scholarly journals Circulating tumor DNA for comprehensive noninvasive monitoring of lymphoma treated with ibrutinib plus nivolumab

Author(s):  
Alessio Bruscaggin ◽  
Lodovico Terzi di Bergamo ◽  
Valeria Spina ◽  
Brendan Hodkinson ◽  
Gabriela Forestieri ◽  
...  

To advance the use of circulating tumor DNA (ctDNA) applications, their broad clinical validity must be tested in different treatment settings, including targeted therapies. Utilizing the prespecified longitudinal systematic collection of plasma samples in the phase 1/2a LYM1002 trial (NCT02329847), we tested the clinical validity of ctDNA for baseline mutation profiling, residual tumor load quantification, and acquisition of resistance mutations in patients with lymphoma treated with ibrutinib plus nivolumab. Inclusion criterion for this ancillary biological study was the availability of blood collected at baseline and cycle 3 day 1. Overall, 172 ctDNA samples from 67 patients were analyzed using LyV4.0 ctDNA CAncer Personalized Profiling by deep Sequencing assay. Among baseline variants in ctDNA, only TP53 mutations (detected in 25.4% of patients) were associated with shorter progression-free survival; clones harboring baseline TP53 mutations did not disappear during treatment. Molecular response, defined as a >2-log reduction in ctDNA levels after 2 cycles of therapy (28 days), was achieved by 28.6% of patients with relapsed diffuse large B-cell lymphoma who had ≥1 baseline variant and was associated with best response and improved progression-free survival. Clonal evolution occurred frequently during treatment, and 10.3% new mutations were identified after 2 treatment cycles in nonresponders. PLCG2 was the topmost among genes that acquired new mutations. No patients acquired C481S BTK mutations implicated in resistance to ibrutinib in CLL. Collectively, our results provide the proof of concept that ctDNA is useful for noninvasive monitoring of lymphoma treated with targeted agents in the clinical trial setting.

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 ◽  
...  

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.


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 (21) ◽  
pp. 5466
Author(s):  
Sang Myung Woo ◽  
Min Kyeong Kim ◽  
Boram Park ◽  
Eun-Hae Cho ◽  
Tae-Rim Lee ◽  
...  

Genomic instability of circulating tumor DNA (ctDNA) as a prognostic biomarker has not been evaluated in pancreatic cancer. We investigated the role of the genomic instability index of ctDNA in pancreatic ductal adenocarcinoma (PDAC). We prospectively enrolled 315 patients newly diagnosed with resectable (n = 110), locally advanced (n = 78), and metastatic (n = 127) PDAC from March 2015 through January 2020. Low-depth whole-genome cell-free DNA sequencing identified genome-wide copy number alterations using instability score (I-score) to reflect genome-wide instability. Plasma cell-free and matched tumor tissue DNA from 15 patients with resectable pancreatic cancer was sequenced to assess the concordance of chromosomal copy number alteration profiles. Associations of I-score with clinical factors or survival were assessed. Seventy-six patients had high genomic instability with I-score >7.3 in pre-treatment ctDNA; proportions of high I-score were 5.5%, 5.1%, and 52% in resectable, locally advanced, and metastatic stages, respectively. Correlation coefficients between Z-scores of plasma and tissue DNA at segment resolution were high (r2 = 0.82). Univariable analysis showed the association of I-score with progression-free survival in each stage. Multivariable analyses demonstrated that clinical stage-adjusted I-scores were significant factors for progression-free and overall survival. In these patients, ctDNA genomic I-scores provided prognostic information relevant to progression-free survival in each clinical stage.


