(1) Bioresource Overview

Project description

The BLUL was initially created using the human-based biomaterials and related clinical/questionnaire data collected from the “Role of multidrug transporters in pharmacokinetics and toxicology – in vitro tests in pharmaceutical and clinical practice” project (Supported by the Polish POIG grant 01.01.02-10-005/08 TESTOPLEK from the European Regional Development Fund). The main goal of TESTOPLEK project (in a part of genetic study) was to create a genetic profile of Polish population [1, 2, 3, 4]. Over 10.000 individuals nationwide were involved to create a retrospective POPULOUS collection (POPUlation – LOdz UniverSity Biobank) and registered in 2013 in the BBMRI catalogue of the population collection (Biobanking and Biomolecular Resources Research Infrastructure). In 2014 Biobank Lab started to operate as a separate scientific unit of the Department of Molecular Biophysics. The main goal of the BLUL is to promote research via sharing biospecimens and related clinical/questionnaire data with interested scientific institutions. Our next step is to implement policies to share genomic data (microarrays, whole exome sequencing data, microbiome, targeted genotyping data) related to a different collection. The BLUL policies and procedures have been formed and formulated according to the ISBER Best Practices for Repositories Guidelines [5].

The BLUL is composed of two main complexes. CORE LAB – principal place of preparation of biological material for biobanking (e. g. blood fractionation, isolation of nucleic acids), place of storage of biological material, conducting mass genetic assays (e. g. the study of polymorphisms, gene expression (Q-PCR) and quantitative assessments of selected parameters). BIG DATA LAB – the spare/emergency storage location of biological material, automated microarrays analysis (e. g. SNP, gene expressions microarrays, analysis of the methylation status) and analysis using the NGS technology [6, 7]. Additionally, all bioinformatics analyzes are carried out with the use of widely available commercial software.

Classification (1)

Human

Species

Human

Classification (2)

BLUL collection includes biological samples with associated anthropological, clinical, molecular data, based on questionnaires, pathology reports, physical examinations – depending on collection.

Context

Spatial coverage

Description: Main collection of the BLUL is POPULOUS, which is based on general Polish population

Northern boundary: 54º50’ N

Southern boundary: 49º00’ N

Eastern boundary: 24º09’ E

Western boundary: 14º07’ E

Temporal coverage

Since 2010 to present, on-going with no fixed expiry date.

Temporal coverage for accessibility

N/A

(2) Methods

Steps

All laboratory methods related to the collection of biomaterials have been evaluated and standard operational procedures (SOPs) have been established (e.g. biomaterial collection, aliquots sampling, DNA isolation, measurement of DNA concentration, DNA normalization, quality testing of DNA samples). Starting from 2015 routine lab methods and SOPs have been validated during Biospecimen Proficiency Testing Programme IBBL (Integrated BioBank of Luxembourg) endorsed by ISBER (International Society for Biological and Environmental Repositories). The BLUL collects samples of different origin – mainly saliva and DNA and for some registered collections blood, serum, plasma or FFPE tissue. All the data records are anonymized to ensure the security and privacy protection of the participants.

All the steps involved in biomaterial preparation are recorded in the BLUL Sample Management System (SMS) by laboratory personnel. Only well-trained Biobank Lab staff are authorized to manage the samples.

Stabilization/preservation

All samples (saliva, blood) are stored in monodimensional barcoded tubes.Aliquotes are stored in 2D barcoded tubes. FFPE sections are stored in monodimensional barcoded tubes.

Saliva is stored in ORAGEN Kit DNAGenotek;

DNA for the purpouse of backup storage is kept in DNA Stable Plus (Biomatrica).

Type of long-term preservation

Freezing in mechanical freezers (DNA aliquots, blood).

For long-term preservation saliva and DNA samples are stored in Oragene (DNA Genotek Inc.) and Biomatrica, respectively.

Storage temperature

Depending on material (e.g. 80°C; 20°C; 4°C; room temperature).

Shipping temperature from patient/source to preservation or research use

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

Shipping temperature from storage to research use

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

Quality assurance measures

Different and rigorous quality control measures are applied to all procedures performed by the Biobank Lodz. The host laboratory’s operational quality system is validated within Proficiency Testing Programme performed by IBBL [8] in order to guarantee high quality standards in terms of procedures and sample preservation. The principal measures for ensuring the quality of the samples include a number of procedures to:

  • govern the sterilisation of reagents and laboratory materials
  • guarantee the integrity of nucleic acids using real time PCR sex testing [9], MultiNA, and concentration measurement
  • ensure an immediate intervention in case of an electrical blackout to safeguard samples with proper alarm systems for all freezers
  • have a back-up storage for each sample in separate freezers and boxes in separate buildings
  • maintain data bases up-to date

Source of associated data

Source of the associated data: collected during the research projects aiming at the collection setting up, depends on the collection type and can include hospital medical records and laboratory reports, both paper and electronic; instrumental data obtained from post-processing analysis and questionnaires within the specific research project can be added.

The BLUL uses an in-house biobank database and biobank information management system designed for both the registration of biomaterials and sample management. Next goal is to prepare web-based interface for the database to enable external users to search and find appropriate samples for their research project(s). The system for genetic data storage and sharing is in preparation phase.

Ethics Statement

The Biobank Lab operates regarding to:

  1. Declaration of Helsinki: ethical principles for medical research involving human subjects [10].
  2. Polish Data Protection Authority, Data Protection Code [11].

