Genetic Engineering 2 (T401) : DNA Analysis in Forensic Science & Archaeology

Genetic Engineering 2
(T401)
DNA Analysis in Forensic Science & Archaeology
Prof. Dr. Samir A. Ibrahim

Outlines
 DNA analysis in the identification of crime suspects
 Studying kinship by DNA profiling
 Six identification by DNA analysis
 Archaeogenetics using DNA to study human
prehistory (To be continue next week)
DNA Analysis in Crime Suspects
Identification
It is probably impossible for a person to commit a crime
without leaving behind a trace of his or her DNA.
 The applications of molecular biology in forensics center

largely on the ability of DNA analysis to identify an
individual from hairs, bloodstains, and even conventional
fingerprints contain traces of DNA, enough to be studied
by the polymerase chain reaction (PCR).
In the popular media, these techniques are called genetic

fingerprinting, though the more accurate term for the
procedures used today is DNA profiling.
Genetic fingerprinting by hybridization
probing
This technique is depending on hypervariable dispersed
repetitive sequence which is repeated sequence (contains
initially GGGCAGGANG (where N is any nucleotide)).
This sequence occurs at various places (―dispersed‖) in the

human genome. The key feature of these sequences is that
their genomic positions are variable
Fingerprint preparation includes, sample of DNA is
digested with a restriction endonuclease, the fragments
separated by agarose gel electrophoresis, and a Southern blot
prepared.
Hybridization to the blot of a labeled probe containing the
repeat sequence reveals a series of bands, each one
representing a restriction fragment that contains the repeat.
insertion sites of the repeat sequence are
variable, so it give a different pattern of bands.
Limitations of Finger printing in Forensic
 A relatively large amount of DNA is needed because the technique
depends on hybridization analysis.
 Interpretation of the fingerprint can be difficult because of variations in

the intensities of the hybridization signals.
 Insertion sites of the repeat sequences are hypervariable, there is a limit

to this variability and therefore a small chance that two unrelated
individuals could have the same, or at least very similar, fingerprints.
DNA profiling by PCR of short tandem
repeats (STRs)
STR: is a short sequence, 1–13 nucleotides in length,
which is repeated several times in a tandem array.
In the human genome, the most common type of STR is

the dinucleotide repeat [CA] n , where ―n‖, the number of
repeats, is usually between 5 and 20
 The number of repeats in a STR is variable
because repeats can be added or, less frequently,
removed by errors that occur during DNA
replication.
 In the population, there might be as many as ten

different versions of a STR, each of the alleles
characterized by a different number of repeats.
 In DNA profiling, the alleles of a selected

number of different STRs are identified.
 This can be achieved quickly and with very small

amounts of DNA by PCRs with primers that
anneal to the DNA sequences either side of a
repeat.
 PCR products can be examined by agarose gel electrophoresis. The
size of the band or bands that are seen in the gel indicate the allele or
alleles present in the DNA sample that has been tested.
 Two alleles of an STR can be present in a single DNA sample

because there are two copies of each STR, one on the chromosome
inherited from the mother and one on the chromosome from the
father.
Combined DNA Index System
CODIS
 Methodology of using 12 STRs with sufficient variability to give only
a one in 1015 chance that two individuals, other than identical twins,
have the same profile.
Each STR is typed by PCRs with primers that are fluorescently
labeled, and which anneal either side of the variable repeat region.
The alleles present at the STR are then typed by determining the sizes
of the amplicons by capillary gel electrophoresis.
Studying Kinship by DNA Profiling
Related Individuals Have Similar DNA
Profiles
Your DNA profile, like all other aspects of your genome, is inherited
partly from your mother and partly from your father. Relationships within
a family therefore become apparent when the alleles of a STR are marked
on the family pedigree
DNA Profiling and Remains of Romanovs
 Extracted DNA from bones from each individual and five STRs typed
by PCR to test the hypothesis that the three children were siblings and
that two of the adults were their parents, as would be the case if indeed
these were the Romanovs.
STR Analysis of Romanov Bones
 The results immediately showed that the three children could be
siblings, as they have identical genotypes for the STRs called
VWA/31 and FES/FPS and share alleles at each of the three other
loci.
 The THO1 data show that female adult 2 cannot be the mother of
the children because she only possesses allele 6, which none of the
children have. Female adult 1, however, has allele 8, which all three
children have. Examination of the other STRs confirms that she
could be the mother of each of the children, and so she is identified
as the Tsarina.
 The THO1 data exclude male adult 4 as a possible father of the

