Name : ‫ساره محمد طه محمود زاهر‬

Assignment for : forensic medicine

Assignment on :DNA finger printing as anew tool of
identification from the forensic point of view.
Faculty of veterinary mansoura university FSH level 5
:Introduction
DNA fingerprinting, one of the great discoveries of the late 20th century,
has revolutionized forensic investigations. This review briefly
recapitulates 30 years of progress in forensic DNA analysis which helps
to convict criminals, exonerate the wrongly accused, and identify victims
of crime, disasters, and war. Current standard methods based on short
tandem repeats (STRs) as well as lineage markers (Y chromosome,
mitochondrial DNA) are covered and applications are illustrated by
casework examples. Benefits and risks of expanding forensic DNA
databases are discussed and we ask what the future holds for forensic
DNA fingerprinting.

Uses of DNA fingerprinting

DNA fingerprinting is commonly used in forensics, a field that applies science in a
legal setting. For example, investigators often collect DNA – in the form of blood,
hair, semen, saliva or tissue samples – from crime scenes. These samples are then
analyzed, and the resulting DNA profiles can be compared with the genetic
fingerprints of suspects to find matches, helping to convict the guilty and to exonerate
the wrongly accused. Paternity investigations often rely on DNA fingerprinting as
well. Here, the technique is used to compare the child's DNA with the alleged father's
DNA. Additionally, in situations such as natural disasters, DNA fingerprinting can be
applied to teeth or bones to help identify the victims.

Beyond its use In forensics, DNA fingerprinting has found applications in multiple
other sectors, including diagnostics, medical research, ecology, microbiology and
genealogy. This article will focus on the technique's applications in forensics, but we
would briefly like to mention that it can also be used to:
Track the inheritance of diseases;
Understand genetic disorders;
Develop more effective and personalized treatments for patients;
Characterize the variety of microorganisms in an environmental sample;
Investigate foodborne outbreaks and pinpoint their source;
Determine evolutionary relationships between organisms.
Moreover, genealogists use DNA fingerprinting to trace lineages and establish
familial connections. This has opened up new ways for people to explore their
ancestry and understand their heritage.

The DNA fingerprinting process

While DNA fingerprinting relies on variations in the genome to generate an
individual's DNA profile, not all polymorphic regions are examined during this
technique. Instead, only certain sequences are analyzed. For example, the short
tandem repeat (STR) approach – commonly used in forensics – focuses on specific
loci that contain sequences of 2 to 6 base pairs that are repeated multiple times.5
Since the number of repeats is highly variable among individuals, and since every
individual has 2 alleles of each loci – one inherited from the mother and one from the
father – they provide an ideal basis for DNA fingerprinting. However, the specific
method used for STR analysis varies from country to country; 20 so-called 'CODIS
core loci' are routinely used by the US FBI to create a fingerprint,6 while the UK
relies on 16 loci plus a gender identifier.
The process of performing STR analysis is described step-by-step in the section
below. For information on other ingerprinting techniques, please refer to the 'Types of
forensic DNA analysis

DNA fStep 1: sample collection

A wide variety of samples – including blood, saliva, semen, genital or rectal swabs,
skin or tissue cells, fingernails, hairs and urine – can be collected from crime scenes
and used for STR analysis. Blood, oral swabs and plucked hairs are the most common
sample types obtained from suspects or individuals involved in paternity
investigations or other genetic relationship inquiries.8 It is important that correct
aseptic sample collection techniques are followed to ensure reliable results.
Step 2: DNA extraction
Once the sample reaches the lab, the next step is to extract DNA from the cells. This
process includes cell lysis, inactivation of nucleases, and purification to separate the
DNA from cellular debris. Several different methods – each with its own pros and
cons – can be used for DNA extraction, and an overview of the different techniques
can be found in our blog entitled 'Comparison of RNA and DNA extraction methods

Step 3: DNA amplification

To ensure that there is sufficient DNA for downstream analysis, the STR sequences
are amplified using polymerase chain reaction (PCR) methods. However, to be able to
effectively differentiate and identify the various STR sequences during the subsequent
analysis step, the standard PCR protocol has to be modified. When performing a PCR
workflow for STR amplification, you not only require a specific primer pair for each
locus, but the primers also need to attach a unique fluorescent tag to the resulting PCR
products.

