Which cells and DNA belong to whom? Scientists unmix blood samples

It’s a familiar problem in forensic genetic identification: a human trace has been found at a crime scene, but it contains DNA from more than one person. Consider, for example, the forensic DNA analysis of a cotton swab swiped past a door handle. Which DNA belongs to whom? Genetically characterizing and identifying persons from mixed traces often is impossible in forensic practice.

Mixed traces

Researchers at Erasmus MC show that a technique long used in biomedical sciences can in the future provide a helping hand for solving the forensic problem of mixed traces. Using this technique, they managed to separate the cells according to the different donors of the mixed blood samples. Up to nine individuals.

Moreover, they correctly inferred the biogeographic origin and sex of the contributors. And they correctly identified them individually. All based on genomics and bioinformatics. They describe their work in Communications Biology.

Barcode

The researchers use so-called single-cell transcriptome sequencing. In this process, the DNA of all individual cells in the blood mixture is given a unique label. Each cell gets a barcode, so to speak, that helps identify which cells belong together.

‘The great advantage of this approach is that we separate the cells and DNA of the different individuals before we do the forensic genetic analyses. That prevents a lot of problems afterward, which we do have with current methods’ explains Prof. Manfred Kayser, head of the Department of Genetic Identification. He led the research together with dr. Eskeatnaf Mulugeta of the Department of Cell Biology.

Ph.D. student Lucie Kulhankova conducted the research. Bioinformatician Diego Montiel-Gonzales built the software needed to analyze the vast amount of data. They called their software De-goulash, after the mixed multi-ingredient stew from Eastern Europe, as Lucie originates from the Czech Republic.

Hold up in court

The researchers tested the method with mixed blood samples. These contained blood from two to nine people, in varying proportions. In all cases, they managed to separate the cells of the different donors and characterize as well as individually identify them correctly. ‘With each person we added, it became a little more difficult. But it kept succeeding, with a precision that would hold up in court,’ Mulugeta said. The next step is to test the approach on other types of samples, such as skin cells or saliva.

To apply the technique in forensic practice, it also needs to be made cheaper and simpler. This is what they are working on right now.

Kayser and Mulugeta call their discovery the result of the ultimate form of collaboration between disciplines and one of the nice examples of how collaboration between departments works successfully at Erasmus MC. Kayser is an expert in forensic genetics and genetic identification and realized that single-cell sequencing could solve the long-lasting forensic problem of mixed traces. A few floors below his office works Mulugeta, an expert in single-cell genomics and bioinformatics. ‘We started talking about it and it clicked right away’, Mulugeta says.