NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program.

Next-generation sequencing (NGS) is being integrated into routine clinical practice in the field of (hemato-) oncology to search for variants with diagnostic, prognostic, or therapeutic value at potentially low allelic frequencies. The complex sequencing workflows used require careful validation and continuous quality control. Participation in external quality assessments (EQA) helps laboratories evaluate their performance and guarantee the validity of tests results with the ultimate goal of ensuring high-quality patient care. Here, we describe three benchmarking trials performed during the period 2017-2018 aiming firstly at establishing the state-of-the-art and secondly setting up a NGS-specific EQA program at the national level in the field of clinical (hemato-) oncology in Belgium. DNA samples derived from cell line mixes and artificially mutated cell lines, designed to carry variants of clinical relevance occurring in solid tumors, hematological malignancies, and BRCA1/BRCA2 genes, were sent to Belgian human genetics, anatomic pathology, and clinical biology laboratories, to be processed following routine practices, together with surveys covering technical aspects of the NGS workflows. Despite the wide variety of platforms and workflows currently applied in routine clinical practice, performance was satisfactory, since participating laboratories identified the targeted variants with success rates ranging between 93.06% and 97.63% depending on the benchmark, and few false negative or repeatability issues were identified. However, variant reporting and interpretation varied, underlining the need for further standardization. Our approach showcases the feasibility of developing and implementing EQA for routine clinical practice in the field of (hemato-) oncology, while highlighting the challenges faced.

Alternative Sample-Homogeneity Test for Quantitative and Qualitative Proficiency Testing Schemes.

Proficiency Testing (PT) External Quality Assessment (EQA) schemes are designed to ascertain the ability of individual laboratories to perform satisfactorily with respect to their peer laboratories or to limits imposed by external sources. Observed deviation of a laboratory result for a PT sample must be entirely attributed to the laboratory and not to the PT provider. To minimize the probability that deviations could be attributed to the PT provider, sample homogeneity should be assured. It is generally required that for quantitative parameters, the standard deviation among PT units should be calculated on the basis of duplicate measurements of at least 10 samples chosen at random, and the standard deviation among PT units should not exceed 0.3 times the standard deviation used to evaluate laboratories. Because this approach has important drawbacks, an alternative procedure is proposed by applying the theory of acceptance sampling to the assessment of sample heterogeneity for both quantitative and qualitative data and deriving acceptance limits on the basis of minimizing the probability of falsely evaluating laboratories. For obtaining acceptance limits for quantitative parameters, a distinction is made between laboratory evaluation using fixed limits on the one hand and laboratory evaluation using limits that are based on the variability of the reported results on the other hand. Sequential tests are proposed to evaluate sample heterogeneity by means of a comparison with the χ2 distribution. For qualitative parameters, acceptance-sampling plans are proposed that are based on minimizing the joint probability of rejecting batches that have a satisfactory amount of defective samples and accepting batches unnecessarily. The approach for quantitative parameters is applied on samples for a PT scheme of ethanol quantification and for qualitative parameters on the presence of monoblasts in a blood smear. It was found that five samples could already be enough to prove that the batch was homogeneous for quantitative parameters, although more than 20 samples were needed to prove homogeneity for qualitative parameters. This study describes a direct relation among the objective of an PT round, the criteria for evaluating the results, and the sample heterogeneity. When samples are effectively homogeneous, less measurements are needed than current practices require. A drawback of the proposed approach is that the number of samples to be tested is not known beforehand, and good knowledge of the analytical variability is crucial. The formulas to be applied are relatively simple. Despite the drawbacks, the proposed approach is generally applicable for both quantitative and qualitative data.

Cyclooxygenase-2 network as predictive molecular marker for clinical pregnancy in in vitro fertilization.

The gene expression of human endometrium on the day of oocyte retrieval of pregnant and nonpregnant patients in a stimulated IVF cycle was compared in two independent groups with different GnRH-antagonist ovarian stimulation protocols. The present data suggest that increased gene expression of cyclooxygenase-2, together with the expression of other molecules in the cyclooxygenase-2 network, on the day of oocyte retrieval in GnRH-antagonist cycles coincides with a lower probability of achieving a clinical pregnancy in this cycle.

In GnRH antagonist/rec-FSH stimulated cycles, advanced endometrial maturation on the day of oocyte retrieval correlates with altered gene expression.

BACKGROUND: Previously, advanced endometrial maturation on the day of oocyte retrieval in GnRH antagonist and -agonist IVF cycles was observed. In these cycles, endometrial advancement exceeding 3 days between the histological dating and the cycle day never resulted in an ongoing clinical pregnancy. In this study, the gene expression of human endometrium on the day of oocyte retrieval in GnRH antagonist/rec-FSH cycles was analyzed, in correlation with the morphological dating. METHODS: Biopsies were taken on the day of oocyte retrieval in 47 patients with 1 or 2 embryos replaced on Day 3 in the same cycle. Endometrial dating was performed according to Noyes' criteria. Biopsies from 11 patients were analyzed for gene expression with the Affymetrix HG U133 Plus 2 microarray. Data analysis, clustering and pathway analysis were performed with GCOS, GeneSpring 7.3 and Ingenuity, respectively. RESULTS: According to Noyes' criteria, all endometria taken on the day of oocyte retrieval showed an advanced maturation, ranging from +d2 to +d4. The patients with a subsequent clinical pregnancy all showed a histological dating corresponding to +d2 or +d3. When comparing endometria +d2-3 to +d4, the microarray results showed a differential expression of 2550 probe sets. Significantly up-regulated genes were SERPINB6, FOXO3A, SOX17 and CDC42. Down-regulated genes of interest were NRP1, HOXA10 and OSF2. Principal component analysis and hierarchical clustering demonstrated two distinct clusters. CONCLUSIONS: In stimulated cycles, endometrial gene expression on the day of oocyte retrieval discriminates between women with and without histologically advanced endometrial maturation exceeding 3 days and supports histological dating results by Noyes' criteria.

Genomic activation of the EGFR and HER2-neu genes in a significant proportion of invasive epithelial ovarian cancers.

BACKGROUND: The status of the EGFR and HER2-neu genes has not been fully defined in ovarian cancer. An integrated analysis of both genes could help define the proportion of patients that would potentially benefit from targeted therapies. METHODS: We determined the tumour mutation status of the entire tyrosine kinase (TK) domain of the EGFR and HER2-neu genes in a cohort of 52 patients with invasive epithelial ovarian cancer as well as the gene copy number and protein expression of both genes in 31 of these patients by DGGE and direct sequecing, immunohistochemistry and Fluorescent in Situ Hybridisation (FISH). RESULTS: The EGFR was expressed in 59% of the cases, with a 2+/3+ staining intensity in 38%. HER2-neu expression was found in 35%, with a 2/3+ staining in 18%. No mutations were found in exons 18-24 of the TK domains of EGFR and HER2-neu. High polysomy of the EGFR gene was observed in 13% of the invasive epthelial cancers and amplification of the HER2-neu gene was found in 10% and correlated with a high expression level by immunohistochemistry.Mutations within the tyrosine kinase domain were not found in the entire TK domain of both genes, but have been found in very rare cases by others. CONCLUSION: Genomic alteration of the HER2-neu and EGFR genes is frequent (25%) in ovarian cancer. EGFR/HER2-neu targeted therapies should be investigated prospectively and specifically in that subset of patients.