Approvals obtained from University of Lodz’s Review Board:

  1. Resolution of KBBN-UŁ from 17/06/2010.
  2. Resolution of KBBN-UŁ/I/9/2013.
  3. Resolution of KBBN-UŁ/I/10/2013.
  4. Resolution nr 7/KBBN-UŁ/II/2014.
  5. Resolution nr 8/KBBN-UŁ/II/2014.

The Contributors who have been responsible for recruitment of the participants evaluate all access requests to ensure compliance with the informed consent documentation.

All donors were recruited within approved research protocol by the Institutional Review Board (IRB) of the University of Lodz or other IRBs from the Institutions collecting biological material. All operations on collected biospecimens (reuse) within approved research protocol by the IRB of the University of Lodz.

To get an access to the services of BLUL, the following procedures have been implemented:

  1. initial contact with the staff manager of the Biobank.
  2. sample contributor provides a signed copy of the Informed consent form
  3. agreement form is signed to accept the rules and policies of the BLUL
  4. assignment of an individual and unique code to samples and collection is granted by the director of BLUL
  5. samples are coded in data storage system BIMS (Biobank Information Managing System).

The BLUL use the model of sharing in which the Contributor (institution/contributor/principal investigator) maintains ownership of the collection (including related clinical/questionnaire data). The biospecimens are governed by the Contributor. Reuse of collected biomaterials depends on the agreement of the Contributor and opinion of IRB of the University of Lodz. The Contributor has agreed to share collected biomaterials with related data based upon scientific merit and correlation with studies subjects. All biospecimens with related data (stored in the BLUL) have been consented to secondary use by the study participants or by the IRB of the University of Lodz.

There are no limitations in sharing samples and related data from POPULOUS collection. Restrictions of sharing of other collections deposited in BLUL depend on Contributors.

Constraints

None, except the Polish regulation on personal data and biological material.

(3) Bioresource description

Object name

Human Genomics and Genetic samples and data.

Bioresource name

Biobank Laboratory, Department of Molecular Biophysics, Faculty of Environmental Protection, University of Lodz

BLUL, Biobank Lodz

Bioresource location

Biobank Lab, Department of Molecular Biophysics, Faculty of Environmental Protection, University of Lodz

CORE LAB – Faculty of Biology and Environmental Protection, Building A, 5th floor, 12/16 Banacha Street, 90-237 Lodz

BIG DATA LAB – Building of the Dean of the Faculty of Biology and Environmental Protection, Ground floor, 14 Pilarskiego Street, 90-237 Lodz

Biobank Lab, 14 Pilarskiego Street, 90-237 Lodz, Poland

Bioresource URL

www.biobank.uni.lodz.pl

Identifier used

N/A

Bioresource type

Genomic and Genetic Biobank

POPULOUS – population based; Contributor – BLUL/Biobank Lodz; 10.000 donors with detailed information; material collected: saliva.

BREAST – breast cancer; Contributor – BLUL/Biobank Lodz; 800 patients with detailed diagnosis information; material collected: FFPE.

PANC – pancreatic cancer; Contributor – BLUL/Biobank Lodz; 100 patients with clinical follow-up; material collected: blood.

PUPILS – schoolchildren’s collection; Contributor – Department of Anthropology, University of Lodz; 800 donors with detailed information; material collected: saliva.

BREAST ICZMP – breast cancer; Contributor – Polish Mother’s Memorial Hospital Research Institute; 100 patients with clinical follow-up; material collected: blood.

ENDOMETRIOSIS ICZMP – endometriosis; Contributor – Polish Mother’s Memorial Hospital Research Institute; 170 patients with clinical follow-up; material collected: blood.

BREAST IBUL – breast cancer; Contributor – Department of Molecular Genetics University of Lodz; 250 patients diagnosed; material delivered: DNA.

Type of sampling

Depends on stored collection: population, disease based, longitudinal cohort.

Anatomical site

N/A

Disease status of patients/source

Pancreatic cancer, breast cancer, obesity, other.

Clinical characteristics of patients/source

Age:18–80, sex: male and female. Availability of treatment information, inclusion criteria or/and stage of the disease at time of collection depends on various projects specifications.

Size of the bioresource

The BLUL at University of Lodz is not a project but rather a research infrastructure of the university with no expiry date. The number of full time employees working at BLUL is 4.

Vital state of patients/source

Alive at the sampling.

Control samples

General population from POPULOUS and PUPIL collection.

Biospecimen type

Saliva samples: 12000 (3 ml)

Full blood: 400 (3 ml)

Section of FFPE: 800

DNA aliquots: 40000 with different volumes (0.05–0.4 ml)

Release date

Data and samples are currently available.

Access criteria

The research group in Poland or in other countries are entitled to apply for a research project through a formal application (objectives, description of sample, methods, data needed, timetable); the PI must have a permanent position in his/her organization, all legal and ethical authorizations must be provided. A financial contribution is determined depending on the number and nature of data needed.

For the process of applying for sampling, individual contact with Head of the BLUL is needed. Contact data are available on the BLUL website in English: www.biobank.uni.lodz.pl

(4) Reuse potential

Those who are interested in reuse of BLUL samples and/or data for further laboratory and/or data analyses, replication of previous findings or meta-analyses must contact the Head of BLUL directly. The reuse is possible on a collaborative basis, with the permission of the respective contributor and after obtaining the IRB’s positive opinion.