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Estonian Genome Center of University of Tartu [EGC] Download as PDF

GENERAL INFORMATION

Name Estonian Genome Center of University of Tartu
Acronym EGC
Last update 02/19/2010

Principal investigator

Andres Metspalu (Population-based biobanks /Prof.)
EGP, University of Tartu

Contact

Andres Metspalu (Population-based biobanks /Prof.)
EGP, University of Tartu
Tartu 50410
Phone: +372 7 440243
Email: andres.metspalu@geenivaramu.eeMail

Website

Funding agencies

  • EGeen Inc. (from 2002 until 2004)
  • Estonian Government

BACKGROUND

The Estonian Genome Project Foundation was founded by the Government of the Republic of Estonia in 2001. The Estonian Genome Project of University of Tartu is a research institute reorganised from the Estonian Genome Project Foundation in April 1st 2007. The Estonian Genome Project of University of Tartu carries out the Estonian Genome Project (EGP) with the goal to create a database (biobank) of health, genealogy and genome data from 100 000 individuals by 2010.
The database will make it possible to carry out research both in Estonia and outside to find links between genes, environmental factors, lifestyles and common diseases (cancer, diabetes, depression, cardio-vascular diseases, etc).
The legal framework for the activities of the EGP consists of the Constitution of the Republic of Estonia, the Human Genes Research Act (HGRA), the Personal Data Protection Act, the Databases Act and the Council of Europe Convention on Human Rights and Biomedicine.
In 2001 the EGP started developing a quality management system and in 2003 received an ISO 9001:2000 certificate.
EGP has laboratory for DNA research, IT unit and data (health information and biological samples) collection unit. There are 40 employees in EGP at the moment.

OBJECTIVES

The goal of the Estonian Genome Project is to create a database of health, genealogy and genetic data that would comprise a large part of the Estonian population – The Biobank. The database will make it possible to carry out research both in Estonia and outside to find links between genes, environmental effects and common diseases (cancer, diabetes, depression, cardio-vascular diseases, etc.) and to apply the information gained from research in making new discoveries in genomics and genetic epidemiology, which eventually lead to increasing the efficiency of health care.

Besides the Estonian medical system the database of the Estonian Genome Project will give an impetus also to the biopharmaceutical industry and will hopefully bring direct investments and resources to Estonia for the financing of scientific research projects.

METHODS

Legend Yes No Unknown

General design

Study design Cohort, mixed design
Type of participants Individuals
Target or final number of participants 50000
Target or final number of DNA 50000

Participant selection / Characteristics of the population

Selection criteria

Yes Age Minimun: 18 years   
Yes Country of residence Estonia

Recruitment procedures

People will be asked by their family physicians or data collectors to become gene donors, they get information about the EGP and after deciding they have to sign the informed consent form, will go through computer assisted questionnaire and 50 ml blood sample will be taken afterwards.

Data Sources

  Cross-sectional Repeated/continuous
Yes Questionnaires to participants/respondents Yes Yes
Yes Direct physical measures Yes Yes
Yes Biological samples Yes Yes
Yes Medical paper
No Electronic databases
No Genealogical records  

Collection procedures

The data collection process at the data collector's office consists of three steps:
• obtaining a Gene Donor Informed Consent
• taking a tissue sample
• filling the questionnaire of Health and Genealogical Data.
As the first step the doctor introduces person, who wishes to become a gene donor, EGP and its goals and the role of a gene donor in the project. If the person wishes to become a gene donor, he or she signs the Gene Donor Consent Form.

After that the data collector fills digital Questionnaire of Health and Genealogical Data by interviewing the gene donor. The questionnaire consists of 15 modules and contains in total 182 questions and filling order is Computer Aided Personalized Interview. Filling of the questionnaire takes approximately 1–1.5 hours. Health questions are according to ICD10 structure.
The filled-in questionnaires are sent to EGP via internet in the form of encrypted documents.

A tissue sample (50 ml of blood) is taken from a gene donor before or after filling of the questionnaire. Each tissue sample is marked with a special bar code. Samples are stored in the data collector’s office in a definite temperature range (6 ± 2 °C) until its delivery to a transportation company.
A courier service delivers tissue samples to EGP within 36 hours from the moment of taking the tissue sample, observing the security and other regulations established.

