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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: Genome Biology, Springer Science and Business Media LLC, Vol. 24, No. 1 ( 2023-04-30)
    Abstract: Circulating tumor DNA detection using next-generation sequencing (NGS) data of plasma DNA is promising for cancer identification and characterization. However, the tumor signal in the blood is often low and difficult to distinguish from errors. We present DREAMS (Deep Read-level Modelling of Sequencing-errors) for estimating error rates of individual read positions. Using DREAMS, we develop statistical methods for variant calling (DREAMS-vc) and cancer detection (DREAMS-cc). For evaluation, we generate deep targeted NGS data of matching tumor and plasma DNA from 85 colorectal cancer patients. The DREAMS approach performs better than state-of-the-art methods for variant calling and cancer detection.
    Type of Medium: Online Resource
    ISSN: 1474-760X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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  • 3
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2020-06-03)
    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
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  • 4
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 6 ( 2015-09-15)
    Type of Medium: Online Resource
    ISSN: 1664-8021
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2015
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 79, No. 13_Supplement ( 2019-07-01), p. 466-466
    Abstract: Background: Colorectal cancer (CRC) is characterized by marked inter-tumor heterogeneity, both molecularly and clinically. Patient stratification using transcriptional subtyping show promise to resolve the heterogeneity and guide precision medicine. This requires high quality RNA, which can be purified from fresh frozen (FF) tissue, but not from clinically collected formalin-fixed paraffin-embedded (FFPE) tissue. Consequently, transcriptional subtyping is not applicable to most CRC patients. Aim: To establish a DNA methylation-based approach for molecular characterization and subtyping, which is compatible with both FF and FFPE tissue, and use this to improve patient prognostication as compared to histopathological TNM staging. Methods: Using paired RNA expression and DNA methylation profiles (450K array) from 394 CRCs, we identified 200 CpG sites genome-wide, whose methylation levels correlated best with expression for each gene. With this information, we 1) devised an approach, methCORR, that can infer RNA expression in both FF and FFPE samples using only DNA methylation profiles, 2) established a methCORR network that clusters genes according to overlap in the CpG sites associated with their expression level and 3) used the network to determine and characterize biological traits associated with tumor aggressiveness. Results: The methCORR-inferred RNA expression profiles in FF tissue consistently exhibited high correlation to matched RNA-seq. profiles (median Pearson r=0.97; range 0.91-0.98). We found a higher correlation between FF RNA-seq. and FFPE inferred RNA profiles (median r= 0.97; range 0.96-0.98) than between FF and FFPE RNA-seq. profiles (median r= 0.78; range 0.51-0.92). Gene expression profiles were inferred in two FF (n=231, n=203), and two FFPE cohorts (n=113, n=56). Clustering of these profiles identified the same two CRC subtypes independently in all cohorts. Characterization using the methCORR network showed that the two subtypes resembled conventional and serrated CRC. Moreover, methCORR network analysis identified subtype-specific traits that associated strongly with tumor aggressiveness, such as T-cell, fibroblast, and epithelial-mesenchymal transition activity, and thus allowed identification of subtype-specific prognostic biomarkers. These better predicted relapse-free survival (HR=3.22, 95%CI 2.00-5.17) than TNM staging (HR=1.99, 95%CI 1.28-3.08). Finally, we derived four simple and clinically applicable DNA methylation-specific PCR assays for subtyping and prognostication of CRC FFPE samples. Conclusion: We have developed a novel method for characterization, subtyping, and prognostication of CRC, which is compatible with FF and FFPE samples. We envision that application of the methCORR approach to other cancer types will generate similar fruitful results. Citation Format: Trine B. Mattesen, Mads H. Rasmussen, Juan Sandoval, Halit Ongen, Sigrid S. Árnadóttir, Anders H. Madsen, Søren Laurberg, Emmanouil T. Dermitzakis, Manel Esteller, Claus L. Andersen, Jesper B. Bramsen. A novel DNA methylation-based approach for molecular subtyping and improved prognostication of colorectal cancer using formalin-fixed and paraffin-embedded tissue [abstract] . In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 466.
    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: 2019
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 20 ( 2014-10-15), p. 5758-5771
    Abstract: Exosomes are small secreted vesicles that can transfer their content to recipient cells. In cancer, exosome secretion has been implicated in tumor growth and metastatic spread. In this study, we explored the possibility that exosomal pathways might discard tumor-suppressor miRNA that restricts metastatic progression. Secreted miRNA characterized from isogenic bladder carcinoma cell lines with differing metastatic potential were uncoupled from binding to target transcripts or the AGO2–miRISC complex. In metastatic cells, we observed a relative increase in secretion of miRNA with tumor-suppressor functions, including miR23b, miR224, and miR921. Ectopic expression of miR23b inhibited invasion, anoikis, angiogenesis, and pulmonary metastasis. Silencing of the exocytotic RAB family members RAB27A or RAB27B halted miR23b and miR921 secretion and reduced cellular invasion. Clinically, elevated levels of RAB27B expression were linked to poor prognosis in two independent cohorts of patients with bladder cancer. Moreover, highly exocytosed miRNA from metastatic cells, such as miR23b, were reduced in lymph node metastases compared with patient-matched primary tumors and were correlated with increments in miRNA-targeted RNA. Taken together, our results suggested that exosome-mediated secretion of tumor-suppressor miRNA is selected during tumor progression as a mechanism to coordinate activation of a metastatic cascade. Cancer Res; 74(20); 5758–71. ©2014 AACR.
