Fragment Length Polymorphism

11. Examples of DNA Molecular Testing: Testing Using PCR Approaches

13. DNA Typing

14. Applications of DNA TypingExamples of DNA typing used to analyze samples include:• Crime scene invetigation• Population studies to determine variability in groups of people.• Proving horse pedigrees for registration purposes.• Conservation biology to determine genetic variation in

endangered species.• Forensic analysis in wildlife

crimes, allowing body parts of poached animals to be used as evidence.

• Detection of pathogenic E. coli strains in foods

• Detection of genetically modified organisms (GMOs) in bulk or processed foods