EGP accepts tissue samples according to the procedures of the ISO standard developed. All tissue samples which conform with requirements are accepted for processing in the EGP laboratory before 48 hours have passed from taking the tissue sample. During the processing the tissue sample is separated into different blood components (plasma, erythrocytes and leucocytes), and DNA is separated from leucocytes. Considering the large number of tissue samples processed, an environment-friendly technique has been developed for DNA separation.

The total amount of DNA separated from each tissue sample is measured, and the quality testing of the DNA separated is carried out with three different methods. The results obtained are stored in the EGP database in a digital form, which allows to supply each DNA sample issued from the gene bank with a document proving its quality. 3.5 ml of blood plasma, 1 ml of leucocytes in a special freezing compound and the total DNA which conforms with quality requirements are stored in the storage facility of the EGP. Special CBS™ Mapi straws are used for packaging and storage. Straws are stored in containers filled with liquid nitrogen, at ultra-low temperature (from -150 to -185 °C), the data are stored in the database under the storage addresses.

The data of gene donors are stored anonymously in the EGP database and they can be connected to the gene donor, i.e. decoded, only in cases stipulated in the Human Genes Research Act.

The data collection process of EGP is in accordance with the international standard GCP (Good Clinical Practice) and the ISO 9001:2000 certificate No. 199057A has been issued to it. According to the Human Genes Research Act, the Data Protection Inspectorate exercises supervision over data collection and data processing by EGP.

Follow up procedures

No information available

Baseline principal variables of interest

Health information

  • Yes Diseases history - ICD-10 All conditions
    • ICD 10; all conditions
  • Yes Familial disease history
  • No Early life
  • Yes Women's health
  • No Quality of life

Physical / Biochemical measures

Yes Body structure measures No Biochemical measures
Yes Body function measures  

Sociodemographic Characteristics

Yes Birth location No Parents birth location
Yes Ethnicity/Race Yes Gender
No Marital status Yes Date of birth

Socioeconomic Characteristics

Yes Education level No Income
Yes Working status  

Life habits / Behaviours

Yes Physical activity Yes Smoking / Tobacco Use
Yes Nutrition Yes Alcohol intake

Physical environment

Yes Passive smoking No Mobile phone use

Sample management

Biological samples

Yes Blood No Buccal cells
No Cord blood No Tissues
No Saliva No Urine

Biological samples format

  Fresh Frozen Dried (paper) Other Specification
Blood No Yes No No

Genome-Wide Association (GWA) analyses

  • Yes Already or currently generating GWA data. Approximate number of participants : 12500

GOVERNANCE

Legend Yes No

Allow access to data or samples to external researchers

Yes Data (questionnaire-derived, measured…)
Yes Biological samples

STATUS

Current status

Phase Start End
Preparation phase/Pilot 1999 2003
Recruitment / initial data collection 2003 2010
Follow-up of participants -- --
Current number of participants recruited 42000 in date of 02/01/2010
Current number of collected DNA samples 42000 in date of 02/01/2010

AVAILABLE DOCUMENTS

  Document type Availability
1 General study protocol
2 Specific protocols/procedures (data collection, samples management, etc.) Andres.metspalu@geenivaramu.eeMail
3 Questionnaires Andres.metspalu@geenivaramu.eeMail
4 Physical and cognitive measures
5 DNA processing
6 IT
7 Ethics
8 Consent forms
9 Pamphlet / project description
10 Governance / ethics documentation
11 Human Genome Research Act

PUBLICATIONS AND RELEVANT DOCUMENTATION

1
Metspalu The Estonian Genome Project Drug Development Research 2004 97-101

2
Laschinski, Ganten, Roots, Köhler, Metspalu [The Estonian Genome Project in the context of European genome research] Dtsch Med Wochenschr 2004 S25-8


General Information

Name Estonian Genome Project Questionnaire
Last update 03/17/2009
Version or reference year EGP-Q-1.00; EGP-Q-2.00; EGP-Q-3.00

