Research activities

CLINICAL FOCUS AREAS AND NATIONAL INFRASTRUCTURES

The research activities within the center are categorized into 5 Clinical Focus Areas (CFA) addressing cancer detection and treatment, and 5 National Infrastructures (NI), encompassing the entire process from sample collection to implementation in the clinic.

Covering cancer treatment from discovery to final outcome

Clinical Focus Area (CFA)

The ctDNA Center comprises five Clinical Focus Areas (CFA) that include screening and diagnosis, treatment decisions, treatment monitoring, residual disease detection, and relapse surveillance. All projects within the center align with one or more of the CFAs.

CFA participants may help guide the clinical protocols and ensure national collaborations. The CFA leaders' roles involve facilitating the initiation of national ctDNA studies and trials by organizing CFA workshops and meetings, fostering knowledge transfer, and promoting collaborations.

Further details about the Clinical Focus Areas can be found below.

OBJECTIVE ...

... To investigate the potential roles for minimal-invasive ctDNA detection in early detection of cancer in asymptomatic individuals

We will investigate the potential of using ctDNA as a primary cancer screening tool, and as a tool to supplement ongoing screening. In some screening programs only 60% of invitees take the offered test, potentially participation can be increased if non-responders are offered a blood-based test, after refusing the standard test.

LEADERS

Claus Lindbjerg Andersen
Department of Molecular Medicine
Aarhus University Hospital

Christina Therkildsen
The Gastro Unit
Hvidovre Hospital

OBJECTIVE ...

... To investigate if postoperative ctDNA analysis is a better tool for identifying the patient population likely to benefit from adjuvant therapy, than the risk markers used today.

We will initiate interventional trials aimed at investigating, if postoperative ctDNA-stratification can be used to personalize the adjuvant therapy decision and thereby reduce the fraction of patients receiving futile treatment. In the clinic today it is impossible to define which patients are disease-free after surgery (cured) and who has minimal residual disease and will develop recurrence if no further treatment is given.

For most cancer types it is estimated that more than 60% of patients treated with adjuvant therapy are already cured by surgery alone. Postoperative ctDNA detection is an effective method for distinguishing patients with and without postoperative residual disease, and its implementation in decision making could potentially spare cured patients from undergoing toxic adjuvant chemotherapy while at the same time identify those patients who are most likely to benefit from adjuvant therapy.

LEADERS

Karen-Lise Garm Spindler
Department of Oncology
Aarhus University Hospital

Morten Mau-Sørensen
Department of Oncology
Rigshospitalet

OBJECTIVE ...

... To investigate the benefit of ctDNA guided postoperative surveillance compared to the current “one-size fits all” imaging-based surveillance strategies.

Disease recurrence is a major problem for nearly all cancer types. With current imaging-based surveillance programs, less than 20% of the recurrence events are detected sufficiently early to enable curatively intended intervention. ctDNA analysis enables detection of microscopic residual disease after end of definitive treatment, and moreover detects recurrence up to 16 months before standard radiological surveillance. Hence, ctDNA analysis represents a promising new approach for pinpointing the patients likely to benefit from high-intensity surveillance or to identify patients likely to benefit from early treatment of micro-metastatic disease before detectable by standard imaging methods.

Within the frame of this CFA we will initiate and conduct several clinical studies comparing personalized radiological surveillance, guided by longitudinal ctDNA analysis, to the current “one-size-fits all” surveillance strategies. With a paradigm shift to ctDNA stratified surveillance, we aim for 1) early detection of recurrence, 2) increasing the fraction of patients receiving curative treatment of the recurrence, and 3) improving survival. In essence, a re-allocation of surveillance resources without compromising patient quality of life.

LEADERS

Lars Dyrskjøt Andersen
Department of Molecular Medicine
Aarhus University Hospital

Kåre Gotschalck
Department of Surgery
Horsens Regional Hospital

OBJECTIVE ...

... To investigate if monitoring of ctDNA levels during treatment (including neo-adjuvant and palliative chemo-, targeted-, and immunotherapy) is a better measure of treatment efficacy compared to standard imaging methods.

We will design and initiate interventional trials to compare ctDNA based monitoring approaches to standard imaging strategies performed during neo-adjuvant and palliative treatment. Monitoring of response to treatment in the metastatic setting is performed by standard computed tomography (CT), and while imaging techniques offer an assessment of the tumor burden, the monitoring potential is restricted by a suboptimal detection limit and inherent variability in measurements. Evaluation of treatment efficacy is therefore a major clinical challenge.

It would be beneficial to only continue therapeutic treatment in patients that show a clear response and change treatment when possible. Changes in ctDNA levels during treatment are correlated with tumor burden and outcome. ctDNA analysis may provide predictive information regarding treatment efficacy.

