The researchers have also compiled a reference DNA database during the development process, which goes a long way towards confirming the country’s rich genetic diversity.
To the untrained eye, a DNA profile may appear as no more than a series of squiggly waves of peaks and valleys. But within each of those mysterious DNA chromatograms, as they’re called, vital snippets of unique genetic information can be found.
Those personalised markers are the reason why DNA profiles are famously deployed as a forensic technique for investigators to identify and compare the DNA profiles of suspects against evidence found at the scene of a crime. As with fingerprinting, each human’s DNA profile is unique.
But unlike the sleek depictions of the technique in crime series like ‘CSI’, where DNA evidence is portrayed as the gospel truth, DNA science in the real world is messy and requires intense rigour from those who compile and analyse it. This is particularly true in cases of rape, where DNA samples are likely to contain the DNA of both victim and perpetrator or perpetrators.
That’s one of the reasons why researchers at the Forensic DNA Laboratory (FDL) at UWC have spent almost two decades developing and finessing kits that can clearly distinguish between the DNA of a female victim and that of a male perpetrator. To do so, the kit needs to zero in on male DNA and take into account the genetic diversity of South Africans.
For this work, the FDL – led by Professor Maria Eugenia D’Amato – is collaborating with two industry partners: Inqaba Biotec, who work in the field of genomics, and a local biotech company that is exploring commercialisation and opportunities in neighbouring SADC countries.
Why the Y-chromosome?Typically, DNA profiling is done using what is known as ‘autosomal testing’. In this technique, scientists look at autosomal chromosomes, which are long stretches of DNA that make up the lion’s share of a person’s DNA store.
Of each human’s 23 pairs of chromosomes (i.e. 46 chromosomes), 22 are autosomal. Across these pairs, individualised information can be found at hundreds of thousands of DNA locations or ‘markers’ known as Short Tandem Repeat (STR) markers. A person can be identified by the number of times this small sequence of DNA is repeated at each marker. The number of STR repeats varies from individual to individual.
STR markers are so useful because they mutate much faster than other DNA sequences, even from one generation to the next. This makes it possible to tell the DNA profile of a father apart from the DNA profile of his son, for example.
But for all the wealth of data to be found within autosomal chromosomes, it contains no information on the gender of a person. For that information, you have to turn to the 23rd pair, the sex chromosomes. Biological females typically in that pair have two X chromosomes (one passed on from the mother, the other from the father’s mother), while biological males have one X (from the mother) and one Y chromosome (passed on only from a father to a son).
DISCOVER BIOTECHNOLOGY AT UWC
UWC’s new FDL kit is designed specifically for what’s known as ‘Y-STR testing’ in other words looking at the information stored in those short tandem repeats on the male Y-chromosome.
In certain contexts, this information is significant. “In cases of rape where the victim is female, autosomal profiles often result in mixtures of DNA from victim and perpetrator and can be difficult to interpret,” explains Dr Mohaimin Kasu, a researcher in the FDL who ran several tests on the DNA kit for his doctoral work. “In these cases, Y-chromosome information is a highly valuable tool.”
Shortcomings in technology have historically limited the use of Y-STR testing, points out Professor D’Amato. “Y-chromosome analysis is currently not being implemented routinely in South Africa,” she says, “as the lack of valuable DNA markers and population data have been major limitations for several years.”
The lab’s kit, known as UniQ-Typer™ Y-10 kit – a prototype launched in 2018 – hopes to address those limitations. It targets 10 highly informative markers, with the potential to differentiate between two males, even if they are close relatives.
As to the shortcoming around population data, this is addressed in the part of the process that follows the extraction of a DNA profile, explains Professor D’Amato. “The work doesn’t stop once you have a profile,” she says. “The real question is, now that you have a profile, what do you do with that?”
The necessary DNA databaseAs with fingerprints, DNA profiles, while unique, can be very similar. This is especially true in the cases of close relatives like full siblings. (In twins, profiles are identical.)
When its being used in criminal cases or paternity tests, a DNA profile must stand up to one question: what is the statistical chance or probability that two people have that exact same profile?
To answer that question, scientists need to understand the genetic variation within a community or society. It’s understood, for instance, that DNA profiles can be similar for those in any one ethnic or language group. Historically, DNA profiling in South Africa has relied heavily on international reference data compiled by researchers in other parts of the world. “So we have been using data largely from America, based on African-American and Hispanic groups, which is not representative of South Africa,” explains Professor D’Amato (pictured).
To make up for this obvious shortcoming, the FDL has recently completed what it sees as the first stage of a comprehensive and representative DNA database of males in South Africa. The database is distinctively different from the criminal National Forensic DNA Database of South Africa, or NFDD, held by the South African Police Service. “Ours is a reference database, which is used for statistical analysis,” says Professor D’Amato. “We are interested in the metadata of the anonymous participants in our database, not in the individual.”
The FDL database covers males across 16 population groups in South Africa. The groups are broadly identified by ethnolinguistic measures, meaning that it takes into account ethnic identity, language, and geography. It includes indigenous KhoiSan and ‘black African’ populations, as well as ‘Out of Africa’ (or OoA) groups such as British and Dutch descendants.
The FDL database currently holds DNA profiles of 2,188 males, based on samples collected from across the country between 2008 and 2018. This study is the first large-scale Y-STR analysis for South Africa and is outlined in detail in an article - ‘The Genetic Landscape of South African males: A Y-STR perspective’ - published recently.
The paper both outlines the forensic statistical analysis that was conducted for the kit and offers a glimpse into the rich genetic diversity found in South Africa. A significant focus of the paper was to characterise the genetic relationships between the 16 population groups. It also sought to provide a comprehensive geospatial analysis that looks at how that genetic diversity is grouped and spread across the country.
In doing so, the authors made some novel findings on African paternal ancestry in particular regions of the country, reflecting the complexities of South African history, says Dr Kasu.
The kit is still some time away from completion, explains D’Amato. And once it is completed, there will be certain legal and scientific hoops it has to go through before being used in the South African legal system. That said, it has already been applied at least once in Zimbabwe, where it was used to exonerate a suspect. In the meantime, the FDL is also doing Y-STR analyses for population samples from Lesotho and Nigeria.
The UWC team is confident that UniQ-Typer™ Y-10 will prove to be a powerful tool in the analysis of DNA. “The collection of markers that we use represent a good balance between DNA that mutates very fast from one generation to another, and markers that do not change so fast, providing more comprehensive information,” says Dr Kasu.
Adds Prof D’Amato: “With this tool, we have access to dual sets of information. Not only can it discriminate between individuals, but we can also recover deeper ancestry information, as shown in our article.”
That means that the kit can be used to both identify sexual offenders and innocent suspects while also revealing much about the genetic melting pot that is South Africa.