Genetic fingerprinting: a look inside Understand article

In popular TV detective series, genetic fingerprinting is commonly used to identify criminals. Sara Müller and Heike Göllner-Heibült take a look behind the scenes.

Image courtesy of Alex Mit /
iStockphoto

The idea of distinguishing people by their genetic characteristics is not new. Discovered in 1900 by Karl Landsteinerw1, ABO blood typing was the first genetic marker to be used in forensics, later complemented by MN blood groups (1927) and the Rhesus factor (1937).

Even when we analyse all three blood group systems simultaneously, however, about one in ten people give identical results; this is what makes blood transfusions possible. For forensic purposes, however, it is a disadvantage: the results may tell you that your blood sample does not come from Suspect X, but they cannot tell you with any acceptable level of certainty that it does come from Suspect Y.

Advances were made in the 1970s and 80s, with the analysis of different forms of enzymes (isoenzymes) in red blood cells and blood serum. The certainty that the sample really came from the suspect depended on the number of proteins analysed (usually four); we call this certainty the power of discrimination. The power of discrimination that these combined techniques offered was still only 1:1000, better than the 1:10 power of blood group analysis, but still not good enough. To get a better power, we needed to take a closer look at our genetic composition.

Our genetic composition – who we are

From base pairs to
chromosomes (not to scale):
how DNA is packaged.
Click on image to enlarge

Image courtesy of Darryl Leja,
NHGRI / NIH

The human genome consists of 46 paired chromosomes: 23 from our mother, 23 from our father. We therefore have two of each chromosome (except – in the case of men – sex chromosomes) and thus two copies of each gene.

The main component of chromosomes is deoxyribonucleic acid (DNA), which contains information for building the proteins we need for life. However, of our 3 billion base pairs (bp), only about 4% actually code for proteins; the rest is often just ‘filling’ consisting of repetitive sequences organised in clusters. If you compare the DNA of two humans, most of it is identical, with the variability found largely in these repetitive sequences.

Different people can have different numbers of repetitions of these sequences: one person may have five repeats at a specific DNA locus (site); another person may have seven. Using samples, e.g. from blood or semen, we can analyse the repetitive sequences at several DNA loci; we call this analysis a genetic fingerprint. Like fingerprints, genetic fingerprints can be used to distinguish individuals.

Although the term ‘genetic fingerprinting’ (or genetic profiling) is commonly used, not everybody is aware that it actually encompasses two very different techniques, only one of which is commonly used in forensics today.

Early genetic fingerprinting: restriction fragment length polymorphism

Image courtesy of Arno
Bachert / pixelio.de

The first method of genetic fingerprinting was invented in 1984 by Alec Jeffreysw2, who used repeated DNA sequences known as variable number tandem repeats (VNTRs; e.g. sequence D1S80, (AGGACCACCAGGAAGG)n). These sequences, 10-100 bp per repeat, can be investigated using restriction enzymes, which work like molecular scissors to cut the DNA at defined sequences (recognition sequences). In our entire genome, a 6 bp recognition sequence will occur around 730 000 times.

This means that if you cut the genome with a particular restriction enzyme, you will get around 730 000 restriction fragments of varying lengths. And this is where the VNTRs become important: the number of repeats in a particular VNTR cluster may vary between individuals, which means that the length of the corresponding restriction fragment will vary between individuals too (Figure 1). We call this phenomenon restriction fragment length polymorphism (RFLP).

Figure 1: Overview about two VNTRs from two different individuals. Sites cut by restriction enzymes (molecular scissors) are indicated by an arrow. Depending on the number of VNTR repeats, DNA fragments of different sizes are generated (see also Figure 2, Step 4)
Image courtesy of Sara Müller

Of the 730 000 restriction fragments, only some will differ between individuals – too few to be detected by eye. Instead, scientists used a technique called Southern blotting, which allowed only the sequences of interest to be visualised. To do this, they separated the restriction fragments according to size by gel electrophoresis, using an electric current to pull the charged molecules of DNA through a gel. The distance travelled was determined by the fragment size (Figure 2, Step 1). Next, they transferred the DNA to a membrane (Figure 2, Step 2) and applied a radioactively labelled probe that was complementary to the VNTR(s) of interest. The probe hybridised (stuck) to the matching sequences (Figure 2, Step 3) and by placing the membrane on an X-ray film, the scientists got a picture of the radioactively labelled bands, each of which represented a different length of fragment (Figure 2, Step 4). This picture was the genetic fingerprint.

