What is DNA Fingerprinting?
A collection of techniques used to determine the genetic identity of an organism based on its unique DNA patterns
Based on known DNA polymorphisms, usually in the non-protein coding regions of the genome
Can use trace amounts of hair, skin, body fluids Based on the fact that every individual’s DNA sequence is unique (except identical twins)
SNPs Single Nucleotide Polymorphisms
SNPs are produced when individuals in a population have different nucleotides (A,T,C or G) at specific locations.
Each sequence change represents a potential allele
SNPs are differences in specific sequence locations among individuals in a population.
Example of SNP use • Recent genome wide study of SNPs to identify
genes under positive selection in human populations living at high altitudes – Compared SNPs in Tibetan genomes (live at high
altitudes) with Han Chinese and Japanese genomes (both do not live at high altitudes)
– Study identified 1 gene known to affect regulation of RBC production
– 2 other genes linked to adult and fetal Hb showed a high correlation.
• Source: Science, Vol 329, 2 July 2010, p.72, Simonson et.al.
RFLPs Restriction Fragment Length
Polymorphisms
Utilizes restriction enzyme analysis of total genomic DNA to identify regions with SNPs
SNPs produce RFLPs
SNPs & RFLP (1) • A change in a specific nucleotide at a specific
location produces a change in the DNA sequence
• DNA Sequence changes alter Restriction Enzyme recognition sites – Add a restriction site – Delete a restriction site
• In this example, RE3 no longer exists due to a sequence change in Person 2
• Person 1 has a different set of restriction fragments than Person 2 – a RFLP
RE1 RE2 RE3 RE4 Person 1
RE5
Person 2
Fragment 1 Fragment 2 Fragment 3
Fragment 1 Fragment 2 Fragment 4 Fragment 3
•RE = Restriction Enzyme Site
SNPs & RFLPs (2) • A change in restriction sites will change the
resulting pattern of Restriction Fragments – RFP: Restriction Fragment Pattern
• In or across populations, different nucleotide changes, SNPs, occur in different individuals:
• In or across populations, SNPs produce RFP variations, these RFP variations are termed RFLPs
SNPs & HAPLOTYPES • Populations: Individuals with a common pool
of genetic variations. (SNPs, Indels, rearrangements, etc).
• HAPLOTYPE: a genotype with a single or a group of variations.
• HAPLOTYPES can be defined by the presence of a single variation (1 SNP) or a collection of variations.
Steps in RFLP analysis: 1. Collect sample (need a fair amount) 2. Purify DNA from the sample 3. Digest with restriction enzymes 4. Run on agarose gel 5. Transfer to nitrocellulose 6. Hybridize with labeled probe 7. Detect bands by autoradiography
DNA Fingerprint from Identical Twins No RFLPs present
DNA Fingerprints from a Sexual Assault Case
Which Suspect can be Ruled Out?
Which bands implicate the defendant? Why?
Paternity Testing: DNA Evidence
BASICS OF PCR (Animation) http://highered.mcgraw-hill.com/olc/dl/120078/micro15.swf
PCR (Polymerase Chain Reaction)
PCR of STRs (Short Tandem Repeats) Another Tool Used for DNA Fingerprinting
• Usually only 3-4nucleotides in each repeat • Advantages Can be done using very small amounts of DNA DNA can be very old or partially degraded
• Routinely used in forensic analysis • FBI has chosen 13 STRs for CODIS database Combined DNA Index System • Odds of matching someone else at all 13 STRs loci is greater than one in a billion • Main problem is sample contamination
STRs
Applications for DNA Fingerprinting
• Forensics (exclude or implicate a suspect) • Exoneration of falsely accused (Innocence
Project) • Paternity cases • Evolutionary studies • Want to Know More: Genetic Justice
Haplotypes & Genotypes for Alu insertion at PV92 Locus
• Alu insert = 300bp • Haplotypes
– PV92 locus with NO Alu insertion (400bp) – PV92 locus WITH Alu insertion (700bp)
• Genotypes – Homozygous NO Alu insertion (Alu -/-) – Heterozygous for Alu insertion (Alu +/-) – Homozygous for Alu insertion (Alu +/+)
