scholarly journals Circulating tumor DNA (ctDNA) detection is associated with shorter progression-free survival in advanced melanoma patients

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Gabriella Taques Marczynski ◽  
Ana Carolina Laus ◽  
Mariana Bisarro dos Reis ◽  
Rui Manuel Reis ◽  
Vinicius de Lima Vazquez

Abstract BRAF, NRAS and TERT mutations occur in more than 2/3 of melanomas. Its detection in patient’s blood, as circulating tumor DNA (ctDNA), represents a possibility for identification and monitoring of metastatic disease. We proposed to standardize a liquid biopsy platform to identify hotspot mutations in BRAF, NRAS and TERT in plasma samples from advanced melanoma patients and investigate whether it was associated to clinical outcome. Firstly, we performed digital polymerase chain reaction using tumor cell lines for validation and determination of limit of detection (LOD) of each assay and screened plasma samples from healthy individuals to determine the limit of blank (LOB). Then, we selected 19 stage III and IV patients and determined the somatic mutations status in tumor tissue and track them in patients’ plasma. We established a specific and sensitive methodology with a LOD ranging from 0.13 to 0.37%, and LOB ranging from of 0 to 5.201 copies/reaction. Somatic mutations occurred in 17/19 (89%) patients, of whom seven (41%) had ctDNA detectable their paired plasma. ctDNA detection was associated with shorter progression free survival (p = 0.01). In conclusion, our data support the use of ctDNA as prognosis biomarker, suggesting that patients with detectable levels have an unfavorable outcome.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e16799-e16799
Author(s):  
Liu Yang ◽  
Jiahong Jiang ◽  
Song Ye ◽  
Yaping Xu ◽  
Dongsheng Huang

e16799 Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer death, partly due to the high recurrence rates for patients with resectable PDAC. Current postoperative surveillance methods including monitoring of clinical symptoms, tumor markers and CT imaging, lack sensitivity and specificity to identify minimal residual disease (MRD). Methods: We investigated whether the detection of circulating tumor DNA (ctDNA) could identify MRD and predict relapse in postoperative patients with PDAC. In this study, we performed panel-captured sequencing to detect somatic mutations. Matched tissue samples were obtained to verify mutation. Results: A total of 27 patients and 65 plasma samples were included. Among the somatic mutations, KRAS and TP53 were the most recurrent genes in both tissue and plasma samples. The detectable rate of ctDNA increased with the stage of PDAC. The maximal variant allele fraction (VAF) of ctDNA had a positive correlation with tumor largest diameter (p = 0.0101). Patients with ctDNA-positive status postoperatively had a markedly reduced disease-free survival (DFS) compared to those with ctDNA-negative status (HR, 5.20; p = 0.019). Positive vascular invasion significantly influenced disease-free survival (DFS) (p = 0.036), and positive postoperative ctDNA status was an independent prognostic factor for DFS (HR = 3.60; 95% CI, 1.15-11.28; p = 0.028). Conclusions: Postoperative ctDNA detection provides strong evidence of MRD and identifies patients with a high risk of relapse. ctDNA detection is a promising approach for personalized patient management during postoperative follow-up.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1600-1600
Author(s):  
Charles Macaulay ◽  
Stefan Alig ◽  
David M. Kurtz ◽  
Michael C. Jin ◽  
Stephen Opat ◽  
...  