Questionnaire owner

  • Estonian Genome Project of University of Tartu

Contact

Andres Metspalu (Population-based biobanks /Prof.)
Estonian Genome Project EGP
Tartu 50410
Phone: +372 7 440243
Email: andres.metspalu@geenivaramu.eeMail

Information on validity

Validation of the questionnaire has not been carried out yet

Methods

Legend Yes No

Respondent

  • Yes Participant
  • No Proxy

Administration environment

  • No Over the phone
  • Yes Hospital, clinic, university or recruitment center
  • No Respondent / Proxy residence

Administration mode

  • No Auto administered
  • No Auto administrated with face to face validation by trained personnel
  • Yes Administrated by trained personel / Physician

Administration format

  • No Paper questionnaire
  • Yes Computerized

Administration language

  • Estonian

Documents

Available Format

  • Adapted questionnaireWeb page
  • Original questionnairePDF

NOTICE: HTML document format may differ slightly from the actual questionnaire. Please refer to the original PDF document for exact reproduction.

General Information

Name Estonian Genome Project Questionnaire
Number of Question Blocks 46

Questionnaire and Question Block List

Click on the View block to see the block of questions related to a domain or a group of domains.
Block 1 View block
  • Sociodemographic Characteristics / Birth location
Block 2 View block
  • Sociodemographic Characteristics / Citizenship
Block 3 View block
  • Sociodemographic Characteristics / Language
Block 4 View block
  • Social Environment / Familial and social environment
  • Sociodemographic Characteristics / Age/Birth Date / Subject's Relatives Age / Birth Date
Block 5 View block
  • Health Information / Familial Disease History (ICD10*) / Certain conditions originating in the perinatal period
  • Health Information / Familial Disease History (ICD10*) / Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
  • Health Information / Familial Disease History (ICD10*) / Diseases of the circulatory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the digestive system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the genitourinary system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the musculoskeletal system and connective tissue
  • Health Information / Familial Disease History (ICD10*) / Diseases of the nervous system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the respiratory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the skin and subcutaneous tissue
  • Health Information / Familial Disease History (ICD10*) / External causes of morbidity and mortality
  • Health Information / Familial Disease History (ICD10*) / Neoplasms
  • Health Information / Familial Disease History (ICD10*) / Pregnancy, childbirth and the puerperium
  • Health Information / Familial Disease History (ICD10*) / Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
  • Health Information / Familial Disease History (ICD10*)
  • Health Information / Familial Disease History (ICD10*) / Endocrine, nutritional and metabolic diseases
  • Health Information / Familial Disease History (ICD10*) / Mental and behavioural disorders
  • Social Environment / Familial and social environment
Block 6 View block
  • Health Information / Familial Disease History (ICD10*) / Certain conditions originating in the perinatal period
  • Health Information / Familial Disease History (ICD10*) / Diseases of the circulatory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the digestive system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the genitourinary system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the musculoskeletal system and connective tissue
  • Health Information / Familial Disease History (ICD10*) / Diseases of the nervous system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the respiratory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the skin and subcutaneous tissue
  • Health Information / Familial Disease History (ICD10*) / Endocrine, nutritional and metabolic diseases
  • Health Information / Familial Disease History (ICD10*) / External causes of morbidity and mortality
  • Health Information / Familial Disease History (ICD10*) / Mental and behavioural disorders
  • Health Information / Familial Disease History (ICD10*) / Pregnancy, childbirth and the puerperium
  • Health Information / Familial Disease History (ICD10*) / Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
  • Health Information / Familial Disease History (ICD10*)
  • Health Information / Familial Disease History (ICD10*) / Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
  • Health Information / Familial Disease History (ICD10*) / Neoplasms
  • Sociodemographic Characteristics / Age/Birth Date / Subject's Relatives Age / Birth Date
  • Sociodemographic Characteristics / Kinship
Block 7 View block
  • Social Environment / Familial and social environment
  • Sociodemographic Characteristics / Age/Birth Date / Subject's Relatives Age / Birth Date
Block 8 View block
  • Health Information / Familial Disease History (ICD10*) / Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
  • Health Information / Familial Disease History (ICD10*) / Diseases of the digestive system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the genitourinary system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the musculoskeletal system and connective tissue
  • Health Information / Familial Disease History (ICD10*) / Diseases of the nervous system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the respiratory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the skin and subcutaneous tissue
  • Health Information / Familial Disease History (ICD10*) / Endocrine, nutritional and metabolic diseases
