DNA-17 Profiling

• Introduction
• DNA Profiles
• DNA-17: Introduction
• DNA-17: Benefits
• DNA-17: Risks
  • Discordance
  • Partial Matches
  • Contamination
• Implementation
• Match Probabilities
• Expert Evidence (including Streamlined Forensic Reporting)

Introduction

DNA-17 is the term that has been adopted to describe the next generation of DNA (Deoxyribonucleic Acid) profiling methodologies to be utilised by the National DNA Database (NDNAD).

Currently, samples are profiled using the SGMPlus methodology, but from 24 July 2014, samples will be profiled using a DNA-17 profiling methodology.

This guidance is intended to assist with understanding the changes that are occurring in the profiling of DNA and the consequences of these changes.

DNA Profiles

DNA profiling is now routinely used to provide evidence in prosecutions of criminal cases. It allows the comparison of DNA found at crime scenes with profiles from known sources. It helps to convict criminals, exonerate the wrongly accused, and identify victims of crime.

DNA profiles relating to crimes in England and Wales are held on the National DNA Database (NDNAD), managed by the National DNA Database Delivery Unit (NDU) at the Home Office. Each profile records the variation at a defined set of locations (loci) in a person's DNA. The loci that are profiled have been selected because of their suitability for forensic applications and high level of variation between individuals. This variation is due to the difference in the number of times a short sequence of DNA is being repeated over and over again, end to end. The loci are known as short tandem repeat (STR) loci.

The majority of each person's DNA is normally organised into 23 chromosome pairs. It is expected that a person will inherit one chromosome within a pair from each of their parents, in other words, they will inherit half of their chromosomal DNA from each parent. This means that for each locus there will be a copy of DNA that has originated from each parent, i.e. the loci is normally made up of two DNA components. Statistical methods have been developed to calculate the probability of one DNA profile matching another DNA profile by chance, based on the DNA samples coming people belonging to a large mixed population rather than from people in closer relationships, such as close relatives, siblings or ethnic groups.

DNA-17: Introduction

DNA profiling relies upon two things:

• the application of the polymerase chain reaction (PCR), which allows the rapid replication of a piece of DNA generating thousands to millions of copies in a controlled fashion (the process is usually referred to as amplification); and
• the variation of DNA at STR loci between different individuals.

Early versions of DNA STR profiling involved the use of just a few loci, but as the technology improved, more loci were included in the analysis. When the Forensic Science Service (FSS) first started DNA STR profiling in 1994, it used a methodology based on four STR loci. This was not very discriminating and in 1995 an improved methodology, Second Generation Multiplex (SGM), was introduced. SGM DNA profiles were based on six STR loci (i.e. twelve DNA components) and the gender identifier. SGM profiles were loaded to the NDNAD, which became operational in the UK in April 1995. In 1996 the profiles from the analysis of biological materials from crime scenes were uploaded to the NDNAD. SGM was followed in 1999 by SGMPlus, which uses ten loci (i.e. a total of 20 DNA components) and the gender identifier. All loci used in SGM are within SGMPlus.

SGMPlus was introduced to reduce the probability of getting a chance DNA profile match (also known as an adventitious match) between individuals. The probability for a chance match, between any two unrelated individuals' DNA profiles, is one in trillions with SGMPlus, though the possibility of a chance match between very common loci is greater. Despite this improvement, a conservative random match probability of one in a billion has become standard for court reporting purposes. This threshold provides very strong evidence that matching DNA profiles have originated from the same individual.SGMPlus is being replaced with DNA-17 as the standard profiling method in England and Wales. DNA-17 is based on the 10 STR loci used in SGMPlus, in addition to a further six STR loci (giving a total of 32 DNA components) and a gender identifier.

As part of the transition programme, the NDU upgraded the NDNAD software in 2013 to enable the storage of the SGMPlus portion of a DNA-17 profile. Profiles produced using DNA-17 have subsequently been loaded to the NDNAD. Until 24 July only the SGMPlus portions of the DNA-17 profiles have been accessible for comparison purposes in England and Wales. From the 24 July 2014, the NDNAD will be able to store and search full DNA-17 profiles.

DNA-17: Benefits

DNA-17 is the latest DNA profiling methodology to be approved by the NDU Delivery Unit, on behalf of the Chair of the NDNAD Strategy Board, for profiles to be uploaded to the NDNAD. The United Kingdom Accreditation Service (UKAS) will accredit the DNA-17 methods used by Forensic Science Providers (FSP) to develop DNA profiles before profiles are loaded to the NDNAD.

