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Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis

SIMPLE SUMMARY: Despite the progress in diagnostics and therapeutics, epithelial ovarian cancer (EOC) remains a fatal disease. Using shallow whole-genome sequencing (WGS), we identified copy number variations (CNVs). In addition, we quantified chromosomal instability using genome-wide instability an...

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Detalles Bibliográficos
Autores principales: Bak, Seong Eun, Kim, Hanwool, Ho, Jung Yoon, Cho, Eun-Hae, Lee, Junnam, Youn, Sung Min, Park, Seong-Woo, Han, Mi-Ryung, Hur, Soo Young, Lee, Sung Jong, Choi, Youn Jin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9857189/
https://www.ncbi.nlm.nih.gov/pubmed/36672479
http://dx.doi.org/10.3390/cancers15020530
Descripción
Sumario:SIMPLE SUMMARY: Despite the progress in diagnostics and therapeutics, epithelial ovarian cancer (EOC) remains a fatal disease. Using shallow whole-genome sequencing (WGS), we identified copy number variations (CNVs). In addition, we quantified chromosomal instability using genome-wide instability and found that it could detect newly diagnosed EOC. In addition, the data showed RAB25 amplification (alone or with CA125), and disease-free survival and overall survival. Our data demonstrated that cfDNA, detected by shallow WGS, represents a potential tool for diagnosing EOC and predicting its prognosis. ABSTRACT: Despite the progress in diagnostics and therapeutics, epithelial ovarian cancer (EOC) remains a fatal disease. Using shallow whole-genome sequencing of plasma cell-free DNA (cfDNA), we investigated biomarkers that could detect EOC and predict survival. Plasma cfDNA from 40 EOC patients and 20 healthy subjects were analyzed by shallow whole-genome sequencing (WGS) to identify copy number variations (CNVs) and determine the Z-scores of genes. In addition, we also calculated the genome-wide scores (Gi scores) to quantify chromosomal instability. We found that the Gi scores could distinguish EOC patients from healthy subjects and identify various EOC histological subtypes (e.g., high-grade serous carcinoma). In addition, we characterized EOC CNVs and demonstrated a relationship between RAB25 amplification (alone or with CA125), and disease-free survival and overall survival. This study identified RAB25 amplification as a predictor of EOC patient survival. Moreover, we showed that Gi scores could detect EOC. These data demonstrated that cfDNA, detected by shallow WGS, represented a potential tool for diagnosing EOC and predicting its prognosis.