Background: While the majority of diffuse large B-cell lymphoma (DLBCL) patients are cured with R-CHOP immunochemotherapy, a significant proportion of patients still experience disease relapse. Studies using interim PET (iPET) to select patients for therapy intensification have failed to improve survival, at least partially, due to imperfect risk stratification. Circulating tumor DNA (ctDNA) is an emerging biomarker in lymphoma and ctDNA dynamics early in therapy have been shown to predict treatment outcomes in DLBCL (Kurtz, JCO 2018). Here, we assess the utility of interim ctDNA after 3 cycles of front-line therapy, in the context of standardized interim PET/CT imaging and PET-driven adaptive therapy. Methods: We quantified ctDNA levels using Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) in plasma samples collected before treatment and prior to cycle 4 in 39 patients with de novo DLBCL. 28 patients were from the NHL21 trial of the Australasian Leukaemia Lymphoma Group, in which patients initially received R-CHOP14 as frontline therapy (Hertzberg, Haem 2017). Patients with positive iPET after cycle 4 were escalated to R-ICE (rituximab, ifosfamide, carboplatin, etoposide) followed by 90Y-ibritumomab tiuxetan-BEAM (BCNU, etoposide, cytarabine, melphalan) and autologous stem cell transplant (ASCT). iPET negative patients continued R-CHOP14 for a total of 6 cycles. iPET was evaluated centrally by 2 nuclear imaging specialists according to the International Harmonization Project (IHP) criteria. An additional group of 11 patients received 6 cycles of R-CHOP as standard therapy at Stanford University. All survival analyses are calculated from date of diagnosis. Matched germline DNA was sequenced in 28/39 cases and all samples were uniformly processed at Stanford. Results: Median follow-up for progression-free survival (PFS) for the patients from the NHL21 cohort was 2.6 years [95%CI 2.23; 2.97]. Within the 28 NHL21 patients evaluated, mean baseline metabolic tumor volume was 898.76 cm3(+/- 112.01). Of the 28 patients with interim PET data, 10 were iPET-positive. Agnostic to ctDNA detection, the 2 year mean progression free survival (PFS) for these 10 patients was 60.0% [95% CI 36.2; 99.5%] as compared to 66.7% [95% CI 48.1%; 92.4%] within the iPET-negative group (Hazard Ratio (HR) 1.649 [95% CI 0.50; 5.4], p=0.4, Fig 1A). Within the 39 patients monitored across both cohorts, 17 patients possessed detectable disease by ctDNA at C4D1 with a mean disease burden of 3.59 haploid genome equivalents per milliliter of plasma (hGE/mL, +/- 1.23). Plasma genotyping within the 28 patients from the NHL21 cohort discovered an average of 112.9 single nucleotide variants (SNVs) which were then used to monitor plasma samples at the C4D1 timepoint, comparable to a broader cohort of NHL cases previously described (Kurtz, JCO2018). 2-year PFS of the 22 patients with undetectable disease as assessed by ctDNA at C4D1 was 81.82 [95% CI 67.2; 99.6] compared to 47.1% within the 17 patients with detectable ctDNA [95% CI 28.4; 77.9] (HR 4.42 [95% CI 1.32; 13.76],p=0.006, Fig. 1B). Detection of ctDNA at C4D1 also has a prognostic value for overall survival (p=0.02, Fig. 1C). iPET concordance with with C4D1 ctDNA-positivity was 50% and within the 18 patients who were iPET-negative as part of the NHL21 study and did not receive therapy escalation, 9 patients with undetectable disease by ctDNA demonstrated 88.9% 2-year PFS [95% CI 70.6; 1.00] compared to 44.4% [95% CI 21.4; 92.3] for the 9 patients with detectable ctDNA (p=0.03, Fig. 1D). Conclusions: Late in the course of DLBCL therapy, ctDNA carries promising value as a biomarker for stratifying predicted patient response to therapy as evidenced by additional detection of additional 50% detection of relapsing cases not categorized as iPET-positive. Data from additional patients and relationships between ctDNA response as measured by EMR (C2D1), MMR (C3D1), and C4D1 will be presented at the meeting. Disclosures Kurtz: Roche: Consultancy. Opat:Gilead: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; AbbVie: Consultancy, Honoraria, Research Funding; Mundipharma: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Beigene: Research Funding; Pharmacyclics LLC, an AbbVie Company: Research Funding; Amgen: Research Funding; Merck: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Epizyme: Research Funding; CSL: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Consultancy, Research Funding; Novartis: Consultancy; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Hertzberg:BMS: Honoraria; MSD: Consultancy; Roche: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Janssen: Consultancy. Gandhi:Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Honoraria; Roche: Honoraria, Other: Travel Support; Merck: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Gilead: Honoraria, Research Funding; Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees, Research Funding. Diehn:BioNTech: Consultancy; Novartis: Consultancy; AstraZeneca: Consultancy; Quanticell: Consultancy; Roche: Consultancy. Alizadeh:Pfizer: Research Funding; Chugai: Consultancy; Celgene: Consultancy; Gilead: Consultancy; Pharmacyclics: Consultancy; Janssen: Consultancy; Genentech: Consultancy; Roche: Consultancy.


