Since 2003, the Institute of Biotechnology (IBT) in Vietnam has been working on a project to identify the many thousands of Vietnamese dead from the Vietnam war. Recently, with support from the International Commission on Missing Persons (ICMP), which has its headquarters in The Hague, and consultants from Bioglobe GmbH, Hamburg, they have begun an ambitious project aiming to identify at least 4,000 deceased a year. SelectScience® spoke to Professor Dr Wolfgang Höppner, CEO of Bioglobe, and Christian Starke, QIAGEN, about the challenges of collecting and processing degraded DNA.
“There are some very specific challenges to these kinds of samples”, explained Christian. The samples of bone from which the DNA is extracted are 40-50 years old, with “quite substantial microbial contamination and degradation of DNA”. The technology needed to enable this analysis, as well as the “improvements in protocols and products” has only been available in the last 5 years, agreed Dr Höppner, as has the experience of the ICMP in identifying bodies from the Balkan conflict.
“Generally speaking, there is a lot of PCR inhibition in the bone, the data of the DNA is usually quite fragmented due to age, and depending on how acidic the soil is, there may also be some microbial contamination. Therefore, the quality is bad, as is the quantity”, explained Christian. “The ICMP take as many samples as possible to get as much DNA as possible out of these bones, so it can be concentrated enough to do PCR and STR fingerprinting.”
Markers for matches
The key technology that will be used in this project comes from QIAGEN, who already have a collaboration with the ICMP. “QIAGEN has been very innovative in developing most of the components needed for the workflow, from difficult samples to DNA extraction and to successful genotyping”, revealed Dr Höppner. Currently, 24 Short Tandem Repeats (STR)-markers on different chromosomal loci are utilized for DNA identification. However, “the degraded or contaminated DNA from the old bones may not be able to give positive results to all 24 loci”, explained Dr Höppner. Luckily, 16 markers may already be sufficient to find matches.
The QIAGEN technology, in particular the QIAGEN Investigator 24plex QS kit, has “two build-in quality sensors which gauge the degree of degradation of DNA and the amount of contaminants in the sample which inhibit the amplification reaction”, allowing the best possible results, said Dr Höppner. Bioglobe have also visited Vietnam to consult on “how to equip the Vietnamese labs and train their scientists”.
However, despite this innovation, this will be a long process. “With increasing number of genotyped bones and genotyped reference the hit rate will go up, but in the beginning it will be slow”, explained Dr Höppner. “My guess is that the project in Vietnam will need at least 20 years.”
Here are Dr Höppner’s Lab Essentials, the equipment he couldn’t do without: