Copy Number Variation of Circulating Tumor DNA (ctDNA) Detected Using NIPT in Neoadjuvant Chemotherapy-Treated Ovarian Cancer Patients

• DOI: 10.3389/fgene.2022.938985
• Publication Date: 2022-07-22T16:23:27Z
• Authors: Mina Sharbatoghli; Fahimeh Fattahi; Hamidreza Aboulkh...; Arvand Akbari; Setareh Akhavan; Marzieh Ebrahimi; Mohsen Asadi-Lari; Mehdi Totonchi; Zahra Madjd
• Keywords: CNVs; 0303 health sciences; 03 medical and health sciences; ovarian cancer; copy number variations; Genetics; ctDNA; QH426-470; NIPT; 3. Good health

Analysis of circulating tumor DNA (ctDNA) can be used to characterize and monitor cancers. Recently, non-invasive prenatal testing (NIPT) as a new next-generation sequencing (NGS)-based approach has been applied for detecting ctDNA. This study aimed investigate the copy number variations (CNVs) utilizing in plasma ctDNA from ovarian cancer (OC) patients who were treated with neoadjuvant chemotherapy (NAC). The samples six patients, including stages II-IV, collected during pre- post-NAC treatment that divided into NAC-sensitive NAC-resistant groups follow-up time. CNV analysis was performed using NIPT via two methods "an open-source algorithm WISECONDORX NextGENe software." Results these compared OC patients. Finally, bioinformatics tools data mining Cancer Genome Atlas (TCGA) CNVs indicated fewer changes on chromosomes before rather than are not only observed coding genes but also non-coding genes. identified, HSF1, TMEM249, MROH1, GSTT2B, ABR, NOMO2, comparison illustrated total alteration frequency is amplification, highest incidence (≥35% based TCGA data) found HSF1 chromosome (Chr) 8. Based data, survival showed significant reduction overall among chemotherapy-resistant well high expression level three sensitive (all, p < 0.0001). continued Chr8 revealed modifications prior NAC therapy, no individuals. Our findings low coverage whole-genome could identify after chemotherapy. These different -resistant highlighting potential application this patient management.