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Record W1531621676 · doi:10.1158/1538-7445.am2014-5610

Abstract 5610: Circulating tumor DNA: FOXL2 402C-G mutation can be identified in plasma from adult granulosa cell tumor patients with recurrent disease

2014· article· en· W1531621676 on OpenAlexaff
Melissa K. McConechy, Anniina Färkkilä, Winnie Yang, Noora Andersson, Ying Ng, Leila Unkila‐Kallio, Jessica N. McAlpine, C. Blake Gilks, Mikko Anttonen, David G. Huntsman

Bibliographic record

VenueCancer Research · 2014
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicCancer Genomics and Diagnostics
Canadian institutionsBC Cancer AgencyUniversity of British Columbia
Fundersnot available
KeywordsDigital polymerase chain reactionMutationTaqManPrimer (cosmetics)BiologyMolecular biologyGenotypingSomatic cellCancer researchPolymerase chain reactionMedicineGeneticsGenotypeGeneChemistry

Abstract

fetched live from OpenAlex

Abstract Adult granulosa cell tumors (aGCT) represent 2-5% of all ovarian cancers. Most patients present with stage 1 disease and have a good prognosis, however up to 30% of aGCTs will recur (median=7 years), and 50% of these patients die of aGCT. These women require prolonged surveillance for serum tumor markers. In recent years, the detection of somatic mutations in free circulating tumor DNA (ctDNA) in plasma has been investigated as a non-invasive method to diagnose and monitor different cancers. The analysis of plasma DNA, which is a mixture of ctDNA and normal DNA, can be extended to aGCT patients that are at risk to recur, which would involve testing for the presence of the FOXL2 402C->G mutation. This mutation is known to be present in 95% of aGCTs; FOXL2 mutation testing is currently being used to aid in tumor differential diagnosis. FOXL2 mutations in free ctDNA can be detected in the plasma of aGCT patients and may aid in diagnosis and monitoring of patients. Plasma samples (1-2mL) were extracted for ctDNA using the Qiagen circulating nucleic acid kit. The ctDNA was preamplified for 10 cycles using the C134W FOXL2 Taqman primer/probe, ABI genotyping mix, followed by a 1:5 dilution. Preamplified ctDNA products were subjected to droplet formation and counted on the Raindance Raindrop digital PCR instruments to detect wild type or mutant alleles. All analysis was performed using the Raindrop Analyst V2 software. Of two aGCT cases tested, both showed detectable plasma ctDNA FOXL2 mutations using Raindance Raindrop digital PCR. For case 1, plasma from two subsequent time points were tested. The FOXL2 mutation was not detected in the first time point, 12 years from diagnosis, at which time the patient had relapsed disease and underwent chemotherapy. Surgery for extensive tumor burden was performed at the second time point, 6 months later, and a 16% allelic frequency of the FOXL2 mutation was detected in the plasma DNA. For case 2, two plasma samples were tested, the first from the primary surgery, the second at relapse two years later. The FOXL2 ctDNA mutation was present at 6% in the recurrent plasma sample, but not at primary diagnosis. The recurrence was originally diagnosed as a high-grade serous ovarian carcinoma, however the tumor was FOXL2 mutation positive and later re-diagnosed as a relapsed aGCT. The analysis of two cases of aGCT plasma suggests that the pathognomonic aGCT associated FOXL2 mutation is present in recurrent disease. We also show that the presence of a ctDNA FOXL2 mutation confirms the differential diagnosis of recurrent disease. This is the first proof of principle that plasma DNA may be a non-invasive method to detect recurrent aGCT. Plasma samples from a large prospective cohort with primary or recurrent aGCT will be analyzed to test the sensitive of FOXL2 ctDNA to predict tumor burden. These studies will be imperative to determine the utilization of the plasma FOXL2 ctDNA mutation in routine diagnosis. Citation Format: Melissa K. McConechy, Anniina Farkkila, Winnie Yang, Noora Andersson, Ying Ng, Leila Unkila-Kallio, Jessica N. McAlpine, Blake Gilks, Mikko Anttonen, David G. Huntsman. Circulating tumor DNA: FOXL2 402C-G mutation can be identified in plasma from adult granulosa cell tumor patients with recurrent disease. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5610. doi:10.1158/1538-7445.AM2014-5610

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.001
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Observational · Consensus signal: Observational
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.003
Threshold uncertainty score0.011

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0000.001
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0010.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0030.001

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.019
GPT teacher head0.297
Teacher spread0.278 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designObservational
Domainnot available
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations1
Published2014
Admission routes1
Has abstractyes

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