So how many VNTRs needed to be compared to reliably distinguish between individuals? If the scientists chose VNTRs with enough variation (e.g. D1S80, which may be repeated anything from 15 to 41 times), they only needed to compare four different VNTRs to have a power of discrimination of 1:1 million – much better than the 1:10 offered by ABO blood typing.

Figure 2: RFLP analysis after digesting the DNA with restriction enzymes. Click on image to enlarge
1. Size separation of digested DNA fragments by gel electrophoresis. Large molecules with slow mobility in the gel can be seen at the top of the picture; small molecules with higher mobility in the gel are at the bottom
2.-3. Southern blot technique. Separated DNA is transferred to a membrane and subsequently detected on the membrane with radioactively labelled probes against VNTRs A and B
4. The exposed X-ray film shows an individual fingerprint for each person (compare to Figure 1)

Image courtesy of Sara Müller
Figure 3: A simplified
diagramshowing how
defined DNA fragments are
amplified by PCR.
Click on image to enlarge

Image courtesy of Sara Müller

The current technique: PCR-based genetic fingerprinting

Kary Mullis’ invention, in 1983, of the polymerase chain reaction (PCR) won him the Nobel Prize in Chemistryw3, w4. This invention, together with the discovery in the late 1980s of short tandem repeats (STRs) – 2-9 bp repeated sequences, also called microsatellites – paved the way for the high-speed genetic fingerprinting technique that forensic scientists use today.

PCR enables a DNA locus of interest (e.g. the 4 bp STR known as D18S51, (AGAA)n), to be amplified exponentially, generating a billion copies of a single DNA molecule in a few hours (Figure 3). For forensic scientists, this has the advantage of making the analysis of even very tiny samples possible – as few as 30 cells (see Table 1 for a comparison with RFLP-based genetic fingerprinting).

For PCR analysis, we need STRs flanked by sequences that are identical in all human beings (we say these sequences are conserved). We then use primers – short molecules that are complementary to the conserved flanking sequences (genes 1134 and 1135 in Figure 4) – to initiate the PCR. Once the DNA has been amplified, we can separate it either by gel electrophoresis (Figure 5) or, in modern forensic science, by electrophoretic automated sequencing (Figure 6), and visualise it as a genetic fingerprint.

Figure 4: Schematic view of the STR D1S80 (the nomenclature ‘D1S80’ tells us that the STR is on chromosome 1, in region 80) from two individuals. The black arrows represent the primers used to amplify that specific STR.
Click on image to enlarge

Image courtesy of Sara Müller

We have two copies of each chromosome, so we also have two copies of each STR. If, for each copy of the STR, someone has the same number of repetitions (i.e. the same allele), the PCR analysis reveals only one size of DNA fragment: the person is homozygous for that STR allele (green arrow in Figure 5, corresponding to individual 2 in Figure 4). If the two chromosomes carry non-identical alleles for that STR, we see two sizes of fragment and say that the person is heterozygous (red arrow in Figure 5, corresponding to individual 1 from Figure 4).

Figure 5: Genetic fingerprint of the D1S80 locus generated by school students (channels numbered 1–16) with their own DNA. The lane on the far right, labelled M, contains DNA fragments of known sizes, used as markers.
The individual indicated with the green arrow is homozygous for the D1S80 locus (only one band is visible). The individual marked by the red arrow is heterozygous (two bands). The blue arrows indicate two students who are heterozygous and have the same number of repeats for each allele at the D1S80 locus; this means that they cannot be distinguished by the fingerprint. They may be twins, but it is also likely that two unrelated persons will have the same number of repeats if only one STR is analysed 

Image courtesy of Sara Müller

If we only analyse one STR, the chance of two unrelated people having the same PCR-based genetic fingerprint is high – between 1:2 and 1:100 (blue arrows in Figure 5). This is because STRs have fewer alleles and lower heterozygosity than the VNTRs used in RFLP-based genetic fingerprints. To overcome this disadvantage, we analyse multiple STRs simultaneously; with 16 STRs, as is common in forensic casework in Germany, we can achieve a power of discrimination of 1:10 billion (equivalent to one person in the world’s population; (Figure 6).