LEADERS

Julia S. Johansen
Department of Oncology
Herlev and Gentofte Hospital

OBJECTIVE ...

... To investigate if liquid biopsy analysis can replace or supplement tissue biopsies in the metastatic setting for identification of therapeutically actionable targets and for screening of resistance-causing variants.

With the hypothesis that ctDNA is better suited than biopsies to detect intratumoral subclones and clonal evolution during treatment, we will initiate interventional trials to investigate the clinical benefit of using ctDNA analysis for identification of new therapeutic targets arising during metastatic progression and for tracking the rise of specific variants associated with treatment resistance during disease progression.

LEADERS

Iben Spanggaard
Department of Oncology
Rigshospitalet

Karin Birkenkamp-Demtröder
Department of Molecular Medicine
Aarhus University Hospital

Quality work from biopsy collection to clinical implementation

National Infrastructures (NI)

To bolster the projects within the various CFAs, the ctDNA Center has established five National Infrastructures (NI). The NIs are structured to uphold the highest scientific standards for all associated protocols. They aim to enhance research throughout Denmark by providing expert knowledge and facilities.

Further details about the National Infrastructures and their ongoing projects can be found below.

OBJECTIVE ...

... To establish best practice guidelines for collection and pre-analytical processing of liquid biopsies.

Standardized pre-analytical conditions are of utmost importance in national protocols where samples are collected locally but analyzed centrally. By bringing together information from literature and guidelines/recommendations from national and international workgroups we will investigate which sample type (e.g. plasma, urine, feces, and breath exhale), sample collection time point (e.g. in relation to surgery and treatment), type of collection container and sample storage, is best suited for various clinical situations.

In addition, the influence on ctDNA analyses of pre-analytical processing parameters will be investigated, such as time from sampling until start of processing, DNA purification and centrifugation procedures, endogenous and exogenous specific inhibitors affecting analytical accuracy, and pre-amplification of DNA prior to the ctDNA detection.

LEADERS

Rikke Fredslund Andersen
Department of Clinical Immunology and Biochemistry
Sygehus Lillebælt, Vejle

Estrid Høgdall
The Molecular Unit, Department of Pathology
Herlev Hospital

CONTACT NI1 FOR...

  • Guidelines/SOPs for collection of samples (choice of material, volume, preparation etc.)

  • Advise on biobanking

  • Advise on legal questions

  • Contacts/collaborators within the network


CURRENT PROJECTS

Standard Operating Procedure (SOP)

NI1 makes guidelines to ensure uniform and high quality of plasma aiming for comparable results within and between trials. The Standard Operating Procedures (SOP) undergo continuous revision and are prepared by Regionernes Bio-og Genombank (RBGB).

Danish: SOP for blodprøvehåndtering ved ctDNA analyse RBGB
English: SOP for sampling, preparation and storage of plasma

SOP til håndtering af ascites prøver

See RBGB for more SOP: www.rbgb.dk

Pneumatic tube system transport

Pneumatic tube systems (PTSs) are widely used in most hospitals in Denmark, and their usage and scale are rapidly increasing, particularly due to the construction of larger hospitals. Despite their prevalence, few studies have been conducted to assess the impact of PTSs on the sensitivity of ctDNA analyses. The primary concern is the potential for contamination with high molecular weight DNA due to rupture of leukocytes.

Presently, an investigation of the PTSs is planned at Vejle Hospital (Department of Immunology and Biochemistry) and Aarhus University Hospital (Department of Clinical Biochemistry).

Different materials for cfDNA extraction

A questionnaire have been sent out to 86 members of the scientific group in RBGB to ask what material they use for cfDNA analysis.

The following materials are used besides plasma:

  • Urine
  • Bronchial wash
  • Cerebrospinal fluid
  • Ascites

Relevant laboratories have SOPs for sampling and preparation of the materials, which can be used by others when starting to work with these materials.

Long-term storage of material from clinical studies

Can retrospectively collected samples be used for future studies?

The effect of long-term storage of plasma, and the effect of storage temperature (-70oC vs -80oC) will be investigated. Examine samples in Danish Cancer Biobank/DCB (4 ml plasma) with matched high-quality samples taken during clinical trials (40 ml plasma). Yield?

Can plasma collected routinely through DCB be used for single mutation analyses e.g. KRAS? Exploring studies? Compare results obtained from DCB samples with results from IMPROVE samples. If yes, can they be used for NGS? Small panels/large panels? Old and newly collected samples as well as influence of handling time will be investigated.

OBJECTIVE ...

... To coordinate a national assessment of ctDNA analytical methods with the aim of increasing diagnostic efficacy of current ctDNA practices as well as facilitating optimization of existing methods and the development and implementation of novel methods.