2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Weiwei Feng ◽  
Nan Jia ◽  
Haining Jiao ◽  
Jun Chen ◽  
Yan Chen ◽  
...  

Abstract Background Currently, there is no reliable blood-based marker to track tumor recurrence in endometrial cancer (EC) patients. Liquid biopsies, specifically, circulating tumor DNA (ctDNA) analysis emerged as a way to monitor tumor metastasis. The objective of this study was to examine the feasibility of ctDNA in recurrence surveillance and prognostic evaluation of high-risk EC. Methods Tumor tissues from nine high-risk EC patients were collected during primary surgery and tumor DNA was subjected to next generation sequencing to obtain the initial mutation spectrum using a 78 cancer-associated gene panel. Baseline and serial post-operative plasma samples were collected and droplet digital PCR (ddPCR) assays for patient-specific mutations were developed to track the mutations in the ctDNA in serial plasma samples. Log-rank test was used to assess the association between detection of ctDNA before or after surgery and disease-free survival. Results Somatic mutations were identified in all of the cases. The most frequent mutated genes were PTEN, FAT4, ARID1A, TP53, ZFHX3, ATM, and FBXW7. For each patient, personalized ddPCR assays were designed for one-to-three high-frequent mutations. DdPCR analysis and tumor panel sequencing had a high level of agreement in the assessment of the mutant allele fractions in baseline tumor tissue DNA. CtDNA was detected in 67% (6 of 9) of baseline plasma samples, which was not predictive of disease-free survival (DFS). CtDNA was detected in serial post-operative plasma samples (ctDNA tracking) of 44% (4 of 9) of the patients, which predicted tumor relapse. The DFS was a median of 9 months (ctDNA detected) versus median DFS undefined (ctDNA not detected), with a hazard ratio of 17.43 (95% CI, 1.616–188.3). The sensitivity of post-operative ctDNA detection in estimating tumor relapse was 100% and specificity was 83.3%, which was superior to CA125 or HE4. Conclusions Personalized ctDNA detection was effective and stable for high-risk EC. CtDNA tracking in post-operative plasma is valuable for predicting tumor recurrence.


2021 ◽  
pp. 510-524
Author(s):  
Jeffrey C. Thompson ◽  
Erica L. Carpenter ◽  
Benjamin A. Silva ◽  
Jamie Rosenstein ◽  
Austin L. Chien ◽  
...  

