Abstract 7312: Construction of a gene panel for liquid biopsy-based diagnostics of gynecologic cancer
Authors: Schumacher Sara , Carlsson Therese , Lauesgaard Jacob Malchau , Linder Anna , Widjaja Amanda Olsson , Sundfeldt Karin 
Published: March 2024

Background: Ovarian carcinoma (OC) is the leading cause of death from gynecologic cancers mainly due to late detection, where most patients are diagnosed at advanced stages (51% in stage III; 29% in stage IV). Despite an overall more favorable prognosis, endometrial carcinoma (EC) is the most common gynecologic cancer, with an increasing incidence and where some subtypes are associated with a poor prognosis. Identification of DNA mutations from precancerous lesions or early-stage OC and EC would allow for early intervention. Liquid biopsies through routine sampling such as endocervical sampling, or blood collection for isolation and analysis of ctDNA have previously been assessed for their use in detection of OC and EC. These studies have provided evidence that tumor-derived mutations can be detected in endocervical samples, supporting endocervical liquid biopsies as a potential source of ctDNA. Herein, we aimed to construct a diagnostic gene panel corresponding to common mutation profiles of OC and EC to detect early-stage malignancy through a non-invasive approach.

Methods: Using the NGS-method, Simple multiplexed PCR-based barcoding of DNA for sensitive mutation detection using sequencing (SiMSen-Seq), a gene panel was constructed targeting hotspot mutations in known OC- and EC-associated genes. Hotspots were identified using the Catalogue of Somatic Mutations in Cancer (COSMIC) database or retrieved from the literature and assays were designed for amplification of short DNA fragments. Precise assay development was carried out including multiple steps of careful validation to ensure high specificity and efficient amplification. Individual assays were validated in multiple steps using qPCR and fragment analysis.

Results: The gene panel was designed as two non-overlapping subunits for comprehensive diagnosis of OC and EC. The two constructed multiplexes, together composed of 125 single assays target genomic regions in 34 EC and OC-associated genes e.g., PTEN, TP53, PIK3CA and CTNNB1. Included assays had a median amplicon size of 92 bp (range 57-111 bp). Both multiplexes displayed good performance with distinguishable libraries at low DNA input (10 ng). Validation of individual assays showed high specificity and efficient amplification where &gt;80% of assays displayed a sequencing coverage &gt;500 UMI counts at a consensus depth of 3. Patient coverage calculations of COSMIC data suggested comparable coverage as similar published approaches.

Conclusion: The results suggest that the constructed gene panel has great potential to detect mutations in liquid biopsies collected from the gynecologic tract, despite low tumor DNA levels. Validation of the two multiplexes by fragment analysis and sequencing showed high performance, hence, prospective for the approaching sequencing of liquid biopsies.

Citation Format: Sara Schumacher, Therese Carlsson, Jacob Malchau Lauesgaard, Anna Linder, Amanda Olsson Widjaja, Karin Sundfeldt. Construction of a gene panel for liquid biopsy-based diagnostics of gynecologic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7312.