New methods and technologies for ctDNA profiling are being continuously developed, mainly focusing on increased detection of minute amounts of ctDNA e.g. by mutation detection using ultra-deep panel sequencing, MassArray and ddPCR or by cell free DNA fragmentation analysis using shallow Whole Genome Sequencing.

We will make several efforts to standardize and optimize these methods. First, an overview of the available assays, capture panels, platforms, and expertise will be collected in a database. The database will include information about analysis work-flows, analytical performance (limit of detection, precision, conformity) and validity of the application for clinical purposes. All participants in DCCC can access this curated database and contribute with analyses or look for relevant cancer-specific assays and sequencing protocols. Secondly, a national quality control program will be developed including traceable national calibrators, national quality control guidelines and sample exchange programs. A number of processes in relation to the methods will be sought optimized, including, the conversion rate of cell free DNA fragments to sequence library and robustness of cell-free DNA pre-amplification.

LEADERS

Mads Heilskov Rasmussen
Department of Molecular Medicine
Aarhus University Hospital

Niels Pallisgaard
Department of Pathology
Zealand University Hospital

CONTACT NI2 FOR...

  • Methods for ctDNA detection (ddPCR, NGS, WGS, etc.)

  • Contacts/collaborators within the network


CURRENT PROJECTS

Reference material for ctDNA detection

In the ctDNA center we have developed well-characterized reference material for ctDNA detection, consisting of cell line-derived background DNA and spike-in variants both enzymatically fragmented to ~167 bp-fragments. The reference material is flexible and the catalogue of available variants includes >100 relevant mutations (SNV, INDELS and fusions) from various human cancers including relevant drug targets. Further, the material spans over a wide noise profile and all possible SNV base substitution changes.

The reference material is designed to include variants frequently analyzed by ctDNA laboratories in Denmark and can be analyzed by using common methods like ddPCR and NGS. The final reference material is to be used as a quality assurance for ctDNA analyses among laboratories in Denmark as a way to obtain a common standard across laboratories and facilities.


The reference material is free and available for all members of the center.

The reference material is currently being used for the National Quality Assurance trial for ctDNA detection, but can also be used for:

  • Bank of positive controls
  • Quality certification program
  • ctDNA methods benchmarking
  • Methods development (pre-analytical, analytical, bioinformatics)

Contact Mads Heilskov Rasmussen (mads.heilskov@clin.au.dk) or Maria Hønholt Jørgensen (mhj@clin.au.dk) if you are interested in the reference material.

Database on ddPCR ctDNA assays

Niels Pallisgaard and Malene Green Madsen from Næstved are building a database with the ddPCR assay information described below. The information is a collection of assays from ctDNA laboratories across the country. The assays will be available for the ctDNA Center laboratories for free, except for the transportation costs.

An assay database will save time, money, and work when an assay in the database is needed in ddPCR in the detection and monitoring of clinical samples. As the database grows the ctDNA laboratories will need to develop and validate fewer and fewer assays over time, thus saving resources.

Information included in the database:

  1. Contact lab(s) who have used the assay
  2. PCR conditions
  3. Primer and probe sequences and concentrations (if known)
  4. Available controls
  5. Picture of 2D plot
  6. LoB and LoD if available
  7. Traffic light scoring (red: only used a few times in a single lab, yellow: used in several labs, green: widely used

Database will be made available for the ctDNA research center members.

Quality assurance program on ctDNA purification

Niels Pallisgaard and Malene Green Madsen lead a quality assurance program on ctDNA purification. Plasma samples will be prepared centrally and distributed to ctDNA laboratories who purify the ctDNA samples and send them back to Næstved laboratory. Næstved laboratory analyses ctDNA samples for different parameters like yield, degree of single strandedness, protinaseK carryover, fragmentation - and the participating labs will receive a report with individualized comments.

If you are working in a lab and want to participate in the EQA, write an e-mail to Malene Green Madsen (malemad@regionsjaelland.dk).

OBJECTIVE ...

... We will 1) establish a national bioinformatics infrastructure that ensures the use of consistent, reliable, state-of-the-art bioinformatic ctDNA analyses across Denmark and 2) develop and deploy new computational methods to improve the detection of clinically relevant signals from ctDNA-seq data.

We will set up a national ctDNA-bioinformatics repository containing data, software, workflows and documentation. The repository will be populated with standardised, validated and well-documented software and analysis workflows as well as datasets from the CPs to ensure rapid and consistent quality assessment of both new pipelines and computational methods. We further propose a number of new computational methods that we expect to greatly improve our ability to extract clinically relevant signals from ctDNA-seq data.

LEADERS

Søren Besenbacher
Department of Molecular Medicine
Aarhus University Hospital

CONTACT NI3 FOR...