PURPOSE Although the majority of patients with metastatic non–small-cell lung cancer (mNSCLC) lacking a detectable targetable mutation will receive pembrolizumab-based therapy in the frontline setting, predicting which patients will experience a durable clinical benefit (DCB) remains challenging. MATERIALS AND METHODS Patients with mNSCLC receiving pembrolizumab monotherapy or in combination with chemotherapy underwent a 74-gene next-generation sequencing panel on blood samples obtained at baseline and at 9 weeks. The change in circulating tumor DNA levels on-therapy (molecular response) was quantified using a ratio calculation with response defined by a > 50% decrease in mean variant allele fraction. Patient response was assessed using RECIST 1.1; DCB was defined as complete or partial response or stable disease that lasted > 6 months. Progression-free survival and overall survival were recorded. RESULTS Among 67 patients, 51 (76.1%) had > 1 variant detected at a variant allele fraction > 0.3% and thus were eligible for calculation of molecular response from paired baseline and 9-week samples. Molecular response values were significantly lower in patients with an objective radiologic response (log mean 1.25% v 27.7%, P < .001). Patients achieving a DCB had significantly lower molecular response values compared to patients with no durable benefit (log mean 3.5% v 49.4%, P < .001). Molecular responders had significantly longer progression-free survival (hazard ratio, 0.25; 95% CI, 0.13 to 0.50) and overall survival (hazard ratio, 0.27; 95% CI, 0.12 to 0.64) compared with molecular nonresponders. CONCLUSION Molecular response assessment using circulating tumor DNA may serve as a noninvasive, on-therapy predictor of response to pembrolizumab-based therapy in addition to standard of care imaging in mNSCLC. This strategy requires validation in independent prospective studies.


2018 ◽  
Vol 25 (8) ◽  
pp. 2400-2408 ◽  
Author(s):  
Joel M. Baumgartner ◽  
Victoria M. Raymond ◽  
Richard B. Lanman ◽  
Lisa Tran ◽  
Kaitlyn J. Kelly ◽  
...  

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 4491-4491
Author(s):  
Ana Jimenez-Ubieto ◽  
María Poza ◽  
Alejandro Martín-Muñoz ◽  
Sara Dorado ◽  
Yanira Heredia ◽  
...  

