Sunday Times 2
DNA fingerprinting: A tool for the Post-Modern world Sherlock Holmes
View(s):By Dr. Mangalika Wickramasinghe, Dr. Venura Herath and Dr. Dimanthi Jayatilake
The use of DNA fingerprinting in criminal investigations is no longer a scene from the hit TV series CSI. In many countries DNA fingerprinting is used as a tool in routine criminal investigations. DNA fingerprinting profiles of criminals are maintained in a centralised record system for easy identification of the suspects.
Though this technology has been available in Sri Lanka, it was only limited to research during its early days. The word “DNA fingerprinting” came to the day-to-day vocabulary of the Sri Lankans in the aftermath of the 2004 tsunami catastrophe, when DNA fingerprinting was used for the identification of the biological parents of a lost-and-found baby, famously known as the “tsunami baby – 81″. The case not only made the general public aware of this advanced technology but also led to the build-up of trust in the tools of modern sciences in solving such issues.
Since then, the technique has been used to solve a number of crimes in Sri Lanka. However, the recent rape and murder of the four-year-old Seya Sadewmi of Kotadeniyawa has again put the spotlight on DNA fingerprinting as forensic evidence to find the culprit behind this gruesome act. Even though by now DNA fingerprinting is widely accepted as a criminal justice tool for the identification of criminals, there is an ongoing debate in the media about issues related to the technique.
DNA fingerprinting
In a DNA fingerprinting test a particular individual is identified based on the characteristic imprints of his/her deoxyribonucleic acid strand (aka DNA strand). Even though the focus of this article is on the use of DNA fingerprinting for criminal investigations, in general the technique is used in various disciplines including medicine, agriculture and sciences to identify any organism or its unique characteristic features, genetically inherited diseases and for disease diagnostics.
Why target DNA?
In all organisms, from microscopic bacteria to humans (with the exception of some viruses), DNA is the molecule responsible for inheritance. DNA molecules carry the information that decides the physical appearance and metabolic activities of an individual. In addition, research has revealed that certain behavioural characters are also controlled, up to a certain degree, by DNA.
The DNA of a person is inherited via the biological parents. Of the total DNA content in a cell, half is provided by the father and the other half by the mother. During cell division (a process called meiosis to produce reproductive cells, ie. sperm and ova), there is a possibility of changes happening in the DNA sequence. Thus, it is possible that the offspring may have a combination of the parental characters, or they can have different characters to that of their parents. These reasons create the general differences that one observes between siblings. Therefore, the DNA of an individual is a unique personal fingerprint that can be used for identification purposes.
What is DNA?
DNA is a complex molecule made out of small basic building blocks called nucleotides — Adenine (A), Thyamine (T), Guanine (G) and Cytoscine (C). There are four different types of nucleotides, combined in different orders generating a single stranded DNA sequence. Based on base complementation of nucleotides a second strand will assemble and then the newly formed double stranded DNA will twist in to a helical shape.
In the human genome (all DNA in an individual) DNA consists of 3.2 billion nucleotides divided in to 23 chromosomes (thread-like structures located inside the nucleus of cells). Therefore, when comparing two individuals it is very likely to find many differences in the nucleotide order. The nucleotide order found in certain regions of the genome can be used as a unique fingerprint to individually identify a particular individual. Thus, such regions can be targeted to develop a DNA fingerprinting profile of an individual.
How to spot differences at DNA level?
Even though DNA is a large molecule it is not visible to the naked eye or it cannot be observed using an electron microscope with the highest available resolution. Therefore, one might wonder how these minute differences can be spotted.
Under laboratory conditions targeted DNA regions can be copied using a technique called PCR (polymerase chain reaction). Here, a targeted region of the extracted DNA will be copied in to millions using a machine. These copies will be profiled based on the characteristic pattern they produce, which is called the DNA fingerprint/DNA profile of an individual. Each sample (DNA of the forensic sample and that of the suspects) will generate a different profile and the profiles can be compared to see if they match or not.
Can any region on the genome be targeted?
With the advances in molecular biology and technologies, the human genome has been sequenced (i.e. determination of the precise order of nucleotides within a DNA molecule). Based on the genomic sequence, specific regions carrying simple and short repeated nucleotide sequences (called STR – short repeated repeats) have been identified. Of the four nucleotides — Adenine (A), Thyamine (T), Guanine (G) and Cytocine (C) — these STR regions are rich in short repeats such as AT repeats (ATATATAT). These are the most commonly used target regions of the genome used for DNA fingerprinting. Even though there are specific mechanisms that ensure the accuracy of DNA copies made in the cell, often STR regions are vulnerable for nucleotide order changes and changes in the number of repeats. Such regions therefore are prime targets for DNA fingerprinting. The Federal Bureau of Investigation (FBI) in the United States has identified 13 such STR regions for fingerprinting purposes known as a combined DNA index system (CODIS). Some countries such as Britain follow a different system, but it is still based on STR regions.
Why target 13 STR regions?
When one STR region is considered, there is a limit to the number of changes in the number of repeats that can be in a population. For example the STR region D21S11 of humans can exist in 22 different repeat numbers. These alternative forms of the same region are called allele. So if, for example, only the D21S11 STR was used for fingerprinting in a population there can be many individuals carrying the same alleles. The probability of carrying the same allele for a particular STR region has been estimated as 5-20 percent. Thus, focusing on one STR region alone will not make a unique fingerprint profile of a person.
