DNA Fingerprinting

DNA analysis or ‘DNA fingerprinting’ refers to the identification of an organism using deoxyribonucleic acid. It was first described by Alec Jeffreys, an English geneticist. Jeffreys discovered that DNA contained a number of sequences that were repeated again and again (Jefferys et al, 1985). He then established that the number of repeated sections varied in each individual, rendering their genetic make-up completely unique, with the exception of identical twins (Jefferys et al, 1988). Jeffreys developed a technique in which he could examine the variation of length in each of these sequences which created the ability to discern one person from another.

Two of most common techniques for analysing the genetic fingerprint are: restriction fragment length polymorphisms (RFLP) and polymerase chain reaction (PCR). Each technique has their respective strengths and weaknesses outlined below.

(Jeffreys, 2005)

RFLP was the first technique developed for use in fingerprinting. In this technique the investigator utilizes repeated sequences known as variable number tandem repeats (VNTRs; e.g. AGGACCACCAGGAAGG Nth). The number of repeats in a particular VNTR cluster vary between individuals (Prinz, 2014). This property can be exploited by using restriction enzymes. These enzymes will produce different sized fragments in accordance to how many repeats there are (Prinz, 2014). To visualize the differences between individuals the fragments can be separated by electrophoresis, transferred onto a membrane, and then probed by a marker.

Overview of two different VNTRs from two different individuals. Depending on the number of VNTR repeats, fragments of different size are generated (restriction enzyme indicated by the black arrow). Unique fragments between individuals create a unique banding pattern (Jeffreys, 2005)

This is the new generation of fingerprinting. In this technique the investigator utilizes repeated sequences known as short tandem repeats (STRs; e.g. AGAA Nth). Just as in VNTRs, the number of repeats in a particular STR cluster vary between individuals (Prinz, 2014). But in this case, the property can be exploited by designing primers that flank both ends of a targeted STR. One caveat to this technique is that the primers that are created must be complementary to a conserved region that is present in all individuals. In the end, this will amplify the desired regions and just as before there will different sized fragments in accordance to how many repeats there are (Prinz, 2014). This can be visualized by electrophoresis or florescence.

Schematic view of the STR D1S80 from two individuals (black arrows represent the primers used to amplify the STRs). The individual indicated with the green has homozygous alleles (only one band is visible). The individual marked by the red has heterozygous alleles (two bands). The lane on the far right, labelled M, contains DNA fragments of known sizes, used as a reference point (Jeffreys, 2005).

Genetic profiling is used in wide array of practical applications including: paternity testing, diagnosing genetic diseases, identifying disaster victims, tracing family trees, tracking down missing people, investigating historical figures, conservation purposes (e.g. to analyse confiscated ivory), drug investigations (e.g. by analysing seized cannabis plants), to control food or water quality (e.g. by identifying contaminating microbes), medicine (e.g. to detect viral infections such as HIV, hepatitis or influenza) and bioterrorism investigations (e.g. to identify microbial strains). We will discuss one of the more unique applications that pertain to research below.

DNA fingerprinting can sometimes be used to determine whether a metastasis or recurrence of a cancer represents cells from the primary tumor (ie, the same clone) or a newly arising tumor (ie, a different clone). This is important because doctors choose treatment according to the type of primary cancer. For instance, if cancer cells in the liver are actually breast cancer cells not liver cells, the treatment needs to be for breast cancer. In cases like these, tumors are from the same person, so the choices of target polymorphisms on targets are not going to be as great. One method is to use PCR analysis to define regions of deletion causing the phenomenon of loss-of-heterozygosity (LOH), a common cause of allele drop-out in malignant tumors. Tumor loci representing the same clone should exhibit the same LOH pattern, while those of different clones should show different patterns (Schlechter, 2004). If the patient is female, an alternate strategy can be used, looking for polymorphisms on the maternally and paternally inherited X chromosomes. Recall that in every female cell, one of the 2 X chromosomes is inactivated, forming the Barr body. Which of the 2 X chromosomes that gets inactivated in any cell line is random, but in 2 lines from the same clone, they would be the same. The mechanism of inactivation is DNA methylation, so by using a methylation-sensitive method of amplifying the polymorphisms, one can tell whether the same or the opposite X chromosome is inactivated in the primary tumor vs the metastasis (Banelli, 2010).