DNA-17 offers:

• a methodology that is compatible with the SGM and SGMPlus methodologies that have been used to produce profiles for loading to the NDNAD.
• improved discrimination between profiles - greatly reducing the probability of getting a chance match between any two unrelated individuals' DNA profiles . Despite the improved discriminationn between individual's profiles, the match reporting threshold used for reporting full DNA-17 profile matches will remain the same as that used to report the strength of a full SGMPlus DNA profile match between unrelated individuals (i.e. one in a billion - a billion is one thousand million). It is considered that a move to a more discriminating threshold (as outlined above) will not add any additional evidential value to the probability of the DNA having originated from the individual. As such, the match probability will continue to be reported at one in a billion.
• improved sensitivity - making it possible to produce DNA profiles using standard methodologies from less DNA, or poor quality DNA samples, e.g. samples of DNA that have become degraded or are mixed with chemical inhibitors such as the dyes used on certain clothing such as indigo dye in denim.
• improved comparability between profiles on the NDNAD with profiles produced in other European Union countries and beyond.

DNA-17 has already been introduced successfully in Northern Ireland and Scotland. DNA-17 will be used in England and Wales from 24 July 2014 for producing DNA profiles for loading to the NDNAD.

DNA-17: Risks

Discordance

Small DNA sequences called primers are used to bind to specific areas of DNA and target specific DNA loci in a DNA profiling methodology. Primer sequences are specific to each loci and have a coloured fluorescent dye attached to allow detection. Binding of the primer DNA sequence to the target DNA enables the DNA fragment of interest and the variation at these loci to be amplified, and subsequently detected in a DNA profile.

The SGMPlus methodology was provided by a single manufacturer and was the only kit allowed for producing profiles in the UK for the NDNAD. The use of one manufacturer constrained the methodology to use a single set of primer DNA sequences for the amplification and detection of DNA variations at the target STR loci. Following the opening up of the market for the provision of DNA profiling methodologies to the UK, different versions of the DNA-17 profiling methodology have been developed.

Although each DNA-17 methodology targets the same 16 STR loci (and gender identifier) in order to be uploaded to the NDNAD, different primer DNA sequences may be used by each DNA-17 methodology to detect and amplify the target STR loci. These may also differ to the primer sequences used in the SGM and SGMPlus methodologies. In the vast majority of cases the use of different DNA primer sequences between different profiling methodologies will not be problematic. However, in a very small number of cases, the results obtained using the different DNA-17 methodologies will not be totally compatible, and result in an expected and characteristic difference. This is referred to as a discordant event, or discordance.

Differences in the profiles can be due to a rare event in the DNA of an individual, known as a Primer Binding Site Mutation (PBSM). The mutation in the DNA means that the primer sequence that is used to bind to the target DNA in order to start the amplification of the STR locus is unable to bind effectively to it. Depending on how ineffective the binding is, the DNA at that STR locus will either be poorly replicated or will not replicated during the amplification process. Should a PBSM cause this to happen, the DNA variation at the STR locus will not appear in the DNA profile or will appear only weakly and may not be associated with the overall DNA profile.

Solution

Following the studies into the compatibilities of the different PCR chemistries, the NDU has enhanced its existing integrity programme, which will manage results that have identified any discordant events caused by PBSMs. The programme initially identifies any discordance that the profiles must have produced using different methodologies or different DNA-17 chemistries, and shows a single number at a specific marker in one test, and two numbers (one will be the single number represented in the first test) at a specific marker in the other test. Once any possible a discordance is identified, it is reported to the FSP who will be asked to confirm the analysis of the profile.

The FSP will review the information provided to it, and may choose to reprocess the sample to confirm that a discordance has occurred. This will involve re-analysing one of the samples, either by:

• Reprocessing the sample which produced the profile with the single number at the marker, using the same methodology that generated the profile with the two numbers. You would expect to see that the reprocessed sample would generate both the two numbers; or
• Reprocessing the sample which produced the profile with the two numbers, using the same methodology that generated the profile with the single number. You would expect to see that the reprocessed sample would generate just the single number.

This re-analysis, to verify that the difference in the result was due to discordance, will take place before the result is reported to the police and prosecution, usually via Streamlined Forensic Reporting (SFR).

Further enhancements to the integrity programme will be implemented in early 2015 to further strengthen the ability to identify these rare discordant events. Close monitoring of the performance of the systems will also take place to ensure that should a discordant event be observed, the case is tracked and reviewed. Any learning from this will then be fed into the technical standards that FSPs have to follow when loading profiles to the NDNAD.

Reporting guidelines have been produced by the FSR Specialist Group, which support Reporting Officers in interpreting and reporting cases using DNA-17 chemistries.

Partial Matches

Controlled DNA samples taken from people are expected to result in full profiles, whichever methodology is used. In comparison, the quality of DNA recovered from crime scenes may vary. Where the condition of recovered material is very poor, DNA may have degraded such that the DNA variations at loci are no longer preserved intact, or the amount of DNA present in the sample is extremely low, resulting in a partial DNA profile. Where this occurs, the police unit that submitted the samples for profiling is currently advised to contact the FSP that analysed the crime scene sample for advice on the value of the match.

It should be borne in mind that a partial match using DNA-17 may have more matching areas of DNA compared with a full match using SGMPlus. For example, a 12 loci match would have been a full match for SGMPlus, but will be only a partial match for DNA-17. The partial DNA-17 match probability will still be one in a billion.

