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  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 2306-2306
    Abstract: Introduction: Increasingly, circulating tumor DNA (ctDNA) is proposed as a tool for minimal residual disease (MRD) assessment, with the potential to guide postoperative treatment decisions. Low ctDNA levels immediately after surgery necessitate extremely sensitive detection methods. Additionally, for potential clinical implementation, detection methods should ideally feature short turnaround times (TATs) and low analysis costs. Compared to sequencing-based detection methods, digital PCR is low-cost, and features TATs of less than a day. Consequently, digital PCR is a good candidate for clinical implementation. Here, we present ctDNA detection results from a highly optimized, tumor-informed digital PCR strategy in a large cohort of stage II-III colorectal cancer (CRC) patients. Methods: Stage II-III CRC patients (n=864) treated with curative intent were recruited from Danish surgical centers from 2014 to 2021. Whole exome sequencing was conducted on matched tumor and buffy coat from all patients. After thorough clonality assessment, a mutational target was chosen for digital PCR analysis. Plasma samples (8mL) collected before and within 60 days after surgery, were investigated for ctDNA using digital PCR. Additionally, a subset of patients (n=229) had serial samples collected every three months analyzed for ctDNA. Results: Before surgery, ctDNA was detected in 569/828 (69%) analyzed blood samples. A minimum of 12 months of radiological follow-up was available for 598/864 patients at time of writing, enabling prognostic evaluation of ctDNA detection in these patients. Postoperative ctDNA detection was highly correlated to future recurrence (HR=9.6, 95%CI 6.3-15, P & lt;0.001). The median time to recurrence was significantly shorter for postoperatively ctDNA positive patients (10 months, interquartile range (IQR) 3.8-12 months) compared to ctDNA negative patients (18 months, IQR 12-26 months, P & lt;0.001), indicating a higher disease burden postoperatively in ctDNA positive patients. In a subset of patients with samples collected immediately after adjuvant treatment (n=95) and serially (n=186), ctDNA was also prognostic of recurrence (HR=6.4, CI95% 2.9-14, P & lt;0.001; HR=27, 95%CI 14-52, P & lt;0.001). A minimum of 12 months of follow-up is expected to be available for 700 patients before the AACR meeting 2023. Conclusion: These results from one of the largest ctDNA detection cohorts of stage II-III CRC patients demonstrate that our personalized digital PCR approach effectively detects MRD immediately after surgery. Additionally, our approach shows promise for serial ctDNA detection for recurrence surveillance applications. With digital PCR being a widespread and cost-effective method with low TATs, clinical implementation of ctDNA analysis may be more forthright using this method over cost-intensive sequencing-based methods. Citation Format: Tenna V. Henriksen, Christina Demuth, Amanda Frydendahl, Marijana Nesic, Mads H. Rasmussen, Thomas Reinert, Ole H. Larsen, Anders H. Madsen, Uffe S. Løve, Per V. Andersen, Ole Thorlacius-Ussing, Ismail Gögenur, Jakob Lykke, Allan G. Pedersen, Peter Bondeven, Nis H. Schlesinger, Lene H. Iversen, Kåre A. Gotschalck, Claus L. Andersen. Potential clinical utility of circulating tumor DNA detected by digital PCR in a nationwide Danish cohort of high-risk colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2306.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 2
    In: European Journal of Cancer, Elsevier BV, Vol. 163 ( 2022-03), p. 163-176
    Type of Medium: Online Resource
    ISSN: 0959-8049
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
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  • 3
    In: International Journal of Cancer, Wiley, Vol. 155, No. 5 ( 2024-09), p. 925-933
    Abstract: Tumor‐informed mutation‐based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational features—such as cancer cell fraction (CCF), multiplicity, and error rate—would improve the success rate of tumor‐informed ctDNA analysis. Additionally, we aimed to develop a practical and easily implementable analysis pipeline for identifying and prioritizing candidate mutations from whole‐exome sequencing (WES) data. We analyzed WES and ctDNA data from three tumor‐informed ctDNA studies, one on bladder cancer (Cohort A) and two on colorectal cancer (Cohorts I and N). The studies included 390 patients. For each patient, a unique set of mutations (median mutations/patient: 6, interquartile 13, range: 1–46, total n  = 4023) were used as markers of ctDNA. The tool PureCN was used to assess the CCF and multiplicity of each mutation. High‐CCF mutations were detected more frequently than low‐CCF mutations (Cohort A: odds ratio [OR] 20.6, 95% confidence interval [CI] 5.72–173, p  = 1.73e−12; Cohort I: OR 2.24, 95% CI 1.44–3.52, p  = 1.66e−04; and Cohort N: OR 1.78, 95% CI 1.14–2.79, p  = 7.86e−03). The detection‐likelihood was additionally improved by selecting mutations with multiplicity of two or above (Cohort A: OR 1.55, 95% CI 1. 14–2.11, p  = 3.85e−03; Cohort I: OR 1.78, 95% CI 1.23–2.56, p  = 1.34e−03; and Cohort N: OR 1.94, 95% CI 1.63–2.31, p  = 2.83e−14). Furthermore, selecting the mutations for which the ctDNA detection method had the lowest error rates, additionally improved the detection‐likelihood, particularly evident when plasma cell‐free DNA tumor fractions were below 0.1% ( p  = 2.1e−07). Selecting mutational markers with high CCF, high multiplicity, and low error rate significantly improve ctDNA detection likelihood. We provide free access to the analysis pipeline enabling others to perform qualified prioritization of mutations for tumor‐informed ctDNA analysis.
