(1) Bioresource Overview

Project description

The Assistance Publique Hôpitaux de Marseille (AP-HM) started its biobank activity in 1995 in various hospitals to support internal research. Since 2015, the different biobank sites have been grouped together at Timone Hospital and the biobank still works with all the other AP-HM hospitals, which represent over 900,000 consultations and over 72,000 surgeries per year; furthermore the biobank has partnerships with private hospitals in the city. This network enables the biobank to reinforce its activity on its 3 different sites certified AFNOR NF S 96 900 and ISO 9001 (2015).

Since 2018, the biobank sites have been regrouped administratively at the Biology-Pathology department to reinforce their collaboration and facilitate their management.

The Vascular Hematology (HV) site is located in the Hematology department of the accredited ISO 15189 AP-HM Medical Laboratory, at the Center for Exploration of Hemorrhagic and Thrombotic pathologies (CEHT); and works currently under the direction of Pr. Pierre Morange. Part of its activity also relates to research on Venous Thrombo-embolism (VTE) diseases, for which they started their biobank activity. The HV site of the biobank expanded its activity, related to their expertise in the management of blood and its derivatives, for other diseases towards prognostic research.

The biobank site TAC (Tissues, DNA and Cells) is located in the Medical Genetics Department of the accredited AP-HM Medical Laboratory and is presently represented by Dr. De Sandre-Giovannoli Annachiara. Its activity is focused on DNA samples and cell lines issued from patients affected with rare genetic disorders, namely including extremely rare disorders characterized by premature aging.

Led by Pr. Dominique Figarella-Branger, the biobank’s TBM (Tumorbank and Biobank of Muscles) site works in close collaboration with the pathology department, concentrating its activity on tissue samples. The site initiative focused first on brain neoplasms and developed the biobank activity by implementing more types of neoplasm and muscle disease samples, to support internal medical research as well as future collaboration with national and international institutes.

Classification (1)

Human.

Species

Homo Sapiens.

Classification (2)

Biological samples and associated data.

Keywords

Certified Quality Management System, neoplasm, rare genetic diseases, hematological diseases, cardiovascular diseases

Context

Spatial coverage

Description: Marseille, France

Latitude: 43.288736

Longitude: 5.405637

Temporal coverage

The collection of bioresources started in 1995, with no termination date.

Temporal coverage for accessibility

N/A

(2) Methods

Steps

Biological samples and their clinical data are obtained from patients willing to support research or clinical trials by an agreement that is registered with a written informed consent; ranging from diagnosis with a broad consent for research to a more specific consent to the research project including genetic analyses.

All the samples and the minimal set of clinical data associated, provided by the pathology department and/or medical records, are registered into a Laboratory Information Management System (LIMS) to support the Quality Management System in place in the biobank and to comply with the GDPR (General Data Protection Regulation) requirements.

Samples stored in the biobanks can be collected from different sources, e.g. exceeding biopsy/surgical diagnostic material, or specifically prepared upon request for a given project: formalin-fixed paraffin-embedded (FFPE), frozen tissues, Tissue MicroArrays (TMA), slides, whole blood, serum, plasma, DNA, RNA, Peripheral Blood Mononuclear Cells (PBMC), urine, CerebroSpinal Fluid (CSF) and cells.

Stabilization/preservation

Tissues are Formalin-Fixed Paraffin-Embedded or snap frozen in Liquid Nitrogen with or without Isopentane.

Blood samples are taken on EDTA tubes for DNA extraction and on Heparin Lithium or ACD vials (Anticoagulant Citrate Dextrose solution) for peripheral blood mononuclear cells (PBMC) separation; Plasma on EDTA or citrate tubes and Serum on clot activator tubes.

Blood derivatives (plasma, serum) are processed within 4H after sampling (best within 2H), PBMC separation within 48H and DNA within 5 days.

Fibroblasts culture from skin biopsy kept at room temperature is processed within 24H.

DNA extraction from blood, cells or tissues can be automated or manual.

RNA may be extracted from stabilized blood/tissue samples.

