Genomics in personal identification Flashcards
What are the facts that the legal applications of DNA sequencing depend on
> The genomes of all individuals are unique (even MZ twins)- provides a unique personal identification, eg. blood at a crime scene can be traced to one individual
The genome of every person combines chromosomes from his or her parents- genomes can indicate familial relationships
each person’s genome contains genes that influence recognizable features, eg. hair colour- DNA at a crime scene can be analyzed and then used to suggest a physical description of that individual. Therefore, genomes contain much more information about a person than simple identification- the treatment of this information by governmental authorities raises ethical and legal questions
The use of molecular characteristics to identify people and relationships, eg. classical blood groups- A, B, AB and O. Blood groups can be used to prove innocence and not guilt- a suspect with blood type O must be innocent in a crime committed by a person with blood type A. A person of blood type O could never be the parent of a child with blood type AB. Tests based on a wider panel of serotypes, including the major histocompatibility complex haplotypes have better discrimination. In contrast, DNA sequences can provide positive proof of guilt or paternity.
Name some cases where DNA identification provided evidence
> The trial of OJ Simpson for the murder of his wife- he was acquitted despite evidence of his blood at the crime scene.
a stain on the White House intern’s dress provided evidence of inappropriate behavior by US president William Clinton
Comparison of DNA from descendants of US president Thomas Jefferson and a slave Sally Hemings proved that he was the father of her children
Explain how DNA fingerprinting began
AJ Jeffreys discovered DNA fingerprinting in 1984, when he and his colleagues compared the sizes of the restriction fragments of DNA samples, including a human family group(father, mother and child). Different individuals give different patterns- the gel provided a ‘barcode’ unique to each individual. The pattern from the child’s DNA was a combination of the parents’ DNA.
What are restriction enzymes
A restriction endonuclease cleaves DNA at specific sequences. They cleave both strands and either produce restriction fragments with blunt ends(cleave at opposing positions) or sticky ends(cleaves are different positions leaving dangling bits of single strands)
Explain the use of restriction enzymes in DNA profiling
Two restriction enzymes in common use in DNA profiling are HaeIII, HinfI, and TaqI. HaeIII produces blunt ends, HinfI produces sticky ends and TaqI produces sticky ends. Because the sequences at which the enzymes acts are distributed throughout the DNA, cleavage produces a set of ‘restriction fragments’ of variable length. The average length of a restriction fragment is 4^n. The different fragment lengths can be used to distinguish different DNA molecules. When the restriction fragments are spread out on a gel it produces a characteristic pattern called a ‘restriction map’.
Why do different individuals give different patterns of restriction fragment sizes
One possible cause is a mutation in a restriction site causing the site not to be cleaved. Alternatively, somewhere between two restriction sites there might be a short repetitive stretch of DNA- this is called VNTR (Variable number tandem repeat). VNTRs are usually flanked by recognition sites for the same restriction enzyme, which will excise them, producing fragments of different lengths. It is these fragment lengths that vary between individuals, known as RFLP(restriction fragment length polymorphism). The fragments can be separated on a gel according to size and detected by Southern blotting.
Discuss how personal identification by amplification of specific regions has superceded the RFLP approach
Identification by gel separation of RFLPs has disadvantages- it requires relatively large amounts of undegraded DNA(10-20ng, no shorter than 20000-25000 bp).
PCR can use tiny amounts of DNA to amplify even 100bp regions. The method that is commonly used now is to PCR amplify a STR typically containing 2-5 bp, repeated between a few and a dozen times. Amplification produces fragments about 200-500 bp long. Loci typically show 5-20 common alleles in a population. Typically 11 or 13 autosomal loci are tested and the amelogenin test is used to determine gender.
What is the amelogenin test
It is used to test for gender. The human amelogenin gene appears on the the X and Y chromosomes. The X copy shows a 6 bp deletion in intron 1, relative to the Y version. Then PCR that uses suitable primers amplifies fragments of 106 bp from the Y chromosome(if present) and 112bp from the X chromosome. Two bands on the gel imply its a male and 1 band implies that its a female
Explain mtDNA
Human mtDNA is a circular molecule that is 16568 bp long, containing 37 genes that are densely packed in a coding region. There are 13 genes coding for polypeptides, 2 for rRNAs, and 22 for tRNAs (most mitochondrial proteins are encoded in nuclear DNA and the proteins are imported into the mitochondria). mtDNA contains a single major non-coding region, 1122 bp long, which is hypervariable relative to the coding regions. Formerly, two segments from this region were sequenced for population and forensic studies. However, now it is easier to sequence the entire mtDNA. Each person receives mtDNA exclusively from his or her mother, therefore mtDNA sequence comparisons would be useless in paternity testing. However, they can identify an individual from a sequence match to a specimen, are useful in tracking migratory patterns, and can identify relationships among people linked by a maternal line of descent.
What are some applications of DNA identification techniques to animals
Applications of DNA identification techniques to animals include proof that Dolly the sheep was a clone, testing of horses and dogs to confirm breeders claims of pedigrees, identifying the claimed species origin of supermarket meats, and checking of commercial whale meat for endangered species.
Why do some people have to get dog licences
A number of places have required dog owners to submit DNA samples from their dogs as a condition for issuing dog licences- in order to be able to identify and fine owners who do not clean up after their pets.
How can samples from pets help with crime investigation
Animals can cause harm, or be victims, or provide links to human criminals. The association of hair from a suspect’s pet with trace material found on a victim has contributed to many convictions.
Explain paternity testing
Every child receives VNTRs from their mother and father. For VNTRs on autosomes, the child inherits only one of each chromosome pair from each parent- therefore half of each parent’s VNTRs appear in the child. Also, each VNTR in a child must come from one of the parents. If the child has a VNTR that does not come from the mother or the candidate father then it disproves paternity. If all the child VNTR appears in both the mother and candidate father then the probability of paternity depends on the number of loci that were studied. Typically, 15-20 autosomal loci are tested. The results are the two VNTR lengths at these loci for the child, mother and father. If the father and mother share a VNTR length, then its appearance is uninformative. For each VNTR that is shared by the child and the candidate father(but absent in the mother)- the strength of the inference of paternity varies with the frequency of appearance of that VNTR length in the population. Thus, if a child and the candidate father share a rare allele, the associated paternity index is high(PI).
Explain paternity index
The paternity index, at one VNTR locus, is the likelihood of occurrence of the observed genotypes if the candidate father is the biological father, relative to the likelihood of occurrence of the observed genotypes if a randomly selected man from the appropriate population is the biological father. The values are typically in the range 0-40. The Combined Paternity Index (CPI) is the product of paternity indices at all loci. In many countries, a CPI over 100 is the legal criteria for presumed paternity. CPI is conventionally translated into Probability of Paternity (POP). Test results from over-the-counter paternity test kits are not accepted in courts because the origin of the samples is not properly controlled.
Explain reverse paternity testing
This is used if there is no candidate sample available. If there is an alleged father, and sequences from other children or close relatives of his are available, it is possible to compare them with the data from the mother and child. If not, it might be possible to ‘reconstruct’ the genetic make-up of the father. This might make it possible to identify certain of his phenotypic features or to search for him in genetic sequence databases.