    Type of Medium: Online Resource
    ISSN: 0020-7136 , 1097-0215
    URL: Issue
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    Language: English
    Publisher: Wiley
    Publication Date: 2024
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  • 4
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 38, No. 15_suppl ( 2020-05-20), p. 4009-4009
    Abstract: 4009 Background: The clinical utility of tracking circulating tumor DNA (ctDNA) as a non-invasive biomarker for detecting minimal residual disease (MRD) and stratifying patients based on their risk of developing relapse has been well established in colorectal cancer (CRC). This study evaluates the detection and longitudinal monitoring of ctDNA in CRC patients pre- and post-operatively, during and after adjuvant chemotherapy (ACT). Methods: The prospective, multicenter cohort study recruited patients (n = 193) diagnosed with resected stage I-III CRC. Plasma samples (n = 1052) were collected at various timepoints with a median follow up of 21.6 months (4.6-38.5 months). Individual tumors and matched germline DNA were whole-exome sequenced and somatic mutations identified. Multiplex PCR assays were designed to 16 tumor-specific single-nucleotide variants to track ctDNA in plasma samples. The study evaluated the relationship between ctDNA status and clinical outcomes including radiologic imaging. Cox regression was used to calculate recurrence-free survival (RFS) in patients stratified by ctDNA status postoperatively and post-ACT. Multivariable analysis was performed with all clinical variables. Best model was selected according to Akaike Information Criterion. Results: Pre-operatively ctDNA was detected in 90% (n = 166/185) of the patients. Post-operative ctDNA status prior to ACT was assessed in 152 patients, of which 9.2% (14/152) were identified to be MRD-positive and 78.5% (11/14) eventually relapsed. In contrast, 10.1% (14/138) of MRD-negative cases relapsed (HR: 16.53; 95% CI: 7.19-38.02; p 〈 0.001). Longitudinal ctDNA-positive status, post-ACT (n = 84) and post definitive therapy (n = 139) was associated with a 27.92 HR (95% CI: 9.16-85.11; p 〈 0.001) and a 47.52 HR (95% CI: 17.34-130.3.; p 〈 0.001), respectively. In the multivariable analysis, longitudinal ctDNA status was the only significant prognostic factor associated with RFS (HR: 53.19, 95% CI: 18.87-149.90; p 〈 0.001). Serial ctDNA analysis detected MRD up to a median of 9.08 months (0.56-16.5 months) ahead of radiologic relapse with a sensitivity of 79.1% and specificity of 99%. Conclusions: Postoperative ctDNA analyses detect patients with high-risk of recurrence, with near 100% specificity. Early detection of MRD and longitudinal monitoring of ctDNA could guide treatment decisions. Intervention trials to assess the clinical benefit of ctDNA use are underway.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2020
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  • 5
    In: Clinical Chemistry, Oxford University Press (OUP), Vol. 68, No. 5 ( 2022-05-18), p. 657-667
    Abstract: Droplet digital PCR (ddPCR) is a widely used and sensitive application for circulating tumor DNA (ctDNA) detection. As ctDNA is often found in low abundance, methods to separate low-signal readouts from noise are necessary. We aimed to characterize the ddPCR-generated noise and, informed by this, create a sensitive and specific ctDNA caller. Methods We built 2 novel complimentary ctDNA calling methods: dynamic limit of blank and concentration and assay-specific tumor load estimator (CASTLE). Both methods are informed by empirically established assay-specific noise profiles. Here, we characterized noise for 70 mutation-detecting ddPCR assays by applying each assay to 95 nonmutated samples. Using these profiles, the performance of the 2 new methods was assessed in a total of 9447 negative/positive reference samples and in 1311 real-life plasma samples from colorectal cancer patients. Lastly, performances were compared to 7 literature-established calling methods. Results For many assays, noise increased proportionally with the DNA input amount. Assays targeting transition base changes were more error-prone than transversion-targeting assays. Both our calling methods successfully accounted for the additional noise in transition assays and showed consistently high performance regardless of DNA input amount. Calling methods that were not noise-informed performed less well than noise-informed methods. CASTLE was the only calling method providing a statistical estimate of the noise-corrected mutation level and call certainty. Conclusions Accurate error modeling is necessary for sensitive and specific ctDNA detection by ddPCR. Accounting for DNA input amounts ensures specific detection regardless of the sample-specific DNA concentration. Our results demonstrate CASTLE as a powerful tool for ctDNA calling using ddPCR.