Type of long-term preservation

All frozen samples are stored in freezers or vapor phase nitrogen tanks and the storage temperature is monitored with Oceasoft™.

Formalin-Fixed Paraffin-Embedded (FFPE) are stored at room temperature; TMA blocks and sections in refrigerators.

Lymphoblastoid cells lines: PBMC immortalized with Epstein-Barr virus (EBV), Fibroblast cell lines, tissue biopsies DNA, plasma and serum are stored in freezers.

Storage temperature

Room Temperature (±20°C): FFPE block and slide

+4°C: TMA slide and DNA (extracted from tissue)

–20°C: DNA (extracted from blood), urine (as required by user)

–80°C: Frozen tissue, DNA (extracted from blood), urine, Cerebro Spinal Fluid (CSF) and blood derivatives

–150°C: Frozen tissue, Fibroblasts, PBMC, Lymphoblastoid cell line

Shipping temperature from patient/source to preservation or research use

–150°C (nitrogen vapor phase shipper); –80°C (on dry ice); 0–4°C (on ice); 18–25°C (room temperature).

Shipping temperature from storage to research use

–80°C (on dry ice); 0–4°C (on ice); 18–25°C (room temperature).

Quality assurance measures

Certified Quality Management System (NF S 96 900 and ISO 9001: 2015)

Internal audits and External Audits (EQS)

Medical laboratories – Requirements for quality and competence ISO 15189: 2012 (COFRAC: “COmité FRançais d’ACcréditation”)

Source of associated data

Every sample is registered with a minimal set of clinical information provided at the collection of the samples from medical records. Each designated cohort of samples is associated with specific medical and/or socio-economic data compiled for the disease of interest by the cohort manager. Additional data can be obtained with the institutional medical database, from the clinician, on request to specific approved project.

Ethics Statement

AP-HM’s multi-site biobank activity is declared to the government: site HV: DC-2008-880, site TAC: DC-2008-429 and site TBM: DC-2013-1781; the APHM biobank is authorized to release samples for external research projects: AC-2018-3105.

The informed consent sheets used for the different collections have been submitted and approved by a relevant French Research Ethics Committee (CPP: “Comité de Protection des Personnes”).

The different software used by the biobank are declared to the CNIL (“Commission Nationale de l’Informatique et des Libertés”) in charge of the application of the GDPR.

Constraints

Each project, which requires import and/or export of samples by the biobank to another country, needs to be specifically submitted by the biobank to the French government. Collections must meet ethical and regulatory constraints of the French government and be approved by the relevant French research ethics committee (CPP).

(3) Bioresource description

Object name

The Biological Resource Center of the Assistance Publique Hôpitaux de Marseille.

Bioresource name

The Biological Resource Center of the Assistance Publique Hôpitaux de Marseille.

Bioresource location

Biobank site HV: Hematology biological department, Timone Adults Hospital, 1st floor, 264 rue Saint Pierre, 13385 Marseille cedex 5

Biobank site TAC: Medical Genetic-Cellular Biology department, Timone Children Hospital, 8th floor, 264 rue Saint Pierre, 13385 Marseille cedex 5

Biobank site TBM: Building K, Timone Hospital, 264 rue Saint Pierre, 13385 Marseille cedex 5

Bioresource contact

Biobank site TBM: bcb-tumorotheque@ap-hm.fr

Biobank site HV & TAC: crb.timone.marseille@ap-hm.fr

Identifier used

N/A

Bioresource type

Cancer, Muscles, rare genetic diseases, cardiovascular diseases, venous thrombotic diseases, rare platelet disorders. The main collections available are represented in Figure 1 (HV), Figure 2 (TAC) and Figure 3 (TBM).

Figure 1 

HV site’s main collections of blood samples and derivatives (total N: 120,474 samples). The numbers represent the number of samples of each category.

Figure 2 

TAC site’s main collections of DNA and cells (total N: 17,194 samples). The numbers represent the number of samples of each category.

Figure 3 

TBM site’s main collections of frozen tissues (total N: 11,458 samples). The numbers represent the number of samples of each category.

