Working with degraded samples
So far, scientists have collected a variety of samples from these relatives – hair, fingernails, saliva or blood. But in order to analyze tens of thousands of samples annually, the processes will have to be highly coordinated and highly standardized, as Christian Starke explains: “Our automation guarantees ease of use and reproducible results, helping the laboratories to save probably the most precious factor in this project, which is time.”
Another major challenge for the Vietnamese scientists is the condition of the sample material from the missing persons itself. “I saw bones that were as soft as peat,” says Prof. Dr. Wolfgang Höppner, founder of Hamburg-based Bioglobe and head coordinator for this project. Since the skeletal remains lie in humid soil, often directly under the surface, they are extremely vulnerable to microbial and plant damage, and are in a state of advanced decomposition. “The time span and extreme conditions mean that the DNA in the bones is significantly degraded and contaminated,” says QIAGEN’s Christian Starke.
Just a couple of years ago, it would have been impossible to extract DNA from such material, but recent innovations have given the investigators new tools to work with. In workshops in Hamburg, at QIAGEN’s headquarters in Hilden and at ICMP facilities in Bosnia, the Vietnamese forensics specialists were trained in how to utilize a state-of the art DNA analysis workflow, which relies mostly on QIAGEN technologies.
First, the bone samples are pulverized by means of the TissueLyser II, which simultaneously grinds multiple biological samples to a fine powder through high-speed shaking in stainless steel grinding jars. Afterwards, the powder is lysed (decalcified and protein digested), and the lysate is put in an EZ1 Advanced XL system for automated DNA extraction. As the samples are in a bad shape, the DNA extraction is of great importance. Finally, QIAGEN’s Investigator 24plex QS Kits are used to generate so-called STR profiles.
These kits cover 24 different non-coding positions in the human DNA – a considerably higher number of markers is used than is otherwise common in forensics. The tests, also used by the US federal agency FBI, thereby increase the value of the comparisons with the profiles of close and even distant relatives. At the same time, the specially designed test using very short DNA sequences raises the probability of being able to generate a profile, even for heavily degraded samples.
Following the extensive training period in Europe, the Vietnamese team will now work with actual bone samples from the victims and ramp up operations. “In the upcoming months, the increased working capacity and human resource quality will help to increase our staff’s effectiveness,” explains Dr. Tran.