children, and the VWA/31 results exclude male adults 1 and 2.
When all the STRs are taken into account, male adult 3 could be the
father of the children and therefore is identified as the Tsar.
The STR analysis showed that the skeletons included a family group
as expected, if these were indeed the bones of the Romanovs. But
could they be the remains of some other unfortunate group of people?
To address this problem, the DNA from the bones was compared with
DNA samples from living relatives of the Romanovs.
This work included studies of

mitochondrial DNA
Mitochondrial DNA to link Romanov
Skeletons with living Relatives
Mitochondrial DNA contains polymorphisms that can be used to infer
relationships between individuals, but the degree of variability is not as
great as displayed by STRs, so mitochondrial DNA is rarely used for
kinship studies among closely related individuals such as those of a
single-family group.
Mitochondrial DNA has the important property of being inherited

solely through the female line, the father’s mitochondrial DNA being
lost during fertilization and not contributing to the son or daughter’s
DNA content.
This maternal inheritance pattern makes it easier to distinguish

relationships when the individuals being compared are more distantly
related, as was the case with the living relatives of the Romanovs.
Comparisons between mitochondrial DNA sequences obtained from the
skeletons and that of Prince Philip, the Duke of Edinburgh, whose
maternal grandmother was Princess Victoria of Hesse, the Tsarina
Alexandra’s sister .
The mitochondrial DNA sequences from four of the female

skeletons—the three children and the adult female identified as the
Tsarina—were the same as that of Prince Philip, strong evidence that
the four females were members of the same lineage.
Sex Identification by DNA Analysis
The genetic difference between the sexes is the possession of a

Y chromosome by males, so detection of DNA specific for the
Y chromosome would enable males and females to be
distinguished.
PCRs Directed at Y Chromosome-Specific
Sequences
 The simplest way to use DNA analysis to identify sex is to design a PCR specific
for a region of the Y chromosome.
 The PCR must be designed with care, because the X and Y chromosomes are not
completely different, some segments being shared between the two, but there are
many unique regions within the Y chromosome.
 There are several repeated sequences that are only located in the Y
chromosome, these repeated sequences acting as multiple targets for
the PCR and, hence giving greater sensitivity.
 A PCR directed at Y-specific DNA sequences would give a product
with male DNA but no band if the sample comes from a female.
PCR of Amelogenin Gene
The amelogenin gene codes for a protein found in tooth enamel. It

is one of the few genes that are present on the Y chromosome and,
like many of these genes, there is also a copy on the X
chromosome.
The two copies are far from identical, and when the nucleotide
sequences are aligned several indels, positions where a segment of
DNA has either been inserted into one sequence or deleted from
the other sequence.
 Primers for a PCR anneal either side of an indel, the products obtained
from the X and Y chromosomes would have different sizes.
 Female DNA would give a single band when the products are
examined, because females only have the X chromosome, whereas
males would give two bands, one from the X chromosome and one
from the Y.
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Genetic Engineering 2

Prof. Dr. Samir A. Ibrahim

 The applications of molecular biology in forensics center

In the popular media, these techniques are called genetic

This sequence occurs at various places (―dispersed‖) in the

 Interpretation of the fingerprint can be difficult because of variations in

 Insertion sites of the repeat sequences are hypervariable, there is a limit

In the human genome, the most common type of STR is

 In the population, there might be as many as ten

 In DNA profiling, the alleles of a selected

 This can be achieved quickly and with very small

 Two alleles of an STR can be present in a single DNA sample

 The THO1 data exclude male adult 4 as a possible father of the

This work included studies of

Mitochondrial DNA has the important property of being inherited

This maternal inheritance pattern makes it easier to distinguish

The mitochondrial DNA sequences from four of the female

The genetic difference between the sexes is the possession of a

The amelogenin gene codes for a protein found in tooth enamel. It

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