  • You are going to setup a study using deep targeted sequencing with UMIs.

  • You are currently doing deep targeted sequencing with UMIs and would like
    to compare your current pipeline to our pipeline.

  • Contacts/collaborators within the network


CURRENT PROJECTS

Create pipeline for targeted sequencing of cfDNA data with Unique Molecular Identifiers (UMIs):

The UMIs can help remove PCR errors from deep sequenced data.

OBJECTIVE ...

... To 1) ensure that cost-effectiveness analysis (CEA) is an integrated part of all trials in the ctDNA Research Centre, accompanied by health technology assessment (HTA), business plans and other decision making tools, and 2) planning and supporting data collection for the hospitals and regions to inform and enable clinical implementation of the interventions.

To maintain a preparedness for CEA of ctDNA guided cancer management by ensuring staff with a comprehensive skill set to conduct CEA of ctDNA are part of the Research Centre specialist team. These staff members will help establish economic data collection procedures and employ state-of-the art methodologies to conduct CEA of ctDNA trials and related studies.

LEADERS

Liza Sopina
DaCHE SDU
University of Southern Denmark

Jes Søgaard
DaCHE SDU
University of Southern Denmark

CONTACT NI4 FOR...
Reach out for any support or input regarding:

  • Which QoL/outcomes measures to include

  • How to measure costs/which registers to link to

  • Planning analysis

  • Planning and putting together DHTC/approval submissions


CURRENT PROJECTS

Measuring quality of life in cancer

Mapping EORTC QLQ-C30 on to EQ-5D-5L

  • 2000+ cancer patients (all cancers) surveyed x4 over one year with QLQ-C30 and EQ-5D-5L
  • Data linked to registers for demographics, healthcare utilization, health status, etc.
  • Goal: map EORTC on to EQ-5D to get an algorithm for calculating QALYs without weights

Compare instruments for QoL in Danish Cancer patients

  • Danish value set for EORTC QLQ-C10D (subset of QLQ-C30 for calculating QALYs) about to be published
  • Goal: compare QALY estimates produced by EQ-5D-5L, QLQ-C10D value set and the mapping algorithm to establish the most suitable way of measuring QoL in Danish cancer patients
Inequalities in cancer

Socioeconomic status and quality of life

  • Comparing quality of life and access to services in cancer patients across the socio-economic gradient
  • Education, income, region.

Distributional cost-effectiveness evaluations (DCEA):

  • Looking at how ctDNA interventions impact on not only the efficiency, but also equity
  • Innovative statistical method to combine the two concepts of efficiency and equity
Support and guidance for health economics data collection

Liza Sopina has time set aside to support projects in the ctDNA Center with integrating economic evaluation into study design and funding applications. Do not hesitate to contact her for support and inputs.

OBJECTIVE ...

... A central element in the philosophy of the center is dissemination of knowledge and results within the ctDNA Center, to the scientific community, to the patients, and to the clinical and political decision makers.

Education and knowledge dissemination will take place on several levels:

  1. Workshops and PhD courses. These will be conducted in collaboration with the DCCC ctDNA network and the Graduate Schools at the Universities of Copenhagen, Aarhus, Aalborg, and Southern Denmark

  2. Annual meetings for ctDNA Research Center network. Results, progress and new ideas of the Research Center will be presented and discussed at the annual meetings

  3. Dissemination at national and international meetings and symposiums with participation of international experts. Dissemination at meetings organized in collaboration with patient advocacy groups and aimed at providing the public with information of the results and progress of the Research Center

  4. Following documentation of clinical benefit and cost-effectiveness of ctDNA guided cancer care we will generate and disseminate business analyses and other decision and implementation supporting information to the hospitals and health regions

  5. Dissemination to public awareness portals (radio, television, and social media). In close collaboration with the communication departments of the participating institutions, to target key Health Care Media to provide national media coverage of major events in the Research Center e.g. opening of the center, funding, publication of major findings.


LEADERS

Claus Lindbjerg Andersen
Department of Molecular Medicine
Aarhus University Hospital

Morten Mau-Sørensen
Department of Oncology
Rigshospitalet

CONTACT NI5 FOR...

  • If you have any scientific publications, popular science publications or different kind of dissemination of knowledge and results

  • Ideas for workshops

  • Themes for the Annual Meeting

  • International and national meetings/conferences of interest for the whole ctDNA Center

  • Content on LinkedIn or X to be shared at the ctDNA Center page


CURRENT PROJECTS

Planning events

Events during the year:

  • Annual Meeting
  • Journal Club
  • Seminar Series
  • PhD courses
  • Workshops
  • Public awareness
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ADDRESS FOR THE SECRETARIAT

Science Center Skejby, MOMA
Brendstrupgårdsvej 21, build. A
8200 Aarhus N