The Quebec Respiratory Health Network Biobank

Sabrina Biardel1, Christine Racine1, Yvan Fortier2, Andrea Karen Mogas3, Émilie Maillé4, Emmanuelle Brochiero4,5, François Maltais1, Anne-Marie Lauzon3,6, Sze Man Tse7, Catherine Laprise8,9, Philippe Joubert1, Éric Rousseau2, Élyse Bissonnette1, Michel Laviolette1, Yohan Bossé1,10,* and Simon Rousseau3,6,* 1 Institut universitaire de cardiologie et de pneumologie de Québec, Québec, CA 2 Faculty of Medicine and Health Sciences, Université de Sherbrooke, Centre de Recherche du CHUS, Sherbrooke, Québec, CA 3 Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montréal, Québec,CA 4 Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, CA 5 Département de médecine, Université de Montréal, Montréal, Québec, CA 6 Department of Medicine, McGill University, Montréal, Québec, CA 7 Centre hospitalier universitaire Sainte-Justine, Montréal, Québec, CA 8 Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Québec, CA 9 Centre de santé et de services sociaux du Saguenay, Chicoutimi, Québec, CA 10 Department of Molecular Medicine, Université Laval, Québec, CA * Co-senior authors Corresponding author: Simon Rousseau, Ph.D. (simon.rousseau@mcgill.ca)

The Quebec RHN Biobank was initiated in the late 1990s by founder and visionary respirologist-researcher Dr. Michel Laviolette. The original goal was to facilitate, regulate and ensure optimal research use of human biological specimens in the field of respiratory medicine. The biobank was originally designed for local researchers at the Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ, Québec, Canada). Throughout the years with the help of the RHN of the Fonds de la recherche du Québec -Santé (FRQS), the biobank expanded into a province-wide collaborative biorepository that collects human biological materials for research in a wide range of respiratory diseases. The multisite infrastructure is linked to a centralized database. A coordinating committee is in place to harmonize and standardize specimen handling, technical best practices, data entry and management, as well as ethical and legal issues. Activities at each site vary with time owing to the level of interest of local researchers and evolving clinical workflows. As of today, the physical repository of the Quebec RHN Biobank is distributed across six sites ( Table 1).
Biological specimens are from patients with different respiratory conditions including pediatric and adult asthma, lung cancer, chronic obstructive pulmonary disease (COPD), cystic fibrosis, lung transplant, sleep apnea, pulmonary arterial hypertension, interstitial lung diseases, and acute respiratory distress syndrome (ARDS), as well as healthy controls for selected specimens. A comprehensive set of clinical data is also available, tailored to each specific condition, and denominalized in the database. Researchers using this resource benefit from a well-established biobank network that uses a common and stringent set of procedures allowing a quick access to rare samples needed in specific research fields (e.g. molecular anomalies in pulmonary arterial hypertension), as well as a large number and volume of samples in other fields (e.g. genomics). The maturity and size of sample collections vary by medical conditions. The different collections are built with the long term vision to allow world-class research [1][2][3][4][5]. The Quebec RHN Biobank is also a flexible and dynamic infrastructure that can meet specific user needs for the academic, biotechnology and pharmaceutical sectors including prospective studies.
The performance of the Quebec RHN Biobank has increased progressively throughout the years, which is tracked by annual reports generated by each site. The samples and clinical data from the biobank are now contributing to roughly 20 scientific manuscripts per year and fuel more than 50 ongoing research projects.

Species
Homo Sapiens.

Classification (2)
Biological samples and associated data for epidemiological, biological and genetic research in respiratory health.

Spatial coverage
The Quebec RHN Biobank is a multi-site infrastructure located in the province of Québec, Canada. Participants and samples are from six centers located in four cities (latitude and longitude coordinates are provided):

Temporal coverage
The biological specimen collections were initiated at different time. Figure 1 shows the initial year of sample collection as well as the cumulative number of patients (left panel) and samples (right panel) by respiratory condition. The first collection was established in 1996 to procure bronchial biopsies from patients with asthma. Throughout the years, the types of samples collected have diversified. In 1999, the acquisition of tumor and nontumor lung specimens from lung cancer resection started. Other collections were established in 2001 for COPD and sleep apnea, 2007 for pulmonary arterial hypertension, 2008 for lung transplant and cystic fibrosis, and 2010 for interstitial lung diseases. The recruitment of most of these collections is still ongoing. The rate of recruitment varies among collections based on the frequency of the diseases and the level of interest of researchers involved. For example, the rate of lung tissue acquisition from lung cancer resection has progressively increased with time and we are now collecting samples from 350-400 new patients annually.