  • Health Information / Familial Disease History (ICD10*) / External causes of morbidity and mortality
  • Health Information / Familial Disease History (ICD10*) / Mental and behavioural disorders
  • Health Information / Familial Disease History (ICD10*) / Neoplasms
  • Health Information / Familial Disease History (ICD10*)
  • Health Information / Familial Disease History (ICD10*) / Certain conditions originating in the perinatal period
  • Health Information / Familial Disease History (ICD10*) / Diseases of the circulatory system
  • Health Information / Familial Disease History (ICD10*) / Pregnancy, childbirth and the puerperium
  • Health Information / Familial Disease History (ICD10*) / Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
  • Social Environment / Familial and social environment
Block 9 View block
  • Health Information / Familial Disease History (ICD10*) / Certain conditions originating in the perinatal period
  • Health Information / Familial Disease History (ICD10*) / Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
  • Health Information / Familial Disease History (ICD10*) / Diseases of the digestive system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the genitourinary system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the musculoskeletal system and connective tissue
  • Health Information / Familial Disease History (ICD10*) / Diseases of the nervous system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the respiratory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the skin and subcutaneous tissue
  • Health Information / Familial Disease History (ICD10*) / Endocrine, nutritional and metabolic diseases
  • Health Information / Familial Disease History (ICD10*) / Mental and behavioural disorders
  • Health Information / Familial Disease History (ICD10*) / Pregnancy, childbirth and the puerperium
  • Health Information / Familial Disease History (ICD10*)
  • Health Information / Familial Disease History (ICD10*) / Diseases of the circulatory system
  • Health Information / Familial Disease History (ICD10*) / External causes of morbidity and mortality
  • Health Information / Familial Disease History (ICD10*) / Neoplasms
  • Health Information / Familial Disease History (ICD10*) / Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
  • Sociodemographic Characteristics / Age/Birth Date / Subject's Relatives Age / Birth Date
  • Sociodemographic Characteristics / Kinship
Block 10 View block
  • Health Information / Familial Disease History (ICD10*) / Certain conditions originating in the perinatal period
  • Health Information / Familial Disease History (ICD10*) / Diseases of the circulatory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the digestive system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the genitourinary system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the musculoskeletal system and connective tissue
  • Health Information / Familial Disease History (ICD10*) / Diseases of the nervous system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the respiratory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the skin and subcutaneous tissue
  • Health Information / Familial Disease History (ICD10*) / Endocrine, nutritional and metabolic diseases
  • Health Information / Familial Disease History (ICD10*) / External causes of morbidity and mortality
  • Health Information / Familial Disease History (ICD10*) / Mental and behavioural disorders
  • Health Information / Familial Disease History (ICD10*) / Neoplasms
  • Health Information / Familial Disease History (ICD10*) / Pregnancy, childbirth and the puerperium
  • Health Information / Familial Disease History (ICD10*)
  • Health Information / Familial Disease History (ICD10*) / Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
  • Health Information / Familial Disease History (ICD10*) / Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
  • Social Environment / Familial and social environment
  • Sociodemographic Characteristics / Age/Birth Date / Subject's Relatives Age / Birth Date
Block 11 View block
  • Health Information / Familial Disease History (ICD10*) / Certain conditions originating in the perinatal period
  • Health Information / Familial Disease History (ICD10*) / Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
  • Health Information / Familial Disease History (ICD10*) / Diseases of the circulatory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the digestive system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the musculoskeletal system and connective tissue
  • Health Information / Familial Disease History (ICD10*) / Diseases of the nervous system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the respiratory system
  • Health Information / Familial Disease History (ICD10*) / Diseases of the skin and subcutaneous tissue
  • Health Information / Familial Disease History (ICD10*) / Endocrine, nutritional and metabolic diseases
  • Health Information / Familial Disease History (ICD10*) / External causes of morbidity and mortality
  • Health Information / Familial Disease History (ICD10*) / Mental and behavioural disorders
  • Health Information / Familial Disease History (ICD10*) / Neoplasms
  • Health Information / Familial Disease History (ICD10*)
  • Health Information / Familial Disease History (ICD10*) / Diseases of the genitourinary system
  • Health Information / Familial Disease History (ICD10*) / Pregnancy, childbirth and the puerperium
  • Health Information / Familial Disease History (ICD10*) / Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
  • Health Information / Reproductive history / Number of children
