Rebecca Richards - Biological evidence of the future: the use of sequencing in forensic DNA analysis
London Calling 2019
Forensic DNA profiling uses short tandem repeat (STR) analysis for human identification purposes, i.e. to establish a link between biological evidence and an individual. This technique is currently limited to assessing the length of STR alleles via capillary electrophoresis and relies on the comparison to a reference DNA profile. The advent of DNA sequencing has revolutionised the field of forensic genetics. Alleles with the same length but a different sequence can be distinguished, providing additional discrimination between individuals which can greatly aid in DNA mixture interpretation. Rare sequence mutations can be identified to differentiate identical twins, who cannot be told apart using conventional DNA profiling. Using sequencing, scientists have also begun to harness intelligence-based information that a biological sample can provide which could be of use in an investigation. The analysis of single nucleotide polymorphisms (SNPs) offers new opportunities in the form of forensic DNA phenotyping and forensic epigenetics. Prediction of eye, hair and skin colour, as well as bio-geographic ancestry and chronological age estimations of an unknown individual are all now possible. The introduction of nanopore sequencing technology has the potential to transform the field of forensic genetics even further. The portability and real-time capability of the MinION could shift analysis out of the lab into the field, greatly reducing cost and turnaround time which are critical in an investigation. Research into the feasibility of this technology for forensic applications is currently underway. Sequencing has not only changed the field of forensic genetics, but also has changed the way biological evidence is approached and could be used in investigations which has had a wide-reaching effect in enforcement, legal, governmental and judicial fields. Although not routinely used in forensic casework at present, many forensic laboratories around the world are currently validating sequencing technologies with the expectation that this will be the biological evidence of the future.
Rebecca began her Spotlight talk by introducing the currently-used routine method of forensic DNA profiling: short tandem repeat (STR) analysis. Traditionally, this is achieved by amplification of specific alleles, then a comparison of their length to a reference DNA profile via capillary electrophoresis. However, forensic DNA profiling has its limitations. Firstly, Rebecca asked: what do we do if no link is found? Secondly, the low resolution of STR analysis means that the data may link biological evidence to multiple individuals. This can occur in the case of identical twins; it may also result from partial crime scene profiles which produce links to many individuals. Also, Y-STR profiling for all paternal relatives is the same, resulting in matches for all males in a family. Finally, samples containing a mixture of DNA from several individuals are complicated to deconvolute.
Rebecca described how next-generation sequencing, the decreasing costs involved and commercial availability of forensics-specific kits could tackle these problems. Sequencing of the current STR markers means that analysis is "no longer limited to just the length-based information" for alleles: more differences between individuals can be found from sequence information. Rebecca gave an example in which traditional analysis of STR markers identified the same allele, 10, at the TPOX locus in two individuals, whereas DNA sequencing of the same locus revealed two different subvariants, 10a and 10b: the extra information from sequencing enables increased discrimination between individuals. In a second example, this improved distinction between variants helped to improve deconvolution of DNA from different individuals within a mixture. Rebecca noted the many forms of information possible from sequencing, such as SNPs RNA and DNA methylation, potentially bringing a "whole new realm" of forensic analysis. SNPs, she described, provide much more phenotypic information for profiling, including hair colour, bio-geographic ancestry and even age. Furthermore, it could help in identification of other species, useful in applications such as wildlife forensics for investigating illegal wildlife trade.
Here, Rebecca pointed out that, unlike on CSI, forensic labs tend to be "really slow" at taking up new technology: only a few forensic labs worldwide are currently implementing next generation sequencing. Rebecca then introduced "what we're all here for: what about the MinION?" Its portability and real-time sequencing and analysis could allow for on-site analysis of biological evidence, and reduce turnaround time and costs; Rebecca noted several studies into how the MinION could be used in forensic analysis. Rebecca and her team are currently researching and optimising a workflow for the use of the MinION in forensic analysis, with the aim of maximising DNA recovery, accuracy and ease-of-use, with minimal time and cost. Rebecca asked: could next-generation sequencing provide the "biological evidence of the future?". She stressed the importance of the ethical and legal considerations of DNA evidence and that of ensuring good data security.
Rebecca concluded by demonstrating how DNA evidence could aid the investigation of "who stole The Ring?": with the help of sequencing analysis indicating phenotype, she ruled out other Middle Earth suspects until one culprit remained. Mystery solved: it was Samwise Gamgee.