2019 ◽  
Author(s):  
Λυδία Γιαννοπούλου

Ο καρκίνος των ωοθηκών αποτελεί τον τέταρτο συχνότερα εμφανιζόμενο γυναικολογικό καρκίνο και την πέμπτη αιτία θανάτου σχετιζόμενη με καρκίνο στις γυναίκες. Χαρακτηρίζεται από αξιοσημείωτη ιστολογική και μοριακή ετερογένεια, με κυριότερο υπότυπο τον ορώδη καρκίνο ωοθηκών υψηλού βαθμού κακοήθειας (high grade serous ovarian carcinoma, HGSC), που μελετήθηκε στη διατριβή. Η παρούσα διατριβή έχει σκοπό τη μελέτη της μεθυλίωσης επιλεγμένων γονιδίων στον ορώδη καρκίνο ωοθηκών υψηλού βαθμού κακοήθειας. Τα κλινικά δείγματα που χρησιμοποιήθηκαν είναι δείγματα πρωτοπαθών όγκων, αντίστοιχα δείγματα παρακείμενων ιστών, καθώς και αντίστοιχα δείγματα κυκλοφορούντος καρκινικού DNA (circulating tumor DNA, ctDNA) από τις ίδιες ασθενείς. Οι μεθοδολογίες που εφαρμόστηκαν συνιστούν την real-time MSP για την ανίχνευση της μεθυλίωσης σε δείγματα πρωτοπαθών όγκων, παρακείμενων ιστών και πλάσματος, καθώς και την MS-HRMA για τον ημιποσοτικό προσδιορισμό της μεθυλίωσης σε δείγματα πρωτοπαθών όγκων και παρακείμενων ιστών. Αρχικά εξετάστηκε η μεθυλίωση του ογκοκατασταλτικού γονιδίου RASSF1A, όπου πραγματοποιήθηκε μία συγκριτική μελέτη σε δείγματα πρωτοπαθών όγκων, παρακείμενων ιστών και ctDNA ασθενών με HGSC. Η μεθυλίωση του γονιδίου στα δείγματα πρωτοπαθών όγκων και παρακείμενων ιστών συσχετίστηκε με σημαντικά μειωμένη ολική επιβίωση (overall survival, OS) των ασθενών. Τα συνολικά αποτελέσματα της μελέτης υπέδειξαν για πρώτη φορά την προγνωστική σημασία της μεθυλίωσης του γονιδίου στον HGSC. Στη συνέχεια, ακολούθησε μελέτη μεθυλίωσης του γονιδίου ESR1, όπου πραγματοποιήθηκε μελέτη σε δείγματα πρωτοπαθών όγκων και ctDNA ασθενών με HGSC. Η μεθυλίωση του γονιδίου στα δείγματα πρωτοπαθών όγκων συσχετίστηκε με σημαντικά αυξημένα OS και διάστημα επιβίωσης χωρίς εξέλιξη της νόσου (progression free survival, PFS) των ασθενών. H παρούσα μελέτη αποτέλεσε μία προσπάθεια αποσαφήνισης του ρόλου της μεθυλίωσης του γονιδίου στον HGSC. Ακολούθησαν οι μελέτες μεθυλίωσης γονιδίων που εμπλέκονται σε μοριακά μονοπάτια που διαταράσσονται στον HGSC, όπως τα γονίδια BRCA1 και MGMT που συμμετέχουν σε διαφορετικές πορείες επιδιόρθωσης του DNA, το γονίδιο NR2F1 που συμμετέχει ενεργά στην κυτταρική αδράνεια, τα γονίδιο RASSF10 που εμπλέκεται στην ανάπτυξη χημειοαντίστασης, καθώς και το γονίδιο RKIP που συμμετέχει στην ΕΜΤ διαδικασία. Ύστερα από τη συνολική επεξεργασία των αποτελεσμάτων, παρατηρήθηκε στατιστικά σημαντική συσχέτιση της μεθυλίωσης του γονιδίου NR2F1 στα δείγματα πρωτοπαθών όγκων, με μειωμένο PFS. Επιπλέον, η μεθυλίωση του γονιδίου BRCA1 στο ctDNA συσχετίστηκε με σημαντικά αυξημένο PFS. Τέλος, πραγματοποιήθηκε μελέτη της έκφρασης του γονιδίου PD-L1 σε δείγματα κυκλοφορούντων καρκινικών κυττάρων (circulating tumor cells, CTCs) ασθενών με HGSC, με την εφαρμογή RT-qPCR. Με βάση τα αποτελέσματα της μελέτης, παρατηρήθηκε στατιστικά σημαντική συσχέτιση της έκφρασης του γονιδίου με μειωμένη OS των ασθενών, υποδεικνύοντας μία πιθανή προγνωστική σημασία στον HGSC.


2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 3040-3040
Author(s):  
Charu Aggarwal ◽  
Jeffrey C. Thompson ◽  
Austin Chien ◽  
Katie Quinn ◽  
Martina Lefterova ◽  
...  

3040 Background: Circulating tumor DNA next generation sequencing (ctDNA NGS) is increasingly being used to detect mutations (MT) in patients (pts) with metastatic (m) NSCLC. Limited data exist on the correlation of baseline ctDNA NGS profile and serial ctDNA NGS monitoring to response to immunotherapy. Methods: We conducted a prospective study in pts with mNSCLC receiving pembrolizumab monotherapy. Plasma was collected at weeks 0 (T0), 9 (T1), and 18 (T2). ctDNA NGS was performed using a 73 gene panel. Number of MTs and variant allelic fraction (VAF) were determined at baseline, and serially; change in mean VAF was calculated between T1-T0, and T2-T0. Response rate (RR) was assessed using RECIST 1.1. Correlations were made for pt characteristics, RR, progression free survival (PFS), and overall survival (OS). Results: We analyzed 95 samples from 33 pts, 21 female, median age 69 (range 51-89 years), smokers (n = 29), adenocarcinoma (n = 23), 25 pts enrolled at initial diagnosis, majority had high PD-L1 ≥50% (n = 29, 88%). At T0, 32 pts had detectable MT, median number of MTs was 4 (range 0-21), (non-synonymous MT = 3), most common MT was TP53 (n = 21). Confirmed PR was 27% (n = 9), clinical benefit rate (SD+PR) was 64% (n = 21), and 2 pts were not evaluable for response. Smokers were more likely to have higher number of MT at T0 (4 vs. 1 p = 0.003); there was no correlation with smoking and overall RR (p = 0.17). RR was not related to number of MT at T0, p = 0.37. A decrease in ctDNA VAF was seen in 6/9 pts with PR (mean VAF change range -0.11 to -0.001); 2/5 pts with PD showed an increase in mean VAF while 3 showed decrease. At median follow up of 9.26 months (mos), median PFS and OS were 7.4 and 10.5 mos, respectively. Median PFS was longer for pts with a decrease in ctDNA VAF at both T1-T0 (8.9 vs. 5 mos, p = 0.02) and T2-T0 (9.1 vs. 5.5 mos, p = 0.006). OS and additional biomarker analyses including correlation of response to a 2mb ctDNA plasma-based NGS panel will be reported at the meeting. Conclusions: Our results demonstrate that it is feasible to serially monitor plasma NGS, decline in mean ctDNA VAF correlates with radiographic response and PFS on immunotherapy with pembrolizumab.


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.


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