  • Sociodemographic Characteristics / Age/Birth Date / Subject's Relatives Age / Birth Date
Block 12 View block
  • Socioeconomic Characteristics / Education level
  • Socioeconomic Characteristics / Education level / Subject education level
Block 13 View block
  • Socioeconomic Characteristics / Working status / Subject Working status/history
Block 14 View block
  • Life Habits/Behaviours / Physical activity
Block 15 View block
  • Socioeconomic Characteristics / Working status / Subject Working status/history
Block 16 View block
  • Life Habits/Behaviours / Physical activity / Activities/Exercise and Frequency
Block 17 View block
  • Life Habits/Behaviours / Physical activity / Activities/Exercise and Frequency
Block 18 View block
  • Life Habits/Behaviours / Physical activity / Activities/Exercise and Frequency
Block 19 View block
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Beverages (other than water or alcohol)
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Cereals, Bread, Starches
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Meat, Eggs, Fish and Alternatives
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Milk products
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Sweets, Baked goods
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Vegetables and Fruits
Block 20 View block
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Beverages (other than water or alcohol)
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Caffeine
Block 21 View block
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Cereals, Bread, Starches
Block 22 View block
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Meat, Eggs, Fish and Alternatives
Block 23 View block
  • Life Habits/Behaviours / Nutrition / Food intake and Frequency / Fat Intake
Block 24 View block
  • Life Habits/Behaviours / Tobacco use
Block 25 View block
  • Physical Environment / Environmental exposures / Chemical environmental exposures / Passive Smoke Exposure
  • Physical Environment / Occupational Exposures / Chemical Occupational Exposures / Passive Smoke Exposure
Block 26 View block
  • Life Habits/Behaviours / Alcohol use
Block 27 View block
  • Life Habits/Behaviours / Illicit drug use
Block 28 View block
  • Health Information / Women's health / Menstruation
Block 29 View block
  • Health Information / Medical Health Intervention (C239) / Obstetrical and Fetal Interventions / Termination of Pregnancy
  • Health Information / Reproductive history / Parity/Gravidity
Block 30 View block
  • Health Information / Medication Intake (ATC/DDD) / Genito urinary system and sex hormones (G)
Block 31 View block
  • Health Information / Medication Intake (ATC/DDD) / Genito urinary system and sex hormones (G)
  • Health Information / Women's health / Menopause
Block 32 View block
  • Health Information / Perception of health/quality of life
Block 33 View block
  • Health Information / Individual Disease history
  • Health Information / Medication Intake (ATC/DDD)
Block 34 View block
  • Health Information / Individual Disease history / Neoplasms
  • Health Information / Medical Health Intervention (C239) / Physical/Physiological Therapeutic Interventions
  • Health Information / Medication Intake (ATC/DDD) / Antineoplastic and immunomodulating agents (L)
  • Health Information / Medication Intake (ATC/DDD) / Systemic hormonal preparations, excl. Sex hormones and insulins (H)
Block 35 View block
  • Health Information / Individual Disease history / Diseases of the respiratory system
  • Health Information / Medical Health Intervention (C239) / Diagnostic Interventions / Diagnostic Interventions on the Respiratory System
Block 36 View block
  • Health Information / Individual Disease history / Diseases of the musculoskeletal system and connective tissue
  • Health Information / Medical Health Intervention (C239) / Diagnostic Imaging Interventions / Diagnostic Imaging Interventions on the Musculoskeletal System
Block 37 View block
  • Health Information / Individual Disease history / Endocrine, nutritional and metabolic diseases
  • Health Information / Medical Health Intervention (C239) / Clinical Laboratory Interventions
  • Health Information / Medical Health Intervention (C239) / Diagnostic Interventions
  • Health Information / Medical Health Intervention (C239) / Physical/Physiological Therapeutic Interventions / Therapeutic Interventions on the Genitourinary System
  • Health Information / Medication Intake (ATC/DDD) / Alimentary tract and metabolism (A)
Block 38 View block
  • Health Information / Individual Disease history / Diseases of the eye and adnexa
Block 39 View block
  • Health Information / Individual Disease history / Diseases of the circulatory system
  • Health Information / Individual Disease history / Endocrine, nutritional and metabolic diseases
  • Health Information / Medical Health Intervention (C239) / Clinical Laboratory Interventions
  • Health Information / Medical Health Intervention (C239) / Diagnostic Interventions / Diagnostic Interventions on the Cardiovascular System
Block 40 View block
  • Health Information / Medication Intake (ATC/DDD)
  • Health Information / Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
Block 41 View block
  • Health Information / Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
Block 42 View block
  • Health Information / Familial Disease History (ICD10*)
Block 43 View block
  • Body structures / Anthropometric structures / Anthropometric measures / Height
Block 44 View block
  • Body structures / Anthropometric structures / Anthropometric measures / Weight
Block 45 View block
  • Body structures / Hair
Block 46 View block
  • Body structures / Eye

