Analyzing dna differences
1 / 22

Analyzing DNA Differences - PowerPoint PPT Presentation

  • Uploaded on

Analyzing DNA Differences. PHAR 308 March 2009 Dr. Tim Bloom. Overview. Genetic Differences Why analyze differences? SNP RFLP and PCR. Important Terms to Remember. Locus specific region on a chromosome Allele variant found at a locus Genotype composition of alleles at a locus

I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
Download Presentation

PowerPoint Slideshow about ' Analyzing DNA Differences' - graham-acosta

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.

- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
Analyzing dna differences

Analyzing DNA Differences

PHAR 308

March 2009

Dr. Tim Bloom


  • Genetic Differences

  • Why analyze differences?

  • SNP

  • RFLP and PCR

Important terms to remember
Important Terms to Remember

  • Locus specific region on a chromosome

  • Allele variant found at a locus

  • Genotype composition of alleles at a locus

  • Homozygous same allele each chromosome

  • Heterozygous different allele each chromosome

Genetic differences
Genetic Differences

  • Humans are 99% identical in DNA

    • For 3x109 bases, means 3x107 differences

    • On average a difference every 100 bases

  • Types of differences

    • Deletions

    • Insertions

    • Base changes

  • MAY cause differences in people

Genetic differences1
Genetic Differences

  • Alleles represent genetic differences

    • Blue eye vs. brown

    • Blood type A, B, AB and O

  • Genetic diseases

    • Muscular dystrophy

    • Cystic fibrosis

    • Sickle cell anemia

  • “Non-genetic” diseases or therapeutic targets

    • Increased susceptibility

    • Decreased sensitivity

Genetic differences2
Genetic Differences

  • Majority of differences show no effect

    • Differences in inactive DNA

    • “Silent” differences in protein

      • Neutral change in amino acid

      • Silent codon change

    • Requirement for environmental effects

      • CCR5 receptor on T-cells

Useful genetic differences
“Useful” Genetic Differences

  • Used to identify specific populations

  • “Polymorphisms”

    • Found in sizeable fraction of population

    • Can be used as “markers”

    • Can be made into family tree

    • Can be correlated with other traits

Example of a useful marker
Example of a Useful Marker

Image from Nature Clinical Practice Cardiovascular Medicine (2007) 4, 558-569

Finding genetic variation

Changes with effect



Genetic disease

Still must connect to a specific genetic context

Chromosomal stains

DNA sequence

Changes without effect?

Analyze DNA itself

Determine sequence

Effect of change on DNA analytical techniques

Finding Genetic Variation

Genetic markers
Genetic Markers

  • Detectable difference

  • Can be associated with a condition

    • Down syndrome

    • Schizophrenia

    • Sensitivity to chemotherapy

  • Associated means those afflicted or at risk have or are more likely to have the marker

Single nucleotide polymorphism
Single Nucleotide Polymorphism

  • Variability in one nucleotide

    • Example Rs17822931

      • Chromosome 16, position 46,815,699

      • Either C or T

      • Homozygous T = dry ear wax

      • Heterozygous or homozygous C = wet ear wax

    • Can be used forensically to ID race

      • T > 90% in Asian

      • C > 95% European or African

Seeing snps 1
Seeing SNPs (1)

  • Restriction fragment length polymorphism

    • Because of a change in DNA, restriction enzyme site is created or lost

    • DNA digestion pattern changes

Rflp analysis

RE's cut DNA based on sequence

If recognition sequence present, cuts

If recognition sequence absent, no cut

Compare bands created by digestion with one enzyme

RFLP Analysis

Using rflp
Using RFLP

  • Link an RFLP to a disease as marker

  • Link an RFLP to drug resistance

  • Link multiple RFLPs to make a forensic identification

Image from

Finding rflps
Finding RFLPs

  • Empirical

    • Must have DNA samples from separate sources

    • Must find polymorphism

    • (Many are found in genome projects)

    • Polymorphism must affect restriction enzyme

    • Must be able to show relation to something (for usefulness as a marker)

Seeing snps 2
Seeing SNPs (2)

  • Polymerase chain reaction

  • Technique for targeted DNA replication

    • Uses DNA polymerase

    • Uses synthetic DNA primers

    • Primers direct polymerase action

  • Repeated cycles of replication of DNA target

Simple pcr





















Simple PCR

Using pcr
Using PCR

  • See SNP with PCR

  • Use primer base pairing to detect

    • One primer’s end complements 1 polymorphism



  • If primer doesn’t match, no DNA synthesized

Analyzing dna differences

SNP Maps

All chromosomes are sequenced

SNP location

All SNPs are recorded

SNP Data

Analyzing dna differences

Individual SNP Profiles

SNP profile A

SNP profile F

SNP profile B

SNP profile E

SNP profile C

SNP profile D

Analyzing dna differences

SNP Profiles and Response to

Drug Therapy

Breast Cancer Patients

Individual SNP Profiles Are Sorted

Responds to Standard Drug Treatment

Does Not Respond to Standard Drug Treatment

SNP profile A

SNP profile B

SNP profile E

SNP profile C

SNP profile D


  • DNA variations can be correlated to health problems

  • Common variation is SNP

    • Detect by RFLP

    • Detect with PCR

  • Another variation is VNTR

  • Both variations used as “markers”


  • Slides 19-21 from NCI tutorial “Understanding SNPs and Cancer”