Temporal coverage for accessibility
The Quebec RHN Biobank is building on a vision to sustain the infrastructure in perpetuity. The samples and corresponding clinical data are kept as long as they are of scientific interest, but for a maximum duration of twentyfive years as per the consent form. However, at the end of this period, members of the biobank committee have the option to request an extension of accessibility through the research ethics committees of the affiliated centers.

(2) Methods
The acquisition of biological specimens in the Quebec RHN Biobank follows different biobanking collection strategies. In one typical acquisition strategy, called the biobank strategy, samples of potential interest are stored until needed and are not associated to any specific projects. In the prospective collection strategy, samples are collected to meet the requirements for a specific project or investigator(s). The collection of the Quebec City Case-Control Asthma Cohort [6,7] is an example of this prospective collection model. Finally, the third collection strategy is the clinical trial strategy, where samples are collected from clinical trials. In this scenario, samples are usually obtained exclusively for a specific clinical trial, but additional or residual tissues may become available for biobanking according to the biobank strategy provided that the original consent allows secondary use. It should also be emphasized that the biobank staff is open to evaluate the feasibility of new sample processing requirements to meet the need of specific projects including prospective studies.

Steps
Patients receiving care or research participants at each site are invited to sign the consent form to contribute data and samples to the Quebec RHN Biobank. Blood derived specimens are collected by qualified nurses. Tissues derived from surgeries are collected by pathologists, predominantly from excess tissue not required for diagnosis. Other types of tissues (e.g. bronchial biopsies) are obtained in bronchoscopy by respirologists. The samples collected are then processed by dedicated biobanking staff based on standardized protocols for collection, handling and storage. For each participant, an electronic form is filled, which includes general and disease-specific clinical information, dates of acquisition as well as information concerning sample processing, i.e. identification code, quantity, location of storage, and type of preparation. Electronic data from all sites are entered in a centralized database. A management framework of the Quebec RHN Biobank is approved by the ethics committees of each site and reviewed annually. This framework provides a description of the biobank, ethical principles, measures to assure privacy, administrative management structure, data and database management, as well as rules and procedures of access for researchers.

Stabilization/preservation
Stabilization and preservation are specific to the type of tissues collected. Table 2 describes the types of biological specimens available and corresponding stabilization/preservation methods.

Type of long-term preservation
The biological samples are frozen and preserved in OCT (optimal cutting temperature), cryovial, liquid nitrogen tanks or in FFPE (formalin-fixed and paraffin-embedded) ( Table 2).

Storage temperature
Most types of biological samples are stored in monitored ultra-low temperature freezers equipped with alarms and back-up energy supply ( Table 2). Primary lung cell lines are conserved at -150°C in freezers or at -196°C in liquid nitrogen tanks. In case of electrical failure, a generator will take over and maintain the ideal temperature for adequate preservation of samples. Security will response to the alarm and call the person in charge printed on the front door of the freezers.
Shipping temperature from patient/source to preservation or research use The biobank sites are located in hospitals specialized in respiratory diseases and biological specimens are stored on-site. On rare occasions, biological specimens can be collected at one site and stored at a second site. In such cases, samples are shipped in dry ice for frozen samples or room temperature for others. The transfer of fresh tissues for isolation of primary cells from the patient source to the biobank repository is carried out on ice. Procedures are in place at each site for the packaging and transport of ambient temperature and frozen biospecimens to ensure their integrity and safety. This includes packaging specifications to maintain appropriate temperature conditions (wet ice, dry ice, and liquid nitrogen handling), shipment regulations for hazardous materials, shipment logs, delivery notifications, and confirmation of delivery.

Shipping temperature from storage to research use
Biological specimens are shipped on dry ice or at room temperature depending on the storage temperature.

