Human sample authentication in biomedical research: comparison of two platforms

Samples used in biomedical research are often collected over years, in some cases from subjects that may have died and thus cannot be retrieved in any way. The value of these samples is priceless. Sample misidentification or mix-up are unfortunately common problems in biomedical research and can eventually result in the publication of incorrect data. Here we have compared the Fluidigm SNPtrace and the Agena iPLEX Sample ID panels for the authentication of human genomic DNA samples. We have tested 14 pure samples and simulated their cross-contamination at different percentages (2%, 5%, 10%, 25% and 50%). For both panels, we report call rate, allele intensity/probability score, performance in distinguishing pure samples and contaminated samples at different percentages, and sex typing. We show that both panels are reliable and efficient methods for sample authentication and we highlight their advantages and disadvantages. We believe that the data provided here is useful for sample authentication especially in biorepositories and core facility settings.

A systematic evaluation of stool DNA preparation protocols for colorectal cancer screening via analysis of DNA methylation biomarkers

ObjectivesColorectal cancer (CRC) screening using stool samples is now in routine use where tumor DNA methylation analysis for leading markers such as NDRG4 and SDC2 is an integral part of the test. However, processing stool samples for reproducible and efficient extraction of human genomic DNA remains a bottleneck for further research into better biomarkers and assays.MethodsWe systematically evaluated several factors involved in the processing of stool samples and extraction of DNA. These factors include: stool processing (solid and homogenized samples), preparation of DNA from supernatant and pellets, and DNA extraction with column and magnetic beads-based methods. Furthermore, SDC2 and NDRG4 methylation levels were used to evaluate the clinical performance of the optimal protocol.ResultsThe yield of total and human genomic DNA (hgDNA) was not reproducible when solid stool scraping is used, possibly due to sampling variations. More reproducible results were obtained from homogenized stool samples. Magnetic beads-based DNA extraction using the supernatant from the homogenized stool was chosen for further analysis due to better reproducibility, higher hgDNA yield, lower non-hgDNA background, and the potential for automation. With this protocol, a combination of SDC2 and NDRG4 methylation signals with a linear regression model achieved a sensitivity and specificity of 81.82 and 93.75%, respectively.ConclusionsThrough the systematic evaluation of different stool processing and DNA extraction methods, we established a reproducible protocol for analyzing tumor DNA methylation markers in stool samples for colorectal cancer screening.

Results of in vitro test-KRAStissue reagent kit test to determine indications for target therapy of patients diagnosed with colorectal cancer

As subjects of the clinical trial, 44 samples of paraffin-fixed tissue were used from patients diagnosed with “colorectal cancer.” In the course of clinical trials, 44 samples of paraffin-fixed tissue were analyzed in two series of experiments, that is, 88 clinical-laboratory experiments were carried out, of which 48 experiments with genomic DNA samples with the established negative status of the presence of KRAS gene mutations and 40 experiments with genomic DNA samples with the established positive status of the presence of KRAS gene mutations. Analysis and evaluation of the results of clinical laboratory tests of the medical product “Kit of Reagents for Determination of the Status of KRAS Gene Mutations by PCR-RV Method in a Sample of Human Genomic DNA from Samples of Paraffin-Fixed Tissue (Test-KRAS-tissue) according to TU 21.20.23-006-97638376-2016 “confirmed that it allows to carry out qualitative determination of the status of six mutations of the twelfth codon (Gly12Asp, Gly12Ala, Gly12Arg, Gly12Val, Gly12Ser, Gly12Cys) and one mutation of the thirteenth codon (Gly13Asp) the KRAS gene by real-time allele-specific PCR in human genomic DNA sample from paraffin-fixed tissue samples, with high diagnostic sensitivity rates of 90.9% and diagnostic specificity of 95.0% with a confidence probability of 90%. Reproducibility of results is 100%, which confirms the high reliability of the set.