Following a research conducted in the US using a systematic sample of Americans, the researchers have recommended to target 13 STR regions in a criminal investigation to present a DNA fingerprinting profile as credible evidence to support a conviction without reasonable doubt. The probability of coming across two individuals with the same profile when targeted all 13 STR sites was found to be one in a quadrillion. However, the probability calculation depends on the number of alleles found at each STR site. Though no scientific survey has been conducted to assess the allele variation among Sri Lankans, the population in Sri Lanka is smaller compared to that of the US. Therefore, it is still not wrong to assume that the probability mentioned above will be applicable to Sri Lanka as well.
How to determine the number of repeats in an STR region
Once the copies of the target STR regions are made using PCR technology, the copies are visualised using a technology called electrophoresis, where the amplified copies are separated according to the length. When the number of repeats varies between two individuals, the length of the copied fragment changes. Thus, when separated using electrophoresis a clear difference in the profile can be observed if the two samples under question carry STR regions with different number of repeats.
How accurate is DNA testing?
Based on the scientific basis discussed so far, theoretically the probability of error is very minimal. Therefore, DNA testing is generally accepted as an accurate and reproducible type of evidence. Given that we wish to bring our readers’ attention to the practical limitations that are often associated with DNA testing procedures.
Collection of samples from a crime scene
- The crime scene should not be tampered with.
- The samples need to be collected by a specialised officer with specialised training.
- Collected samples need to be handled according to accepted procedures until the samples reach the testing laboratory.
- Laboratory testing
- Testing should be carried out in a laboratory certified to carry out such testing.
- Personnel handling the samples in the lab should be a scientist or a technician specifically trained to work with such samples and techniques.
- The technique used for the profiling needs to be in accordance with international standards with high precision and resolution power (especially the electrophoresis technique used for separation of the copies).
- The DNA fingerprinting profile needs to be analysed by an expert analyst.
Is DNA fingerprinting strong enough evidence?
According to Sir Alec Jeffries, the scientist who developed the DNA fingerprinting technique, it is not a technique that can be used as sole evidence to determine whether a person is guilty of committing a crime. Therefore, DNA fingerprinting needs to be considered only as one piece of evidence and should not be used as the deciding piece of evidence in the court room.
Can a DNA fingerprinting profile be wrong?
Even though DNA fingerprint profiles have been used as a strong piece of evidence in many cases, there are instances where DNA fingerprinting profiles led to wrong convictions. However, it is important to state that in these cases it was not the DNA fingerprinting as a technology that compromised the case, but was the result of the shortcomings that occurred at sample collection. Some of the common flaws associated with the method are:
- Mixed DNA samples of more than one individual.
- DNA sample collected from the crime scene can be in trace quantities and could often be degraded. Such could lead to an incomplete fingerprinting profile.
- Presence of inhibitors in the samples that will disrupt the downstream processes such as DNA extraction and PCR amplification.
Do we have enough facilities in Sri Lanka to do DNA fingerprinting?
DNA fingerprinting as a criminal justice tool was first used in Sri Lanka in the Hokandara murder case. More than a decade has passed since then, yet we see no significant improvement in the technology and facilities available in Sri Lanka. Even though three laboratories were identified and improved to cater to the need of a functional crime lab, so far fingerprinting and profile interpretation has been conducted only at one private institution, and no other laboratories are available to provide a similar service.
What are the basic essentials for a forensic DNA testing laboratory?
Laboratory requirements
For the past two decades, the standard tool for electrophoresis has been capillary electrophoresis. Conventional polyacrylamide gel electrophoresis (PAGE) is now considered as an outdated technology due to poor resolution, practical limitations, and labour and time inefficiency. State-of-the-art DNA testing laboratories have moved forward to an automated robotic system to minimise errors.
Quality assurance (QA)
Quality assurance needs to be maintained at different stages of the DNA testing process,
- Pre-laboratory QA – during case assessment
- Laboratory QA – from DNA extraction to DNA fingerprint profiling
- Post-laboratory QA – interpretation of results, databasing and statement reporting
At all the above stages contamination of samples and smooth transition should be assured.
Laboratory accreditation
An accepted DNA laboratory should be accredited with the following certificates: ISO17025:2005 (a general requirement for the competence of a testing and calibration laboratory), and 5.10.3.5 from the 2011 ASCLD/LAB – International supplemental requirements for testing laboratories (recommended).
Educational requirements
Minimal requirement for all personnel’s involved in the laboratory process is a BSc degree.
Analyst – the BSc. degree should be in any of the following areas: biology, chemistry, forensics or a related area with course work in genetics, biochemistry, molecular biology, statistics and population genetics.
Leading scientist – a minimum of an MSc in any of the above mentioned fields.
Proficiency testing
The analyst should undergo at least two proficiency tests annually conducted by an external agency to assess the areas in which further improvements are needed.
Certification
Even though certification is voluntary it is highly recommended for an analyst.
Recommended improvements for Sri Lanka
- Setting up of state affiliated molecular laboratories with internationally accepted state-of-the-art facilities to meet the needs of a crime laboratory.
- Development of a nationally accepted regulatory framework regarding crime laboratories.
- Accreditation of laboratories and making certification a mandatory requirement for personnel handling forensic samples.
- Training of experts to interpret the DNA fingerprinting profiles and updating their knowledge on current advancements regularly.
- Making the personnel involved in the judicial process knowledgeable on DNA fingerprinting evidence.
- Creating awareness among journalists on ethical and responsible reporting of DNA fingerprinting findings.
- Creating awareness among the general public regarding DNA fingerprinting as a tool for crime scene investigation.
(The writers are attached to the Department of Agricultural Biology, Faculty of Agriculture at the University of Peradeniya)