Quality assurance measures
The Quebec RHN Biobank is a member of the Canadian Tumor Repository Network (CTRNet) as well as the International Society for Biological and Environmental Repositories (ISBER). The Quebec RHN Biobank adheres to the best practices set forward by these organizations in terms of sample collection, preservation, storage, and distribution. The quality assurance of biological specimens is directly related to the application of the management guide and the content of the procedures manual, which consists of a description of a set of methods concerning personnel, equipment, techniques, and documentation. This includes compliance with Good Laboratory Practice (GLP), clinical practice based on the International Conference on Harmonization (ICH), approved technical protocols, training of personnel, controlled access to facilities, efficient and well-maintained equipment, and security for temperature and fire. This guarantees that the samples are prepared and preserved to ensure optimal research use. Procedures are in place throughout the whole process including consent, collection, handling, preservation, storage, distribution, and transport. Steps involved in the tissue collection are thoroughly coordinated to decrease time between the point of acquisition and storage. For example, the time from surgical removal to storage is less than 30 minutes for the lung cancer collection. Quality standards of tissues are also reviewed by pulmonary pathologists. Finally, quality assurance on samples is also performed iteratively from the results of a large number of projects using the specimens. Feedback from users are consistently taken into account to modify or fine-tune our methods.

Source of associated data
Biological specimens are thoroughly annotated and associated clinical data are tailored to each respiratory condition. The source of data depends on the biobanking collection strategies described above (biobank, prospective collection, and clinical trial strategies). Accordingly, the source of data can come from a specific research protocol or directly from the medical records of patients treated by standard of care. Trained staff at each site extracts clinical data from these sources and ensure data entry manually using electronic forms specific for each respiratory condition. Data are then stored in a centralized database. For the cystic fibrosis collection at the CRCHUM, clinical data are also entered into the Canadian CF Registry.

Ethics Statement
The main ethical principle that governs the Quebec RHN Biobank is respect for human rights with regard to physical integrity, cultural and spiritual values, and dignity. The highest ethical and scientific standards are applied. The samples come from voluntary donations and all participants provide written informed consent. Donors' privacy and the confidentiality of data are preserved at all times. A unified informed consent for adult is shared across sites, but adapted to the needs of each site and specific ethical approvals. The consent allows the use of samples for biomedical and genetic research from academic and industry researchers. For one site (CHUSJ), the consent is intended for minors and also allows health and genetic research for academic and industry researchers.

Constraints
Use of samples and data are limited to research in respiratory diseases. The samples for some collections are exclusive to the investigator(s) in charge and in this scenario; access may be possible through research collaboration only.

(3) Bioresource description Object name
The Quebec Respiratory Health Network Biobank

Bioresource name
The Quebec Respiratory Health Network Biobank

Bioresource location
The biological repositories are located at six sites. Each site stores a unique part of the biobank (no duplicate samples across sites). An example of sample identifier is "IAP 01578-15". The first letter corresponds to the respiratory condition (e.g. asthma, COPD) of the patient. The second letter is the type of sampling (e.g. aliquot, slide) and the third letter is the type of sample (e.g. induced sputum, blood). In the above example, we have a patient with interstitial lung diseases (I) for which we have collected an aliquot (A) of plasma (P). The following five digits number is automatically generated by the central server. Finally, the last two digits indicate the year the sample was collected (2015 in the above example). This seven digits number connects each sample to a site. Accordingly, the origin of samples can be traced without access to sensitive data from the participants. A unique number across all sites is also convenient to manage inventory. All information concerning the identity of the participants is stored in the private section of the database. Each site has its own private section and is responsible for the information contained therein. Mechanisms of security are in place to keep the information confidential. Information in the private section of one site cannot be consulted by other sites. The shared database is housed on a web server and is accessible to authorized personnel only. Credentials are needed (user ID and password) to access the shared database. The shared database contains descriptive information related to the participants (e.g. age, gender, weight, medication, pulmonary function) and their respective samples (e.g. quantity, type of preparation, location of storage). The shared database is denominalized. The link between the nominal and descriptive information is a unique ID number for each subject. This number can be used to trace back the original donor, but only the coordinators at each site can make this link.