Figure 6: Electropherogram of a woman, generated by multiplex PCR and subsequent electrophoretic automated sequencing. Eight STRs (D3, TH01, D21, D18, SE33, vWA, D8 and FGA) and amelogenin (which indicates the sex) were analysed. The blue, green and black curves represent amplified STRs (with repeat numbers below the peaks). The red curve is the marker (DNA fragment size labelled in bp). Click on image to enlarge
Image courtesy of Sara Müller

Table 1: Comparison of RFLP- and PCR-based DNA fingerprinting. After Butler (2010)
   RFLP PCR
Amount of starting DNA 30–50 µg At least 200 pg (about 30 cells) for a complete STR pattern
Sensitivity + +++
DNA quality required for analysis Complete genome No complete genome necessary; degradation products also sufficient because of the short sequences involved (total sequence length of an STR, including multiple repeats and flanking sequences, approximately 50– 500 bp)
Time Days to weeks Hours
Discrimination power per locus +++ 
(More alleles and more heterozygosity per locus)

(Fewer alleles and less heterozygosity per locus)
However, multiplex PCR amplification (PCR with more than one pair of primers) and multi-colour labelling allows more than 16 loci to be examined simultaneously, which provides an excellent power of discrimination
Repeat unit 10 bp to 100 bp 2 bp to 9 bp (in forensic case work, mainly 4 bp)
Automated detection Not possible High-throughput sample processing possible
Number of validated loci (important if relatives are involved) Limited number  Large number 
Risk for contamination + +++
Additional safety measures required? Yes (because of radioactive probing) No (no radioactive probing)

Applications of genetic fingerprinting

Identical twins would
normally have identical
genetic fingerprints

Image courtesy of e3000;
image source: Flickr

We now know what genetic fingerprinting is, but how is it used? PCR-based genetic fingerprinting is widely applicable in forensic investigations: it enables the police to exclude or identify suspects on the basis of genetic material such as hair follicles, skin, semen, saliva or blood (see the story that can be downloaded beloww5). A genetic fingerprint alone, however, is not sufficient evidence for a conviction, as close relatives may have very similar fingerprints (and monozygotic twins will normally have identical ones).

Nicholas II, the last Tsar of
Russia, with Tsarina
Alexandra and their four
daughters. Following the
Russian revolution, the entire
family were murdered in July
1918. Their bodies, found in
1979 (the Tsar, Tsarina and
three daughters) and 2007
(the Tsarevich and the
remaining daughter, Maria)
were identified by genetic
fingerprinting

Image courtesy of the
Romanov Collection, General
Collection, Beinecke Rare Book
and Manuscript Library, Yale
University

And to complicate international forensic investigations, although there is a European recommendation to analyse 16 STRs, each country can decide which STRs to analyse, which makes comparisons difficult.

The PCR-based method is also used in humans for paternity testing, diagnosing many genetic diseases (e.g. Huntingdon’s disease), identifying disaster victims, tracing family trees, tracking down missing people and investigating historical figures (e.g. the last Tsar of Russia and his family). In other organisms, it can be used for conservation purposes (e.g. to analyse confiscated ivory), in drug investigations (e.g. by analysing seized cannabis plants), to control food or water quality (e.g. by identifying contaminating microbes), in medicine (e.g. to detect viral infections such as HIV, hepatitis or influenza) and in bioterrorism investigations (e.g. to identify microbial strains).

RFLP-based genetic fingerprinting, although largely obsolete due to the many advantages of the PCR method (Table 1), is still used for classifying plants and animals in basic research. It is particularly useful when there is insufficient information about the genome of the species – remember that for the PCR method, we need regions that vary widely between individuals and are flanked by conserved regions of known sequence.

Genetic fingerprinting at school

The isolation of DNA at school gives the students a ‘wow’ moment when they realise that they are looking at the complete genetic information coding for an organism – a few cotton wool-like strands of DNA that were precipitated by alcohol. It is easy to perform at school using salivaw6 (or epithelial cells from commercially available kits), peas (Madden, 2006), tomatoes, onionsw7 or calf thymus (although check local restrictions on using calf thymus at school)w8.

