Automated Extraction of DNA from Blood and PCR Setup using a Tecan Freedom EVO Liquid Handler for Forensic Genetic STR Typing of Reference Samples

Approaches to automation of the preanalytical phase of large-scale research in the biobank of the National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Health of Russia

Aim. To create and validate an algorithm for automatic aliquoting of serum and plasma samples for biobanking as part of a large-scale study.

Material and methods. Biobank of the National Medical Research Center for Therapy and Preventive Medicine is equipped with a Tecan automated aliquoting system. When compiling the aliquoting program (script), the following parameters were selected: the time spent on spotting one complete cryobox, with a capacity of 96 cryotubes, the optimal number of vacutainers and tips for a single loading of the device. The program was created to receive 12 aliquots of 0,5 ml of blood serum, plasma with ethylenediaminetetraacetic acid and plasma with sodium citrate in cryotubes per 1 ml from eight participants in total from each in one cycle of device loading. Automatic and manual spotting was assessed in terms of the time spent on sample preparation and the quality of the aliquots obtained.

Results. A methodology for conducting the preanalytical phase of a  large-scale study based on the automation of biosample aliquoting has been developed and validated. We created scripts for aliquoting serum and blood plasma at the automated Tecan Freedom EVO system. An experiment conducted on biomaterial from 64 participants showed, that with an expected flow of 32 participants per day, it took more than 2 hours for manual aliquoting, and for automatic aliquoting (4 launches of the aliquot robot for 24 vacutainers from 8 participants) — less than 1,5 hours with the complete exclusion of human errors.

Conclusion. Automated aliquoting has a following number of advantages in comparison with manual: it allows to guarantee standardization and efficiency of sample preparation, reduce the time and increase the accuracy of aliquoting of biomaterial, save space in long-term storage freezers due to the use of smaller cryotubes. The developed algorithm for creating aliquoting programs and calculating the optimal use of consumables can be used in other projects.

Validation of the Applied Biosystems RapidHIT ID instrument and ACE GlobalFiler Express sample cartridge

Rapid DNA platforms are fully automated systems capable of processing DNA from biological samples and interpreting the results in approximately 90 minutes with minimal human intervention. With a greater reliance on the system than on the analyst, validation data are especially needed to define the performance and limitations of commercially available Rapid DNA systems. Thus, validation studies of a Rapid DNA workflow consisting of the Applied Biosystems RapidHIT ID Instrument and RapidLINK software with a focus on the ACE GlobalFiler Express Sample Cartridge and reference buccal swabs were performed in accordance with Scientific Working Group on DNA Analysis Methods Validation Guidelines. These validation studies included assessments of sensitivity, contamination, concordance, reproducibility and repeatability, stability, inhibition, mixtures, sample reprocessing, precision, and first-pass success rate. Overall, the current Applied Biosystems RapidHIT ID Instrument with the ACE GlobalFiler Express sample cartridge was found to be a reliable tool for generation of STR profiles from reference-type buccal swabs.

The use of FTA cards to acquire DNA profiles from postmortem cases

Filter papers have been used for many years in different applications of molecular biology and have been proven to be a stable way to store DNA waiting to be analyzed. Sampling of DNA on FTA (Flinders Technology Associates) cards is convenient and cost effective compared to alternative approaches involving DNA extractions and storage of DNA extracts. FTA cards are analyzed at many forensic laboratories, and the way to perform direct genetic profiling on buccal swab cards has developed into an almost industrial process. The possibility to include postmortem (PM) samples into an FTA-based workflow would facilitate and speed up the genetic identification process compared to conventional methods, both on a regular basis and in a mass casualty event. In this study, we investigated if FTA cards may be used to carry tissue DNA from deceased and present a high-quality DNA profile from the individual in order to be useful for the identification process. The study also aimed to investigate if a specific body tissue would be preferable, and if decomposed tissue is suitable at all to put on an FTA card in order to obtain a DNA profile. We have compared the quality of the DNA profiles acquired from postmortem tissue on FTA cards, with the results acquired with conventional methods from reference bone/muscle samples from the same individual. Several types of tissues have been tested from different identification cases and scenarios. We concluded that tissue cells from inner organs are suitable to put on FTA cards, and that the obtained DNA profiles have the potential to serve as PM data for identification purposes. In cases including compromised samples, however, it is recommended to keep the tissue sample as a backup if further DNA has to be extracted.

A novel fully automated system for quantification of Hepatitis B virus DNA using magnetic bead-based method combined with real-time PCR

BACKGROUND

Hepatitis B virus (HBV) infection is a major global health problem and causes liver damage as cirrhosis of the liver or liver cancer. Development of an accurate, sensitive and reproducible detection method for detecting and monitoring HBV DNA is very necessary and urgent.

OBJECTIVES

The aims were to evaluate the analytical performances of the fully automated Pre-NAT system comparing to domestic assay, and to explore the role of highly sensitive quantification of HBV DNA in the management of chronic HBV infection.

STUDY DESIGN

Pseudo-viral particles at high HBV DNA concentration were serially diluted to assess linear range. Accuracy and lower limit of detection were assessed by determining a panel of HBV standard substance. HBV DNA positive clinical specimen and internal quality control were measured 20 times to evaluate precision and reproducibility. 20 non HBV-infected specimens were used for the specificity assay. 96 chronic hepatitis B samples were quantified for HBV DNA to evaluating the correlation between the new test and Da-an assay. HBV serological markers were detected using ELISA method.

RESULTS

Pre-NAT quantitated HBV DNA levels covered a wide dynamic range (10 logs) with a close correlation between expected and observed values (r=0.999, P<0.05), satisfactory precision and higher specificity. The lower detection limit was 20IU/mL. Comparability assay showed Pre-NAT had a good agreement with but more sensitive than Da-an assay (t=0.149, P>0.05). HBV DNA level was partially correlated to but more reliable and sensitive than serological evidence in reflecting the viral level.

CONCLUSION

This novel fully-automated real-time PCR assay exhibits good analytical and clinical performances for highly sensitive detection of HBV DNA. It is well suited for monitoring antiviral responses and making treatment strategies according to current clinical practice guidelines for the management of chronic HBV infection.

Biomek 3000: the workhorse in an automated accredited forensic genetic laboratory

We have implemented and validated automated protocols for a wide range of processes such as sample preparation, PCR setup, and capillary electrophoresis setup using small, simple, and inexpensive automated liquid handlers. The flexibility and ease of programming enable the Biomek 3000 to be used in many parts of the laboratory process in a modern forensic genetics laboratory with low to medium sample throughput. In conclusion, we demonstrated that sample processing for accredited forensic genetic DNA typing can be implemented on small automated liquid handlers, leading to the reduction of manual work as well as increased quality and throughput.