Comparison of Automated and Manual DNA Isolation Methods of Liquid-Based Cytology Samples

A prospective randomized noninferiority trial comparing conventional smears and SurePathTM liquid-based cytology in endoscopic ultrasound-guided sampling of esophageal, gastric, and duodenal lesions

BACKGROUND

Several liquid-based cytology (LBC) methods are currently used, but the diagnostic accuracy of each method is not well known. We aimed to compare the diagnostic performance of SurePathTM LBC and conventional smear (CS) cytology in endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) samples of esophageal, gastric, and duodenal lesions.

METHODS

As a prospective randomized noninferiority study, patients who needed EUS-FNA due to subepithelial mass in the upper gastrointestinal tract were randomly assigned 1:1 to the LBC and CS groups. Cytologic preparation was carried out using a crossover design where 1 method was used for the first needle-pass sample and another method was used for the second needle-pass sample. The primary outcome was to compare the diagnostic performance between LBC and CS using the final diagnosis as the gold standard.

RESULTS

A total of 87 patients were randomized and 60 patients were analyzed. There were no differences between LBC and CS in diagnostic accuracy (91.7% vs 86.7%, P = .380), sensitivity (97.7% vs 90.7%, P = .169), specificity (76.5% vs 76.5%, P > .99), negative predictive value (92.9% vs 76.5%, P = .225), or positive predictive value (91.3% vs 90.7%, P = .921). The background of LBC was less bloody than that of CSs (5.0% vs 53.3%, P < .001) and the sample preparation time of LBC was shorter than that of CSs (29 ± 7 seconds vs 90 ± 17 seconds, P < .001).

CONCLUSION

In the EUS-FNA of a subepithelial mass in the upper gastrointestinal tract, the diagnostic performance of LBC was not inferior to that of CS. The field of view was better in LBC, because the background was less bloody and necrotic. As LBC is more convenient to perform and takes shorter time, it is expected that it can replace the CS method for EUS-FNA samples.

Optimization of pre-analytical and analytical steps for DNA and RNA analysis of fresh cytology samples

BACKGROUND

Different cytology preparations can be used for molecular diagnostics, however the influence of pre-analytical and analytical steps on the results are not yet well defined. We aimed to determine optimal steps for efficient extraction of DNA and RNA from fresh cells for molecular diagnostics.

METHODS

MCF7 and FaDu human cell lines, were used as a model to determine fresh cells storage conditions (temperature: 25°C, 4°C, -20°C, -80°C; duration: 0 h, 4 h, 12 h, 24 h, 48 h) and optimal nucleic acids extraction method. Besides, the minimal number of total cells and minimal percentage of mutated cells needed for successful extraction of nucleic acids and subsequent determination of present mutation were evaluated.

RESULTS

Extraction of nucleic acids using spin columns yielded the highest quantity and quality of nucleic acids. Isolation of nucleic acids was feasible in all storage conditions, however higher temperature and longer duration of fresh cells storage were associated with lower quality of isolated nucleic acids and similar quantification cycle of housekeeping genes. Successful molecular testing was feasible with least 10⁴ cells, while specific mutation was detected in as low as 5% of mutated cells.

CONCLUSIONS

Our cell line model, mimicking fresh cytology samples, showed that quantity of extracted either DNA or RNA declined with higher temperatures and longer duration of storage but regardless of the storage conditions, we successfully detected both housekeeping genes and mutated gene using qPCR.

Agreement between L1 and E6/E7-based assays for detection of high-risk HPV in cervical, oropharyngeal and penile cancers

AIMS

Human papillomavirus (HPV) molecular testing targets either the late gene L1 or early genes E6 and/or E7. Loss of L1 during integration is suggested to compromise sensitivity in samples associated with cancer, however, clear evidence for this is lacking. Our aim is to address this by performing a head-to-head comparison between assays targeting L1 vs E6/E7, using a series of high-grade and invasive disease samples within different biological matrices and anatomical sites.

METHODS

We obtained 298 samples comprising of liquid-based cytology and biopsies of cervical cancer and cervical intraepithelial neoplasia grade 3, in addition to biopsies of penile and oropharyngeal cancers. Two commercially available HPV primary screening assays and two assays with extended genotyping were applied to the sample set targeting L1 (Abbott RealTime HR HPV Assay and Optiplex HPV Genotyping Test) and E6/E7 genes (Xpert HPV Test and EuroArray HPV Test).

RESULTS

Agreement for high-risk HPV (hrHPV) for all samples types between the screening assays is over 88% and over 96% for the two genotyping assays. For HPV 16 agreement is over 90% for both screening and genotyping assays. Kappa statistics show good to very good agreement between the screening and genotyping assays for hrHPV and HPV 16.

CONCLUSIONS

Analysis of the valid results from our data indicates that L1 and E6/E7 targeting assays show similar performance for detection of hrHPV in high grade cervical lesions and cancers of cervix, penis and oropharynx.