ECP 2022 Abstract Book

Virchows Archiv (2022) 481 (Suppl 1):S1–S364 13 In collaboration with Dr. G. Douma, Dr. W. van Geffen, Dr. M. Tip (pulmonologists), Dr. C. Klamer-Wardle, Dr. R. Kibbelaar, Dr. H. Sietsma (pathologists) and Dr. E. van der Logt (CSMP) from Treant Zorggroep, Martini Ziekenhuis, Medisch Centrum Leeuwarden, Pathologie Friesland en Ommelander Ziekenhuis Groningen. E-PS-15-009 Assessment of gDNA yield obtained from FFPE samples and from scraped histological and cytological slides of patients with lung adenocarcinoma L. Antonangelo*, F.R.R. Mangone, M.E.M. Agati, A.C. Pavanelli, M.A. Nagai, L.D. Kulikowski, V.R. Figueiredo, C.S. Faria *Universidade de São Paulo, Brazil Background & objectives: Formalin-fixed and paraffin-embedded (FFPE) samples represent a challenge in recovering genetic material. Our objective is to evaluate the yield of genomic DNA from samples of primary tumour and aspirated lymph nodes extracted of paraffin blocks and from scraped histological/cytological slides. Methods: Genomic DNA (gDNA) of 156 samples obtained from tumour resection or endobronchial/transbronchial biopsies (n=81) and mediastinal lymph nodes (MLN) obtained by endobronchial ultrasound with transbronchial needle aspiration (EBUS-TBNA) (n=75) between 2011 and 2019 were extracted with the GeneR- ead® DNA FFPE kit (Qiagen, Hilden, Germany). Of these sam- ples, 61 were from FFPE tissue and 95 from scraped histological/ cytological slides. Results: The average gDNA yield obtained from FFPE samples was 9.45 ng/μL (0.051-53 ng/ μL) for primary tumours (PT) and 2.96 ng/μL (0.04 to 51 ng/ μL) for MLN. In PT samples extracted from scraped histological slides, the average yield was 12.17 ng/ μL (0.051 to 60 ng/ μL) and in samples of MLN from cytological slides was 18.37 ng/μL (0.057 to 217ng/ μL). Conclusion: To obtain gDNA from scarce FFPE samples is an arduous process, especially in those with low cellularity, archived for more than 5 years, as used in this study. We observed an improvement in gDNA yield from histological and cytological slides regards to FFPE samples. The use of samples obtained from scraped slides seems to be an effi- cient tool to improve the gDNA yield for application in genomic tests. Funding: FAPESP 2019-04416-3 E-PS-15-011 OpenHRD - an open source platform for calculation of homologous recombination deficiency scores from OncoScan microarrays A. Lara Gutierrez*, S. Sauer, K. Kashofer *Medical University of Graz, Austria Background & objectives: Homologous recombination deficiency is an important biomarker for PARP inhibitor therapy in ovarian cancer. Existing open-source tools lack standardized parameters and require IT expertise. This project aims to establish a web-based bioinformatic analysis system for robust assessment of genomic instability. Methods: OncoScan-CNV data was obtained from DNA of formalin fixed embedded specimens. The analysis platform uses raw OncoScan microarray images and applies several open-source pipelines such as "Easy Copy Number", "Oncoscan_tools", "Allele- specific copy number analysis of tumours" for the segmentation analysis. HRD calculation was performed by combination of custom R-scripts and the "HRDscore" pipeline. Additionally a commercial diagnostic HRD-test was obtained. Results: The analysis comparison between several pipelines revealed that the combination of "Easy Copy Number" (EaCoN), and "Allele-specific copy number analysis of tumours" (ASCAT) was the best performing setup for raw data normalization and seg- mentation, providing similar results to the proprietary Chromo- some Analysis Suite software (ChAS, Thermo Fisher). The OpenHRD pipeline for homologous recombination deficiency (HRD) calculation is a compilation of EaCoN, ASCAT, our custom R-scripts and "HRDscore". It is run with Django Python and Celery Task Queue web frameworks. Subsequently, the application of the fully automated OpenHRD pipeline with standardized parameters revealed a high correlation to results obtained with the commercial Myriad MychoiceDX test in a cohort of ovarian cancer. Conclusion: Several studies have shown that HRD is a reliable marker for treatment decisions in PARPi therapy. In this study we provided a simple, standardized, web based system to analyse HRD, which is able to process the microarray scan raw image data and generate reliable HRD score values. Initial validation of the HRD platform has been performed in ovarian cancer, and extension to prostate and pancreatic cancer is ongoing. Funding: This research was kindly supported by AstraZeneca Aus- tria GmbH E-PS-15-013 Evaluation of PD-L1 expression in various formalin-fixed par- affin embedded tumour tissue samples using SP263, SP142 and QR1 antibody clones K. Kubelka-Sabit*, D. Jashar, V. Filipovski, M. Kondeva *CH Acibadem Sistina, University Goce Delchev, North Macedonia Background & objectives: Cancer cells can avoid immune destruction through the inhibitory ligand PD-L1. PD-1 is a surface cell receptor, part of the immunoglobulin family. Its ligand PD-L1 is expressed by tumour cells and stromal tumour infiltrating lymphocytes (TIL). Methods: Forty-four cancer cases were included in this study (24 triple-negative breast cancers (TNBC), 10 non-small cell lung can- cer (NSCLC) and 10 malignant melanoma cases). Three clones of monoclonal primary antibodies were compared: QR1 (Quartett), SP 142 and SP263 (Ventana). For visualization, ultraView Universal DAB Detection Kit from Ventana was used on an automated plat- form for immunohistochemical staining Ventana BenchMark GX. Results: Comparing the sensitivity of two different clones on same tissue samples from TNBC, we found that the QR1 clone gave higher percentage of positive cells than clone SP142, but there was no statistically significant difference. Comparing the sensitivity of two different clones on same tissue samples from malignant melanoma, the SP263 clone gave higher percentage of positive cells than the QR1 clone, but again the difference was not statisti- cally significant. Comparing the sensitivity of two different clones on same tissue samples from NSCLC, we found higher percent- age of positive cells using the QR1 clone in comparison with the SP142 clone, but once again, the difference was not statistically significant. Conclusion: The three different antibody clones from two manu- facturers Ventana and Quartett, gave comparable results with no statistically significant difference in staining intensity/ percent- age of positive tumour and/or immune cells. Therefore, different PD-L1 clones from different manufacturers can potentially be used to evaluate the PD- L1 status in different tumour tissues. Due to the serious implications of the PD-L1 analysis in further treatment decisions for cancer patients, every antibody clone, staining pro- tocol and evaluation process should be carefully and meticulously validated. S307