    Type of Medium: Online Resource
    ISSN: 0009-9147 , 1530-8561
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 1590-1590
    Abstract: Early detection of disease recurrence has shown to improve survival in patients with early-stage colorectal cancer (CRC) (Pita-Fernandez et al., 2015). Detection of circulating tumor DNA (ctDNA) postoperatively in patients with stage II colon cancer provides direct evidence of residual disease and identifies patients at high risk of recurrence (Tie et al., 2016). Previous studies have performed ctDNA analysis to monitor tumor burden in early-stage CRC using small gene panel sequencing or digital droplet PCR (ddPCR) assays to detect specific variants (Tie et al., 2016, Reinert et al., 2016). Building upon these previous studies, here we use a personalized multiplex ctDNA technology measuring 16 mutations specific to each patient's tumor respectively to assess minimal residual disease postoperatively and to monitor treatment response in CRC. Our study includes 130 patients diagnosed with stage I-III CRC treated with intended curative surgery. Of the 130 patients, 80 received adjuvant chemotherapy for a duration of six months. For 119 patients, one pre-operative and one post-operative plasma sample were available. In addition, longitudinally-collected plasma samples were available from 78 of 130 patients for early detection of disease recurrence and to determine their relationship with imaging and carcinoembryonic antigen (CEA) during a 3-year post-operative surveillance period. To identify patient-specific tumor mutation signatures, whole-exome sequencing of CRC tissue and germline DNA is used. Patient specific multiplex-PCR assay panels are designed to target 16 tumor-specific single-nucleotide variants (SNVs) in plasma. Targeted sequencing is then performed on plasma samples collected pre- and post-operative and during adjuvant therapy. We then correlate ctDNA status to the clinical outcome, including CEA and radiographic imaging, for each patient. Data collection is ongoing and results will be presented at the AACR 2018 meeting. Conclusion. This study provides a novel methodology to detect minimal residual disease postoperatively and to monitor treatment efficacy in CRC using a personalized multiplex-PCR approach. The performance of this patient-specific ctDNA technology will be compared to the current standard of care for monitoring disease burden. References: S. Pita-Fernàndez, et al. Ann. Oncol. 26, 644–656 (2015). Tie J, et al. Sci Transl Med. 2016 Jul 6;8(346):346ra92. Reinert T. Gut. 2016 Apr;65(4):625-34. Citation Format: Thomas Reinert, Tenna V. Henriksen, Mads H. Rasmussen, Himanshu Sethi, Shruti Sharma, Hsin-Ta Wu, Dina Hafez, Prashanthi Natarajan, Scott Dashner, Mustafa Balcioglu, Ann Nguyen, Derrick Renner, Bernhard Zimmermann, Lene H- Iversen, Mogens R. Madsen, Cheng-Ho Jimmy Lin, Claus L. Andersen. Personalized circulating tumor DNA analysis to monitor colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1590.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 7
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    Online Resource
    American Association for Cancer Research (AACR) ; 2023
    In:  Cancer Research Vol. 83, No. 7_Supplement ( 2023-04-04), p. 6699-6699
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 6699-6699
    Abstract: Introduction: Tumor-informed, mutation-based approaches for the detection of circulating tumor DNA (ctDNA) are among the most common and widely used ctDNA detection approaches. To identify the mutations to be used as ctDNA targets, tumor tissue is often mutation-profiled using broad panel sequencing strategies. Optimally, the strategy for mutation profiling should enable assessment of clonality and copy number of the identified mutations. Hereby, it will be possible to rank the mutations and select those that are clonal and present in multiple copies per cancer cell. Theoretically, this should increase the ctDNA detection likelihood. However, there is no consensus on how best to identify and select the targets. Here, we propose a bioinformatic pipeline for an easy and robust selection of target mutations for ctDNA detection from tumor whole-exome sequencing (WES) profiles. Methods: The pipeline consists of Mutect2 and PureCN, which were both applied to paired tumor and normal WES profiles. The output from the pipeline is a list of somatic mutations, each with estimated measures of clonality, in the form of a cancer cell fraction (CCF), and multiplicity (local mutation copy number). Mutations with CCF above 0.9 were considered clonal. The performance of the pipeline was assessed using matched WES and ctDNA data from 98 colorectal cancer (CRC) and 30 bladder cancer