Abstract Background: Primary mediastinal B-cell lymphoma (PMBCL) is a rare subtype of aggressive B-cell lymphoma. Most relapses occur within the first few months resulting in a dismal prognosis; therefore, it's important to identify primary chemorefractory patients at an early stage, to improve their prognosis. Our group have demonstrated that Circulating Tumor DNA (ctDNA) detected by deep sequencing (DeepSeq) constitute a new non-invasive marker for monitoring response in follicular lymphoma (Jimenez-Ubieto A. et al. ASH 2020). CtDNA monitoring in PMBCL might help to better assess therapeutic response, correct false positive PET/CT results due to residual uptake of the mediastinum and define patients who will benefit from radiation therapy (RT). Here we analyzed the potential value of ctDNA monitoring in 11 PMBCL treated with R-DA-EPOCH between 2018-2020 in the Hospital 12 de Octubre. Methods: Genomic DNA from paraffin embedded (FFPE) lymph node biopsies were obtained from 11 PMBCL cases at diagnosis. Samples were sequenced with a short length Ampliseq Custom Panel (Thermo-Fisher) designed to cover all coding regions of 56 lymphoma specific genes with an average depth of 700x. After annotation and filtering, 5-8 somatic mutations previously described in lymphoma were selected to be screened in plasma samples. The plasma derived cfDNA was obtained from 8-16mL of peripheral blood collected in EDTA tubes and processed in less than 4h by column purification (QIAamp Circulating Nucleic Acid Kit, Qiagen). A total of 31 different plasma time-points were sequenced in triplicates. On average 78ng (9-224 ng) of cfDNA was used for the DeepSeq of the specific mutations selected in each patient. An average coverage of 236.000x per triplicate was obtained for each mutation. The detection cut-off of 1E-4 was defined based on the LOD obtained in healthy controls donors. 18F-fluorodeoxyglucose (FDG) PET/CT scans were performed on a General Electric Discovery MI Scanner at basal, interim (after 4 cycles), end of induction (EOI) and after radiotherapy (RT). Results: The median age was 33 years and 63.6% were female. Most cases (81.8%) were diagnosed with stage I or II disease and 27.3% cases present with extranodal involvement. On interim PET, 4 patients reached Complete response (CR) and 7 Partial Response (PR, DS4). At EOI, the number of CR turned to 6/11 (55%). All patients in PR at EOI (n=5) and two patients in CR (DS3) with residual mass received RT consolidation (median dose 32Gy). After RT the rate of CR was 91% (10/11). One patient progressed to a classical Hodgkin lymphoma (cHL). None of the patients in CR have relapsed after a median follow-up of 22 months. One patient died due to a mediastinal synovial sarcoma. A total of 125 somatic mutations were detected in the 11 baseline samples with a median of 8 per patient (rank 5-35). The three most frequently mutated genes were SOCS1 (73%), B2M (55%) and TNFAIP3 (46%). Despite the reduced size of our cohort, the mutational frequencies were comparable to the described by Mottok A. et al (Blood 2018, Figure 1A). The DeepSeq of six diagnosis plasma samples showed a lower Variant Read Frequency (VRF) in cfDNA. On those paired samples, 25/28 mutations were detected in plasma, with a median VRF of 2% (0-53%) vs 24% (5.5%-87%) in Lymph nodes (Figure 1B). The rest of the plasma samples corresponded to 1st cycle (n=5), 4th cycle (n=6), EOI (n=7) and after RT (n=5). After 1 cycle of chemotherapy 3/4 patients who reached CR at EOI had already undetectable ctDNA (Figure 1C). One patient with positive ctDNA after 1 cycle needed RT to convert to CR. All the CR evaluations by PET-TC who had available ctDNA data, presented undetectable ctDNA (n=9). In the EOI analysis all+ patients except the one who progressed to cHL had undetectable ctDNA. In the PR interim evaluations 2/5 had undetectable ctDNA and converted to CR at EOI. Of the three patients with detectable ctDNA, one progressed to cHL (Figure 1D) and 2 needed RT to convert to CR. Conclusions: Our results demonstrate that disease monitoring using DeepSeq of plasma ctDNA is feasible in PMBCL. Regarding prediction of relapse, the positive predictive value of ctDNA was 100%. An early ctDNA analysis (even after only one R-DA-EPOCH cycle) was able to predict patients in need of RT. Despite the DeepSeq of ctDNA could be useful to disease monitoring to prevent relapse and toxicity reduction by selecting cases in need of RT, more patients are necessary to draw meaningful conclusions. Figure 1 Figure 1. Disclosures Martín-Muñoz: Altum sequencing: Current Employment. Dorado: Altum sequencing: Current Employment. Heredia: Altum sequencing: Current Employment, Current equity holder in publicly-traded company. Rufian: Altum sequencing: Current Employment. Canales: Incyte: Consultancy; iQone: Honoraria; Takeda: Consultancy, Honoraria, Speakers Bureau; Karyopharm: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Celgene/Bristol-Myers Squibb: Consultancy, Honoraria; Sanofi: Consultancy; Eusa Pharma: Consultancy, Honoraria; Sandoz: Honoraria, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; F. Hoffmann-La Roche Ltd: Consultancy, Honoraria, Speakers Bureau; Gilead/Kite: Consultancy, Honoraria. Juarez: Altum sequencing: Current Employment. Sanchez: Altum sequencing: Current Employment. López-Muñoz: Amgen: Consultancy. Ayala: Incyte Corporation: Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astellas: Honoraria; Celgene: Honoraria. Martínez-López: Janssen, BMS, Novartis, Incyte, Roche, GSK, Pfizer: Consultancy; Roche, Novartis, Incyte, Astellas, BMS: Research Funding. Barrio: Altum sequencing: Current Employment, Current equity holder in publicly-traded company.


2019 ◽  
Vol 8 (4) ◽  
pp. e1568812 ◽  
Author(s):  
Arielle Elkrief ◽  
Layal El Raichani ◽  
Corentin Richard ◽  
Meriem Messaoudene ◽  
Wiam Belkaid ◽  
...  