Genetic fingerprinting can be
used in conservation work,
for example to analyse
confiscated ivory

Image courtesy of Ulla
Trampert / pixelio.de

Subsequent PCR of a specific STR in human DNA, for example D1S80 or TH01, can be performed at schoolw6, using reasonably priced commercially available kitsw9 if necessary. If your school has no access to a thermocycler, the thermocycling can be carried out in three water baths, although it is tedious and very hands-on.

If this equipment is not available, there are kits that both simulate and simplify the whole process of genetic fingerprintingw10. These kits contain fragments of DNA that simulate the amplification of different alleles of a single STR or VNTR. (In fact, they are restriction fragments of DNA from plasmid or lambda phage DNA.) The DNA requires electrophoresis and subsequent staining so that students are able to compare ‘amplified’ DNA sequences from a sample of evidence with those of several suspects. Of course, this is very different from detecting amplified STRs using electrophoretic automatic sequencing (and does not even accurately represent the visualisation of VNTRs using Southern blotting, as the DNA is stained directly on the gel), but it nonetheless demonstrates the principles of the analytical process. When using these simulation kits, the students should be made aware that the experiments give the impression that differences between individuals can be easily identified, which is not the case.

Acknowledgement

The authors would like to thank Wolfgang Nellen for his ideas about the article and for allowing the Science Bridge instructions to be made available free of charge.

They are also grateful to Shelley Goodman for her advice on using commercial kits at school.

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References

Web References

Resources

  • To learn more about repetitive DNA and methods (RFLP and PCR), see:
    • Klug WS, et al. (2008) Concepts of Genetics 9th edition. San Francisco, CA, USA: Pearson. ISBN: 9780321524041
  • To find out more about PCR and STRs, as well as worldwide DNA databases and forensic case work, see:
    • Goodwin W, Linacre A, Hadi S (2010) An Introduction to Forensic Genetics. Chichester, UK: Wiley-Blackwell. ISBN: 978-0470710197
  • For a classroom game on DNA detection, see:
  • The University of Arizona, USA, describes how to carry out a school activity on DNA profiling using STRs. See: www.biology.arizona.edu or use the direct link: http://tinyurl.com/7zteg9n
  • The website of the DNA Initiative: Advancing Criminal Justice Through DNA Technology offers a free online course in forensic DNA analysis. Aimed at lawyers, it and the accompanying case study provide an excellent introduction to the topic. See: www.dna.gov/training/otc
  • To investigate a real database of STRs, visit the website of the US National Institute of Standards and Technology: www.cstl.nist.gov/biotech/strbase
  • To learn more about how genetic diseases are diagnosed, see:

Author(s)

Sara Müller studied biology, chemistry and education at the University of Kassel, Germany, and received her teaching degree for secondary schools in 2008. In December 2011, she finished her PhD thesis in the field of epigenetics, also at the University of Kassel. Since February 2012, she has been doing her practical training as a teacher in Göttingen, Germany. She has been a member of the executive board of Science Bridgew6 for the past seven years.

Heike Göllner-Heibült is a DNA forensic science expert with a background in molecular biology. She studied human biology at the Philipps University of Marburg, Germany, spending several months at the Erasmus University of Rotterdam, the Netherlands, and at the University of Cambridge, UK. In 2002, she finished her PhD in molecular biology at the Institute of Molecular Biology and Tumor Research in Marburg and started work in DNA forensics as a DNA expert and reporting officer. She currently works for the Forensic Science Institute of the office of criminal investigation in Berlin, Germany.


Review

The idea of using DNA to identify one individual in the world is mind-blowing. The genetic fingerprinting of an individual relies on the sequences are that not used in coding, but how are these fingerprints created? This article explains.
The ability to identify criminals from DNA databases raises important questions: is it ethical to hold human DNA in such databases or is it a breach of human rights? Should there be a DNA fingerprint for every person or just those who are arrested? How long should the DNA profile be kept?

Students may wish to discuss how genetic fingerprinting can help diagnose genetic diseases, as well as its application in the fight against poaching and species extinction. Ideally they should be able to try the technique for themselves, either as a real or a simulated experiment.


Shelley Goodman, UK




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