patients. For CRC patients, 1-5 mutations per patient within a pre-defined CRC panel were used as ctDNA targets, while an average of 41 selected mutations per patient were used for bladder cancer patients. The performance measure was the mutation detection rate in pre-operative plasma samples, stratified for clonality (CCF), multiplicity, and the combination of CCF and multiplicity. Results: For CRC patients, 51% of mutations with CCF & gt; 0.9 were detected compared to only 17% when CCF & lt; 0.9 (p= 4.3e-09). In bladder cancer patients 21% of mutations with CCF & gt; 0.9 were detected compared to 2 % when CCF & lt; 0.9 (p=1.2e-09). For CRC patients the ctDNA detection rate was 58% when mutation multiplicity was higher than 1 and 31% when multiplicity was 1 (p= 9.175e-06). For bladder cancer, the same numbers were 22% and 16% (p=4.635e-03). Mutations with CCF & gt; 0.9 and multiplicity & gt;1 had significantly increased ctDNA detection rate compared with mutations with CCF & lt; 0.9 and multiplicity 1, in both CRC (p= 1.486e-09) and bladder cancer (p=1.077e-09). Conclusion: The CCF and multiplicity measures provided by the pipeline are highly useful when selecting ctDNA targets. By selecting mutations with CCF & gt; 0.9 and multiplicity & gt;1 the likelihood of detecting ctDNA in plasma cfDNA is significantly improved. Citation Format: Marijana Nesic, Mads H. Rasmussen, Tenna V. Henriksen, Christina Demuth, Amanda Frydendahl, Iver Nordentoft, Lars Dyrskjøt, Claus L. Andersen. What are the characteristics of mutations to use as targets in tumor-informed ctDNA analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6699.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 8
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    Online Resource
    American Association for Cancer Research (AACR) ; 2021
    In:  Clinical Cancer Research Vol. 27, No. 23 ( 2021-12-01), p. 6613-6613
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 27, No. 23 ( 2021-12-01), p. 6613-6613
    Type of Medium: Online Resource
    ISSN: 1078-0432 , 1557-3265
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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  • 9
    In: European Journal of Cancer, Elsevier BV, Vol. 207 ( 2024-08), p. 114186-
    Type of Medium: Online Resource
    ISSN: 0959-8049
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2024
    detail.hit.zdb_id: 1120460-6
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  • 10
    In: Molecular Oncology, Wiley, Vol. 14, No. 8 ( 2020-08), p. 1670-1679
    Abstract: Detection of circulating tumor DNA (ctDNA) post‐treatment is an emerging marker of residual disease. ctDNA constitutes only a minor fraction of the cell‐free DNA (cfDNA) circulating in cancer patients, complicating ctDNA detection. This is exacerbated by trauma‐induced cfDNA. To guide optimal blood sample timing, we investigated the duration and magnitude of surgical trauma‐induced cfDNA in patients with colorectal or bladder cancer. DNA levels were quantified in paired plasma samples collected before and up to 6 weeks after surgery from 436 patients with colorectal cancer and 47 patients with muscle‐invasive bladder cancer. To assess whether trauma‐induced cfDNA fragments are longer than ordinary cfDNA fragments, the concentration of short ( 〈  1 kb) and long ( 〉  1 kb) fragments was determined for 91 patients. Previously reported ctDNA data from 91 patients with colorectal cancer and 47 patients with bladder cancer were used to assess how trauma‐induced DNA affects ctDNA detection. The total cfDNA level increased postoperatively—both in patients with colorectal cancer (mean threefold) and bladder cancer (mean eightfold). The DNA levels were significantly increased up to 4 weeks after surgery in both patient cohorts ( P  = 0.0005 and P  ≤ 0.0001). The concentration of short, but not long, cfDNA fragments increased postoperatively. Of 25 patients with radiological relapse, eight were ctDNA‐positive and 17 were ctDNA‐negative in the period with trauma‐induced DNA. Analysis of longitudinal samples revealed that five of the negative patients became positive shortly after the release of trauma‐induced cfDNA had ceased. In conclusion, surgery was associated with elevated cfDNA levels, persisting up to 4 weeks, which may have masked ctDNA in relapse patients. Trauma‐induced cfDNA was of similar size to ordinary cfDNA. To mitigate the impact of trauma‐induced cfDNA on ctDNA detection, it is recommended that a second blood sample collected after week 4 is analyzed for patients initially ctDNA negative.
    Type of Medium: Online Resource
    ISSN: 1574-7891 , 1878-0261
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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