Step 4: DNA analysis

After amplification, the DNA sample is run through a capillary containing a gel that
allows smaller STR sequences to travel faster through its pores. At the end of the
capillary, a laser beam and a detector register the fluorescent tag of each sequence.
The combination of the travel time and the fluorescent signal allow the capillary gel
electrophoresis system to determine the length of the STR sequences for each locus
analyzed.
Step 5: data comparison and interpretation
The final step in a STR analysis workflow involves comparing the genetic fingerprint
obtained with that of another sample. Capillary gel electrophoresis results –
electropherograms representing each sample – can easily be compared to determine
whether samples match or differ, and this process can be performed manually or
automated.For example, a paternity test will likely include 3 samples – from the child,
mother and alleged father – that will be run through the capillary gel electrophoresis
system. For each locus of interest, you will therefore generate 3 electropherograms
with 2 peaks representing the 2 alleles. Figure 1 depicts a possible result of this test,
and shows a maternal allele (number 8) and a paternal allele (number 13) that have
been passed to the child at this locus. The alleged father could therefore possibly be
the child's biological father, if similar results are observed for the other loci required
in the test.
The process of comparing a DNA fingerprint from a crime scene sample with that of 1
or more suspects works in exactly the same way, but the electropherograms would
match for both alleles if they came from the same individual. Many countries store
genetic fingerprints from previous criminal investigations in DNA databanks,
allowing forensic scientists to search for a match even when there are no direct
suspects.11,12 In some cases and countries, it is even possible to scan genealogy
databanks for suspects or their relatives.13 These databanks allow anyone to register
and submit a DNA sample through an at-home testing kit and, while their main
purpose is to give people more information on their genetic background, they have
proven useful in certain criminal investigations

Types of forensic DNA analysis

Forensic DNA analysis has come a long way since its early beginnings in the 1980s,
with the emergence of several different techniques. STR analysis is now the primary
method18 but, before its invention, restriction fragment length polymorphism (RFLP)
was the dominant technique. Additionally, since the adoption of STR approaches,
other methods such as Y chromosome analysis, mitochondrial DNA (mtDNA)
analysis, single nucleotide polymorphism (SNP) typing and mini STR analysis have
also been developed. This chapter explores the evolution of forensic DNA analysis
techniques, and explains when to use which alternative to STR typing.

Restriction fragment length polymorphism

RFLP analysis begins with the extraction of DNA from a sample. Restriction enzymes
are then used to cut this DNA into thousands of pieces, creating fragments that vary in
length due to polymorphic regions. Next, these fragments are separated by size
through gel electrophoresis and transferred to a membrane.

Following denaturation, the membrane is incubated with radioactive probes binding to

minisatellite regions in the DNA fragments. Minisatellites are similar to STRs – in
that they are short, repetitive, non-coding DNA sequences – but they are longer,
containing to 60 base pairs.20 After incubation, the probes are visualized by exposing
the membrane to X-ray film, producing a pattern of bands – the DNA fingerprint.
Despite its early success, RFLP has been largely replaced by STR
approaches that leverage PCR to enable minute amounts of DNA and
partially degraded samples to be analyzed.19 There are, however,
variations of RFLP that combine the technique with PCR and are still
used today. An example is terminal RFLP (T-RFLP), a popular approach
in environmental microbiology studies to characterize microbial
communities.21 It involves the following steps:

Sample collection;
DNA extraction;
PCR amplification, with primers attaching a fluorescent tag to the
amplicons;
Amplicon digestion by restriction enzymes;
Size separation and data analysis using capillary gel electrophoresis;
Data interpretation

Y chromosome analysis
While STR analysis Is used to study specific loci on various
chromosomes, Y chromosome analysis examines STR markers found
exclusively on the Y chromosome. This technique is particularly valuable
when Investigating male-on-female sexual assaults – where minuscule
amounts of male DNA need to be detected in female samples – or
determining familial relationships among males

Mitochondrial DNA analysis

mtDNA analysis can be more effective than STR approaches when
samples contain a low nuclear DNA content. This can be the case when
samples consist of old bones, teeth or hair shafts. Instead of examining
DNA extracted from the nucleus of cells, this technique analyzes DNA
found in mitochondria. As all maternal relatives share identical mtDNA,
this method can also be used to analyze unidentifiable remains by
comparing them to maternal relatives

Single nucleotide polymorphism typing

SNPs are variations In single base positions In the DNA, and represent
the most common type of genetic mutation. The template size for SNP
typing can be as short as 50 base pairs – compared to the requirement of
300 base pairs for STR analysis – so this technique Is particularly useful
for analyzing degraded samples. For instance, SNP typing was
instrumental in identifying victims of the World Trade Center disaster

Mini STR analysis

Mini STR analysis Is also designed to handle degraded samples. It
attempts to recover information from these samples by reducing the size
of the PCR products needed for STR sequence analysis. This is achieved
by moving the primers as close as possible to the region of Interest
Conclusions:

DNA fingerprinting has come a long way since its discovery in the 1980s.
Although it is mainly used in forensics, its potential is far reaching, with
applications ranging from exploring our genetic heritage to advancing
personalized medicine. However, like any technology, it poses several
challenges, including ethical concerns around the use of DNA databases
for forensic purposes. We hope that this blog has enhanced your
understanding of how DNA fingerprinting works, and the various
techniques available, while demonstrating the importance of valuing both
discovery and privacy during forensic investigations.

References
Saad, R. (2005). Discovery, development, and current applications of
DNA identity testing. Baylor University Medical Center Proceedings,
18(2), 130-133. https://doi.org/10.1080/08998280.2005.11928051
Science Learning Hub (2016). DNA profiling.
https://www.sciencelearn.org.nz/resources/1980-dna-profiling
Jonsson, H. et al. (2021). Differences between germline genomes of
monozygotic twins. Nature Genetics, 53, 27-34.
https://www.nature.com/articles/s41588-020-00755-1