Type of sampling

Disease based; sampled in clinical care; sampled in a research protocol; clinical trial samples; retrospective sampling of pathology archives, familial studies.

Anatomical site

Samples are collected from anatomical site declared by the biobank: Brain, Heart, Lungs, Liver, Pancreas, Intestines, Kidneys, Muscles, Bones, Tendons and ligaments, Bladder, Skin, Peripheral blood, Bone marrow, Soft tissue tumors, Prostate, Lymphoid tissues, Ear, Nose and Throat (ENT), Digestive, Nervous system. Additional anatomical site can be submitted by the biobank to the French Government.

Disease status of patients/source

Thrombophilic patients and relatives

Hemorrhagic patients with platelet defect

Women under progestative pill

Cancer

Myopathy

Genetic disorders (suspected or confirmed)

Clinical characteristics of patients/source

N/A

Size of the bioresource

There are currently over 190,000 samples available for researchers from about 40,000 donors.

Vital state of patients/source

Alive and deceased

Clinical diagnosis of patients/source

Cancer

Myopathy

Atherothrombosis

Acute coronary disease

Venous Thrombo-Embolism (VTE) [1, 2] (ICD I26.9, I80.1, I80.2, Z86.7A, Z86.7B, Z92.1)

Hemorrhagic disease (including constitutional platelet defects)

Neuromuscular diseases

Developmental abnormalities and/or mental retardation

Hemoglobinopathy

Deafness [3]

Epilepsy

Premature aging syndromes [4, 5, 6]

Other constitutional genetic disorders [7]

Normal

Pathology diagnosis

The data from pathology reports are available for the cancer samples collection. The biobank is authorized to collect or requalify samples from diagnostic to a research purpose, each tissue from the “Anatomical Site” listed above; but its main collection of frozen tissues[8, 9] directly available are:

Brain neoplasm (ICD C71, D32, D33, D35)

Thorax neoplasm (ICD C34, C37 C38, etc.)

ENT neoplasm (ICD C02, C06, C08 C10, C14, D11, etc.)

Myopathies (Minor Anomalies, Inflammatory, from Energy Metabolism, Congenital, Muscular Dystrophies, etc.)

Control samples

Healthy volunteers, relatives without any disease (at the age of enrolment).

Biospecimen type

Frozen tissue: number dependent on tissue size

FFPE archival blocks: number dependent on tissue size;

TMA: 3 cores of 20 different patients on average for each block;

TMA section: 5μm each

Blood: Whole blood: 1 to 2 aliquots of 1 ml

Serum: from 1 to 3 aliquots of 500μl

Plasma: from 1 to 6 aliquots of 500μl

Buffy coat: 1 to 2 aliquots of 1 ml

Cells (Fibroblast cell lines, lymphoblastoid cell lines)

DNA: from 20 to 1000μl (at least 50ng/ml)

RNA: 300μl (at least 50ng/ml)

CSF: 1ml

Urine: 5ml and cell pellet

PBMC: 1ml of at least 1.106 cells

Release date

The release date depends on each cohort. Some biological resources under embargo may be available upon request; even for the national collection (eg: Base Clinico Biologique (BCB) Gliomes [10], BCB FREGAT [11], BCB Melbase [12]…).

Access criteria

The application process is by request form completion, accessible from the AP-HM biobank webpage, with submission to the biobank for feasibility review and then to the steering committee. Additional information to be provided to patients and consent forms may be necessary in case of genetic study. Costs are required to cover expenses associated and applicants are required to acknowledge the AP-HM Biobank in scientific publications. All human sample transfers out of the AP-HM hospitals are under the auspices of a Material Transfer Agreement (MTA).

(4) Reuse potential

Terms of the application form and/or the Material Transfer Agreement enjoin researchers to use the biological resources made available as part of the project defined and approved in the application. Researchers are not allowed to transmit the biological material to a third party, except express collaboration within the framework of the project defined in the application and contract.

Researchers are requested to share feedback on the quality of the samples and services provided by the biobank for their research.