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 11535-11535
Author(s):  
Remy B Verheijen ◽  
Tirsa T van Duijl ◽  
Michel M van den Heuvel ◽  
Jos H. Beijnen ◽  
Jan H.M. Schellens ◽  
...  

11535 Background: Epidermal growth factor receptor (EGFR) inhibitors such as erlotinib and gefitinib are routinely used in the treatment of non-small cell lung cancer (NSCLC). Monitoring of EGFR mutations in circulating tumor DNA (ctDNA) derived from plasma has been proposed as an alternative for repeated tumor biopsies. Our aim was to investigate the dynamics of ctDNA in a cohort of NSCLC patients and explore the roles of EGFR driver and resistance mutations in predicting disease progression and progression free survival (PFS). Methods: NSCLC patients treated with either erlotinib or gefitinib as first-line anti-EGFR therapy were included. Clinical data was collected retrospectively from medical records. Plasma samples collected as part of routine care were analyzed. First DNA was isolated from plasma using the QIAsymphony SP (Qiagen). Then EGFR driver (L858R and exon 19 deletions) and resistance (T790M) mutations were quantified using the X100 Droplet Digital PCR and analyzed using QuantaSoft software (Bio-Rad). The dynamics of ctDNA mutations over time and the relationship between copy numbers and progression free survival were explored. Results: 68 NSCLC patients and 249 plasma samples (1-13 per patient) were included in the analysis. In 33 patients, the T790M mutation was detected. The median (range) T790M concentration in these samples was of 7.3 (5.1 - 3688.7) copies/mL. In 30 patients, the L858R or exon 19 deletion driver mutations were found in median concentrations of 11.7 (5.1 – 12393.3) and 27.9 (5.9 – 2896.7) copies/mL, respectively. Using local polynomial regression, the copies/mL of EGFR driver mutations increased several weeks prior to progression on standard response evaluation. In Kaplan-Meier analysis, patients with a detectable T790M mutation during the first 8 weeks of treatment had a shorter PFS (7.6 versus 14.4 months, p < 0.01, log-rank test). Conclusions: Early detection of the T790M mutation in plasma ctDNA is related to poor PFS. Furthermore, an increase in the copies/mL of the EGFR driver mutation over time may predict clinical progression.


2017 ◽  
Vol 12 (11) ◽  
pp. S1908
Author(s):  
S. Lu ◽  
Y. Song ◽  
Z. Xie ◽  
Z. Zhu ◽  
L. Liu ◽  
...  

Cancers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 3101
Author(s):  
Marina Berger ◽  
Andrea Thueringer ◽  
Doritt Franz ◽  
Nadia Dandachi ◽  
Emina Talakić ◽  
...  

We prospectively performed a longitudinal analysis of circulating tumor DNA (ctDNA) from 149 plasma samples and CT scans in Stage III and IV metastatic melanoma patients (n = 20) treated with targeted agents or immunotherapy using two custom next-generation sequencing (NGS) Ion AmpliSeq™ HD panels including 60 and 81 amplicons in 18 genes, respectively. Concordance of matching cancer-associated mutations in tissue and plasma was 73.3%. Mutant allele frequency (MAF) levels showed a range from 0.04% to 28.7%, well detectable with NGS technologies utilizing single molecule tagging like the AmpliSeq™ HD workflow. Median followup time of the tissue and/or plasma positive cohort (n = 15) was 24.6 months and median progression-free survival (PFS) was 7.8 months. Higher MAF ≥ 1% at baseline was not significantly associated with a risk of progression (Odds Ratio = 0.15; p = 0.155). Although a trend could be seen, MAF levels did not differ significantly over time between patients with and without a PFS event (p = 0.745). Depending on the cell-free DNA amount, NGS achieved a sensitivity down to 0.1% MAF and allowed for parallel analysis of multiple mutations and previously unknown mutations. Our study indicates that NGS gene panels could be useful for monitoring disease burden during therapy with ctDNA in melanoma patients.


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