Diagnostic potential of tumor DNA from ovarian cyst fluid

Wang, Yuxuan; Sundfeldt, Karin; Mateoiu, Constantina; Shih, Ie Ming; Kurman, Robert J.; Schaefer, Joy; Silliman, Natalie; Kinde, Isaac; Springer, Simeon; Foote, Michael B.; Kristjánsdóttir, Björg; James, Nathan T.; Kinzler, Kenneth W.; Papadopoulos, Nickolas; Díaz, Luis A.; Vogelstein, Bert

doi:10.7554/elife.15175

Cited by 32 publications

(27 citation statements)

References 62 publications

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“…Benign and malignant cysts contain statistically different levels of protein C inhibitor, apolipoprotein C‐I and C‐III, serum amyloid 4, and transthyretin . Recently, the evaluation of DNA from ovarian cyst fluid using a multiplex polymerase chain reaction‐based assay identified tumor‐specific genetic mutations not found in benign tumors or nonneoplastic cases . The mutated genes include TP53, BRAF, and KRAS, among others …”

Section: Discussionsupporting

confidence: 61%

“…Recently, the evaluation of DNA from ovarian cyst fluid using a multiplex polymerase chain reaction‐based assay identified tumor‐specific genetic mutations not found in benign tumors or nonneoplastic cases . The mutated genes include TP53, BRAF, and KRAS, among others …”

Section: Discussionsupporting

confidence: 61%

“…polymerase chain reaction-based assay identified tumorspecific genetic mutations not found in benign tumors or nonneoplastic cases. 20 The mutated genes include TP53, BRAF, and KRAS, among others. 20 The approach used to triage ovarian cyst FNAs at the study institution, as shown in the data presented herein, is that younger patients with smaller lesions tend to be evaluated with FNA alone, without a surgical biopsy or surgical resection.…”

Section: Cancer Cytopathologymentioning

confidence: 99%

“…20 The mutated genes include TP53, BRAF, and KRAS, among others. 20 The approach used to triage ovarian cyst FNAs at the study institution, as shown in the data presented herein, is that younger patients with smaller lesions tend to be evaluated with FNA alone, without a surgical biopsy or surgical resection. Given the low prevalence of malignant lesions being aspirated, this appears to be effective.…”

Section: Cancer Cytopathologymentioning

confidence: 99%

See 3 more Smart Citations

Performance of ovarian cyst fluid fine‐needle aspiration cytology

Zhou

Levinson

Rosenthal

et al. 2017

Cancer Cytopathology

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show abstract

Section: Discussionsupporting

confidence: 61%

Section: Discussionsupporting

confidence: 61%

Section: Cancer Cytopathologymentioning

confidence: 99%

Section: Cancer Cytopathologymentioning

confidence: 99%

See 2 more Smart Citations

Performance of ovarian cyst fluid fine‐needle aspiration cytology

Zhou

Levinson

Rosenthal

et al. 2017

Cancer Cytopathology

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show abstract

“…For example, it has recently been shown that liquid biopsies of blood can detect minimal amounts of disease in patients with early-stage colorectal cancers, thereby providing evidence that could substantially affect their survival (7). Other studies have shown that circulating tumor DNA (ctDNA) can be detected in the blood of patients with other malignancies, as well as in other bodily fluids such as pancreatic cysts, Pap smears, and saliva (8)(9)(10)(11)(12)(13)(14)(15)(16).…”

mentioning

confidence: 99%

Bisulfite-converted duplexes for the strand-specific detection and quantification of rare mutations

Mattox

Wang

Springer

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The identification of mutations that are present at low frequencies in clinical samples is an essential component of precision medicine. The development of molecular barcoding for next-generation sequencing has greatly enhanced the sensitivity of detecting such mutations by massively parallel sequencing. However, further improvements in specificity would be useful for a variety of applications. We herein describe a technology (BiSeqS) that can increase the specificity of sequencing by at least two orders of magnitude over and above that achieved with molecular barcoding and can be applied to any massively parallel sequencing instrument. BiSeqS employs bisulfite treatment to distinguish the two strands of molecularly barcoded DNA; its specificity arises from the requirement for the same mutation to be identified in both strands. Because no library preparation is required, the technology permits very efficient use of the template DNA as well as sequence reads, which are nearly all confined to the amplicons of interest. Such efficiency is critical for clinical samples, such as plasma, in which only tiny amounts of DNA are often available. We show here that BiSeqS can be applied to evaluate transversions, as well as small insertions or deletions, and can reliably detect one mutation among >10,000 wild-type molecules.next-generation sequencing | bisulfite sequencing | strand-specificity | polymerase chain reaction | mutation

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Identification of DNA mutations in gastric washes from gastric adenocarcinoma patients: Possible implications for liquid biopsies and patient follow‐up

Pizzi

Bartelli

Pelosof

et al. 2019

Intl Journal of Cancer

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Whereas cancer patients have benefited from liquid biopsies, the scenario for gastric adenocarcinoma (GAC) is still dismal. We used next‐generation deep sequencing of TP53—a highly mutated and informative gene in GAC—to assess mutations in tumor biopsies, plasma (PL) and stomach fluids (gastric wash—GW). We evaluated their potential to reveal tumor‐derived mutations, useful for monitoring mutational dynamics at diagnosis, progression and treatment. Exon‐capture libraries were constructed from 46 patients including tumor biopsies, GW and PL pre and post‐treatment (196 samples), with high vertical coverage >8,000×. At diagnosis, we detected TP53 mutations in 15/46 biopsies (32.6%), 7/46 GW‐ (15.2%) and 6/46 PL‐samples (13%). Biopsies and GW were concordant in 38/46 cases (82.6%) for the presence/absence of mutations and, furthermore, four GW‐exclusive mutations were identified, suggesting tumor heterogeneity. Considering the combined analysis of GW and PL, TP53 mutations found in biopsies were also identified in 9/15 (60%) of cases, the highest detection level reported for GAC. Our study indicates that GW could be useful to track DNA alterations, especially if anchored to a comprehensive gene‐panel designed for this malignancy.

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Diagnostic potential of tumor DNA from ovarian cyst fluid

Cited by 32 publications

References 62 publications

Performance of ovarian cyst fluid fine‐needle aspiration cytology

Performance of ovarian cyst fluid fine‐needle aspiration cytology

Bisulfite-converted duplexes for the strand-specific detection and quantification of rare mutations

Identification of DNA mutations in gastric washes from gastric adenocarcinoma patients: Possible implications for liquid biopsies and patient follow‐up

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