In relation to the match probabilities that can be assigned to partial profiles, see Match Probabilities, below.

A match between two profiles on the NDNAD can occur simply by chance. This is an adventitious match. This risk is very low when full SGMPlus and DNA-17 profiles are involved. However, the risk increases if a partial profile is obtained from a sample of DNA. If a very partial profile exists in a match with another profile, there is a risk that this will generate an adventitious match.

Solution

Discordant events and mixed DNA samples (i.e. crime samples that contain the DNA from more than one source) analysed using DNA 17, should not represent a risk to casework provided they are identified and interpreted correctly by the FSP experts.

Similarly, partial matches should not directly represent a risk to prosecuting a case, though the more partial the DNA profile match (between any DNA-17, SGMPlus profile or SGM profile), the more relevance that could be attached to the existence of profile data for the missing STR loci.

The FSP may be asked to upgrade crime stain DNA profiles (wherever possible) that are very partial or were produced using SGM. This would normally be requested following receipt of the original match report from the NDNAD. Whether reprocessing a crime scene sample will produce a more complete profile will depend upon the sample type, the condition of the samples and the sensitivity of the profiling technology available at the time of processing. Such instances need to be dealt with on a case by case basis dependent upon how partial the match is; the strength of the other evidence in the case and the seriousness of the offence.

A match probability can be established from the SGM or SGMPlus portion of the sample. This, together with a consideration of the potential effect of the absent loci are both aspects which should be reported on by the FSP expert. The expert may suggest upgrading a sample's profile from an SGM or SGMPlus profile to a DNA-17 profile.

Match reports from the NDNAD to the police regarding analyses using DNA-17 will have an alert in them regarding issues around eliminating or strengthening information from incomplete profiles.

Irrespective of whether or not DNA-17 has been used in preparing DNA profiles, the evidential value of any SGMPlus or SGM profile matches remains unchanged. Upgrading profiles using the DNA-17 methodology is therefore not necessary for the majority of cases.

If a more complete profile cannot be obtained, the FSP should be asked by the prosecution to report the strength of a partial profile match between unrelated individuals (see Match Probabilities, below). The prosecutor can use this to assess the nature and extent of further evidence required in order to prove the case.

Contamination

Whilst the sensitivity of DNA-17 is such as to increase the risk of DNA contamination from the handling of the samples by the Scenes of Crime Officer (SOCO) and the FSP, it also means that contamination is more easily detected. There is also an increased risk of detecting background DNA, which may have been deposited before and after the deposition of the target DNA.

The ACPO DNA Good Practice Guide contains detailed guidance on dealing with contamination issues before they are reported to the CJS.

Implementation

FSPs will be able to load profiles obtained using DNA-17 onto the NDNAD from 24 July 2014.

Profiles obtained using SGM and SGMPlus will remain as being admissible in criminal proceedings after that date. There is no need to upgrade these profiles for them to be used in criminal proceedings.

Match Probabilities

A full DNA-17 profile obtained from a crime scene samples compared with a full DNA-17 subject profile will provide a match probability estimated in the order of 1 in a billion (a billion is one thousand million).

Partial profiles obtained from crime scene samples with between 19 and 32 matching loci when compared with a full subject profile will also provide a match probability estimated in the order of 1 in a billion. Partial profiles with less matching loci will provide a lesser match probability and this should be included in reports.

Expert Evidence (including Streamlined Forensic Reporting)

In R v Reed and Reed; R v Garmson [2010] 1 Cr. App. R. 23 (at paragraphs 128-132), the Court issued case management guidance where issues are raised in relation to DNA evidence. It is vital that the issues are identified at an early stage in the proceedings. This leaves the jury to focus on the issues in dispute. In particular:

• DNA Experts should provide their reports or statements as early as possible in the proceedings. They should follow Crim. PR 33 and ensure that, where propositions are to be advanced as part of an evaluative opinion, that each proposition must be spelt out with precision in the expert report.
• Expert reports must be carefully analysed by the parties and, where a disagreement is identified, this must be brought to the attention of the court.
• In the case of a dispute, the judge will exercise his powers under Crim. PR 33.6 to order that the experts prepare a joint report. The underlying science should be agreed, where possible, and any points in dispute should be highlighted with precision, for example, the match probability, the interpretation of the electrophoretograms or the evaluative opinion that is to be given.
• The parties' Experts should note that a failure to comply, without good reason, with the rules or judge's directions could result in the judge refusing permission for the party in default to call the expert evidence in question.

Streamlined Forensic Reporting (SFR) allows the prosecution to indicate the existence of a match between a crime scene sample and a profile from a known source (the Defendant). Matches that have been identified from a mixed DNA sample should be stated on every occasion - including information about the type of mixture, and an indication as to what part of the mixture the match refers to e.g. major component, minor component, etc. It is for the Defence to indicate that they disagree with the evidence of the match and what issue is taken with it, setting out in clear terms whether the basic science is agreed and identifying with precision what is in dispute.

For more information about SFR, see the SFR guidance and SFR Toolkit.