Numerous countries have produced computerised databases containing profiles to aid in the comparison of fingerprints and the identification of suspects and victims. The first Government database was established in the United Kingdom in April 1995, known as the National DNA Database (NDNAD). As of 2011, there were over 5.5 million profiles of individuals in the system. Similarly in 1994, the FBI in the US formed their own database, the Combined DNA Index System (CODIS).

With an increasing number of DNA profiles that are stored in DNA databases, a new technology called familial DNA database searching has evolved. An individual who's profile is not in a database can still be caught for a crime using this technique. It is based on near matches between the crime stain and a data-based person, who may be a relative of the true perpetrator (Roewer, 2013). The first search was successfully conducted in the UK in 2004, where the police arrested Craig Harman for manslaughter. He was convicted because of partial matches from his brother (Roewer, 2013). Also, the police in Northern Germany the police arrested a young man accused of rape because they had analyzed the DNA of his two brothers (Roewer, 2013).

Civil rights are crucial for democratic societies and ideas to extend DNA databases to whole populations need to be condemned. Alec Jeffreys questioned the way UK police collects DNA profiles, holding not only convicted individuals but also arrestees without conviction and suspects cleared in an investigation. He also criticized that large national databases are likely skewed socioeconomically (Jeffreys, 2005). Most of the matches refer to minor offences; according to GeneWatch in Germany 63% of the database matches provided are related to theft while <3% related to rape and murder (Roewer, 2013). Also, some individuals do not wish to have their DNA profile stored in a database because of personal issues and privacy concerns (Roewer, 2013).

A majority of the scientific community is convinced that DNA sequencing will replace methods based on fragment length analysis and there are good arguments for this position. With the emergence of Next Generation Sequencing (NGS) technologies, the body of forensically useful data can potentially be expanded and analyzed quickly and cost-efficiently (Roewer, 2013). Time is an essential factor in police investigations which will be significantly reduced in future applications of DNA profiling. There are commercial instruments capable of producing a database-compatible DNA profile within two hours and are currently under validation for law enforcement use . The hands-free 'swab in - profile out’ process consists of automated extraction, amplification, separation, detection, without human intervention (Roewer, 2013).

1. Banelli, B., Casciano, I., Di Vinci, A., Gatteschi, B., Levaggi, A., Carli, F., Del Mastro, L. (2010). Pathological and molecular characteristics distinguishing contralateral metastatic from new primary breast cancer. Annals of Oncology,21(6), 1237-1242.

2. Budowle, B., Chakraborty, R., Giusti, AM., Eisenberg, AJ., Allen RC. (1991). Analysis of the STR locus D1S80 by the PCR followed by high-resolution PAGE. Am J Hum Genet, 48:137–144

3. Jeffreys, A. J., Wilson, V., & Thein, S. L. (1985). Hypervariable ‘minisatellite’ regions in human DNA. Nature, 314(6006), 67-73.

4. Jeffreys, A. J., Royle, N. J., Wilson, V., & Wong, Z. (1988). Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Nature, 345(6334), 278-281.

5. Jeffreys A.J (2005). Genetic Fingerprinting. Nat Med, 11:1035–1039.

6. Prinz, M. (2014). Review of: Forensic DNA Analysis: Current Practices and Emerging Technologies, 6(3), 297-305.

7. Roewer, L. (2013). DNA fingerprinting in forensics: past, present, future. Investigative genetics, 4(1), 22.

8. Schlechter, B. L., Yang, Q., Larson, P. S., Golubeva, A., Blanchard, R. A., de Las Morenas, A., & Rosenberg, C. L. (2004). Quantitative DNA fingerprinting may distinguish new primary breast cancer from disease recurrence. Journal of clinical oncology, 22(10), 1830-1838