Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer
Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more compreh...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-01-01
|
| Series: | Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-7737/13/2/88 |
| _version_ | 1797298889482567680 |
|---|---|
| author | Ricardo Roque Ilda Patrícia Ribeiro Margarida Figueiredo-Dias Charlie Gourley Isabel Marques Carreira |
| author_facet | Ricardo Roque Ilda Patrícia Ribeiro Margarida Figueiredo-Dias Charlie Gourley Isabel Marques Carreira |
| author_sort | Ricardo Roque |
| collection | DOAJ |
| description | Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data collection, and introducing new variables that can be correlated with clinical outcomes. Current NGS strategies can comprise a tumour-informed set of genes or the entire genome and detect a tumour fraction as low as 10<sup>−5</sup>. Despite some conflicting studies, there is evidence that ctDNA levels can predict the worse outcomes of ovarian cancer (OC) in both early and advanced disease. Changes in those levels can also be informative regarding treatment efficacy and tumour recurrence, capable of outperforming CA-125, currently the only universally utilised plasma biomarker in high-grade serous OC (HGSOC). Qualitative evaluation of sequencing shows that increasing copy number alterations and gene variants during treatment may correlate with a worse prognosis in HGSOC. However, following tumour clonality and emerging variants during treatment poses a more unique opportunity to define treatment response, select patients based on their emerging resistance mechanisms, like BRCA secondary mutations, and discover potential targetable variants. Sequencing of tumour biopsies and ctDNA is not always concordant, likely as a result of clonal heterogeneity, which is better captured in the plasma samples than it is in a large number of biopsies. These incoherences may reflect tumour clonality and reveal the acquired alterations that cause treatment resistance. Cell-free DNA methylation profiles can be used to distinguish OC from healthy individuals, and NGS methylation panels have been shown to have excellent diagnostic capabilities. Also, methylation signatures showed promise in explaining treatment responses, including BRCA dysfunction. ctDNA is evolving as a promising new biomarker to track tumour evolution and clonality through the treatment of early and advanced ovarian cancer, with potential applicability in prognostic prediction and treatment selection. While its role in HGSOC paves the way to clinical applicability, its potential interest in other histological subtypes of OC remains unknown. |
| first_indexed | 2024-03-07T22:41:40Z |
| format | Article |
| id | doaj.art-62f7f00011914b5f831c4c302aa6a36b |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-07T22:41:40Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-62f7f00011914b5f831c4c302aa6a36b2024-02-23T15:08:09ZengMDPI AGBiology2079-77372024-01-011328810.3390/biology13020088Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian CancerRicardo Roque0Ilda Patrícia Ribeiro1Margarida Figueiredo-Dias2Charlie Gourley3Isabel Marques Carreira4Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, PortugalCytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, PortugalFaculty of Medicine, Gynecology Department, University of Coimbra, 3004-504 Coimbra, PortugalNicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UKCytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, PortugalCirculating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data collection, and introducing new variables that can be correlated with clinical outcomes. Current NGS strategies can comprise a tumour-informed set of genes or the entire genome and detect a tumour fraction as low as 10<sup>−5</sup>. Despite some conflicting studies, there is evidence that ctDNA levels can predict the worse outcomes of ovarian cancer (OC) in both early and advanced disease. Changes in those levels can also be informative regarding treatment efficacy and tumour recurrence, capable of outperforming CA-125, currently the only universally utilised plasma biomarker in high-grade serous OC (HGSOC). Qualitative evaluation of sequencing shows that increasing copy number alterations and gene variants during treatment may correlate with a worse prognosis in HGSOC. However, following tumour clonality and emerging variants during treatment poses a more unique opportunity to define treatment response, select patients based on their emerging resistance mechanisms, like BRCA secondary mutations, and discover potential targetable variants. Sequencing of tumour biopsies and ctDNA is not always concordant, likely as a result of clonal heterogeneity, which is better captured in the plasma samples than it is in a large number of biopsies. These incoherences may reflect tumour clonality and reveal the acquired alterations that cause treatment resistance. Cell-free DNA methylation profiles can be used to distinguish OC from healthy individuals, and NGS methylation panels have been shown to have excellent diagnostic capabilities. Also, methylation signatures showed promise in explaining treatment responses, including BRCA dysfunction. ctDNA is evolving as a promising new biomarker to track tumour evolution and clonality through the treatment of early and advanced ovarian cancer, with potential applicability in prognostic prediction and treatment selection. While its role in HGSOC paves the way to clinical applicability, its potential interest in other histological subtypes of OC remains unknown.https://www.mdpi.com/2079-7737/13/2/88ovarian cancerliquid biopsycirculating tumour DNAnext-generation sequencing |
| spellingShingle | Ricardo Roque Ilda Patrícia Ribeiro Margarida Figueiredo-Dias Charlie Gourley Isabel Marques Carreira Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer Biology ovarian cancer liquid biopsy circulating tumour DNA next-generation sequencing |
| title | Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer |
| title_full | Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer |
| title_fullStr | Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer |
| title_full_unstemmed | Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer |
| title_short | Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer |
| title_sort | current applications and challenges of next generation sequencing in plasma circulating tumour dna of ovarian cancer |
| topic | ovarian cancer liquid biopsy circulating tumour DNA next-generation sequencing |
| url | https://www.mdpi.com/2079-7737/13/2/88 |
| work_keys_str_mv | AT ricardoroque currentapplicationsandchallengesofnextgenerationsequencinginplasmacirculatingtumourdnaofovariancancer AT ildapatriciaribeiro currentapplicationsandchallengesofnextgenerationsequencinginplasmacirculatingtumourdnaofovariancancer AT margaridafigueiredodias currentapplicationsandchallengesofnextgenerationsequencinginplasmacirculatingtumourdnaofovariancancer AT charliegourley currentapplicationsandchallengesofnextgenerationsequencinginplasmacirculatingtumourdnaofovariancancer AT isabelmarquescarreira currentapplicationsandchallengesofnextgenerationsequencinginplasmacirculatingtumourdnaofovariancancer |