Bioresource type
Respiratory diseases including pediatric and adult asthma, lung cancer, COPD, cystic fibrosis, lung transplant, sleep apnea, pulmonary arterial hypertension, interstitial lung diseases, and ARDS.

Type of sampling
Samples can be obtained in the context of clinical care (e.g. lung cancer resection) of patients treated for various respiratory diseases at different hospitals in the province of Québec. Samples can also be acquired through participation to specific research protocols or clinical trials requiring tissue sampling.

Anatomical site
Most samples are from the lungs, airways, and blood. However, samples from the nose, trachea, quadriceps, uvula, esophagus, thymus and heart ventricle are also available for research in respiratory diseases.

Disease status of patients/source
Pediatric and adult asthma, lung cancer, COPD, cystic fibrosis, lung transplant, sleep apnea, pulmonary arterial hypertension, interstitial lung diseases, and ARDS.

Clinical characteristics of patients/source
Clinical characteristics relevant to each medical condition are collected. Table 3 shows an overview of clinical data available. Table 4 indicates the number of subjects and samples by respiratory condition.

Vital state of patients/source
Post-surgery and long-term outcome including vital status and relapse are available for the lung cancer collection. Vital status is also available for pulmonary arterial hypertension and interstitial lung diseases. Some postmortem samples are also available.

Clinical diagnosis of patients/source
Pediatric and adult asthma, lung cancer, COPD, cystic fibrosis, lung transplant, sleep apnea, pulmonary arterial hypertension, interstitial lung diseases, and ARDS.

Pathology diagnosis
The full pathology report is available for the lung cancer collection as well as for some patients with interstitial lung diseases. Pathological report is also available for specimens collected during autopsies for patients with interstitial lung diseases and pulmonary arterial hypertension. For the lung cancer collection, pathologic classification and staging is updated according to the classification of lung tumors from the World Health Organization and the lung cancer staging project from the International Association for the Study of Lung Cancer (IASLC).

Control samples
Control samples are not systematically collected as part of the biobank. However, some control samples are available for the majority of respiratory conditions. For examples, nasal polyps from participants with or without cystic fibrosis are collected and bronchial biopsies from patients with or without asthma. Moreover, some research protocols require the collection of control samples, e.g. the Quebec City Case-Control Asthma Cohort [6,7]. Trachea, bronchi, and parenchyma samples from lung donor are also collected during lung transplantation. Non-tumor lung samples from lung cancer resection are available for most patients.

Access criteria
Samples are available to academic, biotechnology, and pharmaceutical researchers following requests that are approved by the scientific and ethics committees. The following steps are recommended for samples and data request.
1) Requestors can send an email to the biobank contact to check for tissue and data availability. It is important to specify the type of respiratory disease (asthma, cystic fibrosis, etc.), biological specimens (serum, lung tumor, etc.) and sample size needed. 2) The biobank staff will evaluate tissue availability and feasibility of the project, and may propose alternatives as needed. Collaboration with local researchers may also be proposed. 3) The biobank will provide an estimate of costs associated with the samples and clinical data. 4) Requestor must then provide a research protocol and documentation confirming ethics approval from his/her own institution. 5) The research protocol must also receive approval from the scientific and ethics committees that oversee the specific biobank site. 6) The biobank will then provide a quote and the biological material transfer (MTA) agreement. 7) Once the MTA is signed by both parties, the biological materials and data will be sent to the requestor.

(4) Reuse potential
Biological specimens and corresponding clinical data may be reused according to the access criteria described above.
Approval of submitted projects depends on samples and data availability. Samples and clinical data from a single donor can be used for different projects. For example, if DNA is extracted from samples, residual samples are kept for new projects that will go through the same access criteria. Data/results generated by researchers using the samples do not need to be returned at the Quebec RHN Biobank. However, researchers must return any material that will not be used for the accepted project and are not allow to use residual samples for other purposes. For some collections, research collaboration agreement needs to be established between the requestor(s) and investigator(s) in charge. Partnerships with academic and commercial entities to co-develop companion diagnostics, biomarkers or others are welcome. ful to the dedicated research staff at the Quebec RHN Biobank for storing of biological materials and continuously updating the clinical database.