Publisher Correction: Massively parallel sequencing of cell-free DNA in plasma for detecting gynaecological tumour-associated copy number alteration

Nakabayashi, Makoto; Kawashima, Akitsugu; Yasuhara, Rika; Hayakawa, Yosuke; Miyamoto, Shingo; Iizuka, Chiaki; Sekizawa, Akihiko

doi:10.1038/s41598-018-34168-2

Cited by 3 publications

(1 citation statement)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A recent study using sequencing to analyze plasma cfDNA in patients with known cancers found evidence of abnormal cfDNA patterns in more than 80% of metastatic solid tumor cases and 50% of localized cancers . Our previous study also demonstrated that the incidence of copy number alterations (CNAs) is higher in advanced ovarian and uterine endometrial cancer than that in the corresponding early cancer; moreover, progression‐free survival and overall survival in cases with CNAs were shorter than those without CNAs . Thus, CNAs could be detected in a definite proportion of pregnant women with malignancies, and the alteration might affect the accuracy of NIPT.…”

Section: Discussionmentioning

confidence: 93%

A case of Ewing's sarcoma identified via noninvasive prenatal testing

Miyagami

Matsuoka

Tokunaka

et al. 2020

Clinical Case Reports

Self Cite

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 93%

A case of Ewing's sarcoma identified via noninvasive prenatal testing

Miyagami

Matsuoka

Tokunaka

et al. 2020

Clinical Case Reports

Self Cite

View full text Add to dashboard Cite

show abstract

Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA

Mauger

Horgues

Pierre-Jean

et al. 2020

Sci Rep

View full text Add to dashboard Cite

circulating cell-free DnA (ccfDnA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e., SnVs, cnVs and inDeLS) on ccfDnA that can be used as clinical biomarkers. In this article, five WGS methods were compared: ThruPLEX Plasma-seq, QIAseq cfDNA All-in-One, NEXTFLEX Cell Free DNA-seq, Accel-NGS 2 S PCR FREE DNA and Accel-NGS 2 S PLUS DNA. The Accel PCR-free kit did not produce enough material for sequencing. The other kits had significant common number of SNVs, INDELs and CNVs and showed similar results for SnVs and cnVs. the detection of variants and genomic signatures depends more upon the type of plasma sample rather than the WGS method used. Accel detected several variants not observed by the other kits. ThruPLEX seemed to identify more low-abundant SNVs and SNV signatures were similar to signatures observed with the QIAseq kit. Accel and NEXTFLEX had similar CNV and SNV signatures. These results demonstrate the importance of establishing a standardized workflow for identifying noninvasive candidate biomarkers. Moreover, the combination of variants discovered in ccfDNA using WGS has the potential to identify enrichment pathways, while the analysis of signatures could identify new subgroups of patients. The analysis of circulating cell-free DNA (ccfDNA) from plasma bears great promise for diagnosis, prognosis and monitoring the treatment of cancer 1. In the context of precision medicine, the identification of novel non-invasive biomarkers is crucial but the analysis of ccfDNA is still a challenge. Indeed, ccfDNA is low concentrated, highly fragmented and the abundance depends on the type and the stage of cancer and the pre-analytical steps 2,3-5. Due to its properties, a complete workflow for sample preparation, library preparation, sequencing and data analysis should be performed to ensure standardization of sample analysis especially in the case of clinical cohorts 4,6,7. Pre-analytical steps including sample collection, storage, processing and extraction were compared to maximize the yield and size of ccfDNA 3,5,8-12. Furthermore, size analysis and quantification methods were used to evaluate the extracted ccfDNA. Sensitive approaches such as quantitative PCR, digital PCR, mass spectrometry and next generation sequencing (NGS) are commonly applied to analyze extracted ccfDNA 2. With the improvement of NGS analysis, whole-genome sequencing (WGS) is a great approach to identify all types of genomic alteration including single nucleotide variant (SNV), insertion and deletion (INDEL), copy number variation (CNV) and structural variant (SV) for the identification of candidate biomarkers in cancer 13. In particular, several specific and sensitive low-coverage sequencing approaches have been applied for the analysis of CNVs from cancer plasma samples 14-20. In addition, recent WGS studies allowed the analysis of nucleosome

show abstract

Circulating tumor DNA as a biomarker for predicting progression-free survival and overall survival in patients with epithelial ovarian cancer: a systematic review and meta-analysis

Taliento,

Morciano,

Nero

et al. 2024

Int J Gynecol Cancer

View full text Add to dashboard Cite

ObjectivesCirculating tumor DNA (ctDNA) is emerging as a potential prognostic biomarker in multiple tumor types. However, despite the many studies available on small series of patients with ovarian cancer, a recent systematic review and meta-analysis is lacking. The objective of this study was to determine the association of ctDNA with progression-free-survival and overall survival in patients with epithelial ovarian cancer.MethodsAn electronic search was conducted using PubMed (MEDLINE), Embase, CENTRAL (Cochrane Library), and CINAHL-Complete from January 2000 to September 15, 2023. To be included in the analysis the studies had to meet the following pre-specified inclusion criteria: (1) evaluable ctDNA; (2) progression-free-survival and overall survival reported as hazard ratio (HR); and (3) the patient population had epithelial ovarian cancer at the time of ctDNA detection. We evaluated the association of ctDNA with progression-free survival and overall survival. Secondary outcomes focused on sub-group analysis of genomic alterations and international Federation of Gynecology and Obstetrics (FIGO) stage.ResultsA total of 26 studies reporting on 1696 patients with epithelial ovarian cancer were included. The overall concordance rate between plasma-based and tissue-based analyses was approximately 62%. We found that a high level of ctDNA in epithelial ovarian cancer was associated with worse progression-free survival (HR 5.31, 95% CI 2.14 to 13.17, p<0.001) and overall survival (HR 2.98, 95% CI 1.86 to 4.76, p<0.0001). The sub-group analysis showed a greater than threefold increase in the risk of relapse in patients with positive HOXA9 meth-ctDNA (HR 3.84, 95% CI 1.57 to 9.41, p=0.003).ConclusionsctDNA was significantly associated with worse progression-free survival and overall survival in patients with epithelial ovarian cancer. Further prospective studies are needed.PROSPERO registration numberCRD42023469390.

show abstract

Publisher Correction: Massively parallel sequencing of cell-free DNA in plasma for detecting gynaecological tumour-associated copy number alteration

Abstract: A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Cited by 3 publications

References 0 publications

A case of Ewing's sarcoma identified via noninvasive prenatal testing

A case of Ewing's sarcoma identified via noninvasive prenatal testing

Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA

Circulating tumor DNA as a biomarker for predicting progression-free survival and overall survival in patients with epithelial ovarian cancer: a systematic review and meta-analysis

Contact Info

Product

Resources

About