    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: 2014
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  • 7
    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
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 8
    In: Transfusion, Wiley, Vol. 60, No. S3 ( 2020-06)
    Abstract: Thromboelastometry (TEM) is often used to guide transfusion therapy in patients with massive bleeding. The effect of testing incompletely filled samples and those stored for a prolonged time at 4°C was investigated. METHODS Whole blood samples were collected from 15 healthy blood donors and were pooled according to ABO group. From these pools, aliquots were taken and diluted to produce final whole blood:citrate buffer ratios ranging from 90:10 (fully filled sample) to 40:60 (extremely under filled samples). These samples were then tested by EXTEM, INTEM, and FIBTEM on calibrated ROTEM delta machines. Separately, the four samples at 90:10 dilution were kept at 4°C for 16‐20 hours and then retested on the ROTEM machines. RESULTS All of the samples at the 90:10 and 80:20 (half‐filled sample) whole blood:citrate buffer dilutions demonstrated ROTEM parameters within their respective reference ranges, although the samples from the 80:20 dilution tended to demonstrate slightly longer or slower times, depending on each ROTEM parameter, compared to the completely filled samples. All of the samples with more dilute whole blood to citrate buffer ratios (i.e., 70:30 to 40:60) yielded abnormal TEM results. The TEM results for the 90:10 dilution samples exposed to 16‐20 hours of storage at 4°C were within the reference intervals. CONCLUSION Completely and half‐filled samples, and completely filled samples after prolonged cold storage, produced normal ROTEM results. Tubes that are less than half‐filled should not be used for ROTEM testing.
    Type of Medium: Online Resource
    ISSN: 0041-1132 , 1537-2995
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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  • 9
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2020-04-24)
    Abstract: Transcriptional characterization and classification has potential to resolve the inter-tumor heterogeneity of colorectal cancer and improve patient management. Yet, robust transcriptional profiling is difficult using formalin-fixed, paraffin-embedded (FFPE) samples, which complicates testing in clinical and archival material. We present MethCORR, an approach that allows uniform molecular characterization and classification of fresh-frozen and FFPE samples. MethCORR identifies genome-wide correlations between RNA expression and DNA methylation in fresh-frozen samples. This information is used to infer gene expression information in FFPE samples from their methylation profiles. MethCORR is here applied to methylation profiles from 877 fresh-frozen/FFPE samples and comparative analysis identifies the same two subtypes in four independent cohorts. Furthermore, subtype-specific prognostic biomarkers that better predicts relapse-free survival (HR = 2.66, 95%CI [1.67–4.22] , P  value  〈  0.001 (log-rank test)) than UICC tumor, node, metastasis (TNM) staging and microsatellite instability status are identified and validated using DNA methylation-specific PCR. The MethCORR approach is general, and may be similarly successful for other cancer types.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
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  • 10
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2011-12)
    Abstract: microRNAs (miRNA) are short, endogenous transcripts that negatively regulate the expression of specific mRNA targets. miRNAs are found both in tissues and body fluids such as plasma. A major perspective for the use of miRNAs in the clinical setting is as diagnostic plasma markers for neoplasia. While miRNAs are abundant in tissues, they are often scarce in plasma. For quantification of miRNA in plasma it is therefore of importance to use a platform with high sensitivity and linear performance in the low concentration range. This motivated us to evaluate the performance of three commonly used commercial miRNA quantification platforms: GeneChip miRNA 2.0 Array, miRCURY Ready-to-Use PCR, Human panel I+II V1.M, and TaqMan Human MicroRNA Array v3.0. Results Using synthetic miRNA samples and plasma RNA samples spiked with different ratios of 174 synthetic miRNAs we assessed the performance characteristics reproducibility, recovery, specificity, sensitivity and linearity. It was found that while the qRT-PCR based platforms were sufficiently sensitive to reproducibly detect miRNAs at the abundance levels found in human plasma, the array based platform was not. At high miRNA levels both qRT-PCR based platforms performed well in terms of specificity, reproducibility and recovery. At low miRNA levels, as in plasma, the miRCURY platform showed better sensitivity and linearity than the TaqMan platform. Conclusion For profiling clinical samples with low miRNA abundance, such as plasma samples, the miRCURY platform with its better sensitivity and linearity would probably be superior.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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