Cargando…

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...

Descripción completa

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
_version_ 1784873810833440768
author 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
author_facet 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
author_sort Bak, Seong Eun
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9857189
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-98571892023-01-21 Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis 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 Cancers (Basel) Article 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. MDPI 2023-01-15 /pmc/articles/PMC9857189/ /pubmed/36672479 http://dx.doi.org/10.3390/cancers15020530 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
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
Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis
title Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis
title_full Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis
title_fullStr Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis
title_full_unstemmed Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis
title_short Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis
title_sort shallow whole-genome sequencing of cell-free dna (cfdna) detects epithelial ovarian cancer and predicts patient prognosis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9857189/
https://www.ncbi.nlm.nih.gov/pubmed/36672479
http://dx.doi.org/10.3390/cancers15020530
work_keys_str_mv AT bakseongeun shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT kimhanwool shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT hojungyoon shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT choeunhae shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT leejunnam shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT younsungmin shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT parkseongwoo shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT hanmiryung shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT hursooyoung shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT leesungjong shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis
AT choiyounjin shallowwholegenomesequencingofcellfreednacfdnadetectsepithelialovariancancerandpredictspatientprognosis