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DNA test kit but one result in genotyping research project
IN 2018, the Forensic DNA Laboratory at the University of the Western Cape, Inqaba Biotechnical Industries (Inqaba Biotec), the Lesotho Police and the National University of Science and Technology in Zimbabwe unveiled the first DNA test kit prototype with the potential to help eliminate male perpetrator suspects in sexual assault cases in the Southern African region.
The test kit could not only help police reduce suspect pools in sexual assault cases, but also the time and resources spent on narrowing down the suspect list in subsequent investigations.
The UniQ-Typer™ Y-10 kit prototype uses 10 genetic markers found on the Y chromosome that are able to produce the highest level of discrimination in diff erentiating one male from another and generate a DNA profi le that is unique to a group of related men. The prototype was developed by the laboratory and Inqaba Biotec and was funded by UWC, Inqaba Biotec, the National Research Foundation, the Technology Innovation Agency and BioFISA.
“We were able to identify 10 markers on the Y chromosome with short tandem repeats (Y-STRs) with a high variation from individual to individual after a larger screening using 45 markers,” explains Professor Maria Eugenia D’Amato, a population geneticist and forensic scientist, and head of the laboratory, which is based in the Department of Biotechnology.
Chromosomes are made up of genes that contain genetic material called DNA. A marker is a known region on the chromosome that is highly variable and can thus be used to identify individuals. Currently, the South African Police Service (SAPS) uses kits that rely on STR markers from all the chromosomes in the body to determine perpetrators in sexual assault cases. However, these kits identify both male and female DNA as bodily fl uid obtained from the scene of a rape is usually mixed.
“This makes it very diffi cult to obtain readable genetic profi les, whereas, when you focus on the Y chromosome, you can identify and single out the male DNA from the bodily fl uids recovered,” explains Prof D’Amato.
“Y-STR kits like this prototype are also powerful in eliminating suspects and exonerating innocent individuals,” she says.
Because existing kits used by the SAPS are produced for the European market, they are not as eff ective in more diverse populations like South Africa’s. The prototype, on the other hand, has a higher probability of distinguishing the profi les of paternally related men in Southern Africa.
Prof D’Amato’s research is based on a breakthrough made at UWC in 2003 and published in 2007 when her colleagues, Professors Sean Davison, Mongi Benjeddou and Neil Leat, “discovered many Y-STRs that were unknown then by data mining the published human genome” sequence produced through the Human Genome Project.
“Some of these proved excellent for forensic application for their discrimination power,” she says.
Prof D’Amato furthered their research in 2007 by screening local populations to identify more informative markers. The fi nal selection of the markers for the kit was done in collaboration with the former Director of the South African National Bioinformatics Institute (SANBI), Prof Vlad Bajic, who died in 2019.
“Since 2011, we have been genotyping anonymous donors from all over the country. Currently, we have a collection of 3 000 profi les from Lesotho and South Africa,” says Prof D’Amato. The research that underpins the development of the prototype involved collecting the DNA of anonymous males with ancestry from Africa, Europe and India and local ethnic groups – Venda, Pedi, Zulu, Xhosa, Puthi, Sotho, Vundle, Ndebele, Tswana, Swazi, Tsonga and admixed groups – to understand the natural genetic diversity among men from diff erent ethnic backgrounds.
Other than the testing kit, the research provided the foundation for the development of the UniQTyper Reference Database.
Noting that the prototype has a wider application outside forensics and can be used in genealogy and anthropology studies, Prof D’Amato says, “The reference database is only in its testing phase. We would like to still implement additional functions and statistical tools to evaluate the signifi cance of a match.
Professor Maria Eugenia D’Amato, the head of the laboratory based in the Department of Biotechnology.
“This is important, because when an investigation fi nds a match, it alone says nothing. We need additional information, such as how often that profi le is seen in a country or region, how often that profi le is seen in the population group the suspect belongs to, and what is the probability of fi nding such a profi le among diff erent populations. But, to develop the database, we will need funding.”