General information

Name Physical and cognitive measures
Last update 03/18/2009
Collected at phase Data collecting, III version of EGP questionnaire
Year interval 2007 to 2010

Contact

Andres Metspalu (Population-based biobanks /Prof.)
Tartu 50410
Phone: +372 7 440243
Email: andres.metspalu@geenivaramu.eeMail

Physical and cognitive measures collected

Legend Yes No

BODY STRUCTURES

ANTHROPOMETRIC STRUCTURES

Anthropometric measures

Yes Weight

Yes Height

Yes Standing height

Yes Body circumferences

Yes Waist circumference

Yes Hip circumference

Body composition

Yes Bone density (values of T-sector from medical records of gene donors, if available)

BODY FUNCTIONS

SENSORY FUNCTIONS AND PAIN

Seeing and related functions

Yes Vision and related functions (both eyes dioptries and visuses from medical records of gene donors, if available or the values given by the gene donor)

FUNCTIONS OF THE CARDIOVASCULAR AND RESPIRATORY SYSTEMS

Functions of the cardiovascular system

Yes Blood pressure (at rest)

Yes Heart rate (in 15 seconds has to be measured)

Yes Heart rate at rest

Yes Heart rate under stress

Functions of the respiratory system

Yes Respiratory functions (values of FVC and FEV1 and spirography performing date from medical records of gene donors, if available)

HANDEDNESS / LATERALITY

Yes Handedness functions

Administration mode

Legend Yes No

Administration environment

Yes Hospital, clinic, university or recruitment center

No Participant residence

No Other

Staff administering test

Yes Professionals (nurses, clinicians, etc)

No Interviewers/research assistants

No Other

Documentation on procedures

Administration language Estonian

Standard operating procedures (SOPs) or reference information

General Information

Name DNA Processing
Study name Estonian Genome Center of University of Tartu [EGC]
Last update 02/27/2009

Contact

Merli Hass
 EGP
Email: merli.hass@geenivaramu.eeMail
Utilization conditions None

Samples

Legend Yes No
Sample name Blood
  Main laboratory Laboratory Estonian Genome Project University of Tartu
  Sample labels/traceability (% of samples)
  • No RFID radio frequency identification
  • No Barcode
  • No Printed labels
  • No Handwritten numbers
  • No Others
Pre-extraction sample storage format Substrate storage condition
  • Yes Fresh
  • No Refrigerated
  • No Frozen
  • No Dried (paper)
  • No Liquid Nitrogen
  • No Other
Substrate storage period
  • No Short term
  • No Long term
Protocols
DNA extraction DNA extraction method
  • Yes Salting out
  • No Phenol-chloroform
  • No Columnary-extraction
  • No Magnetic beads
  • No Oragene (saliva)
  • No Others
Automation of handling
  • Yes Manual
  • No Automated
Protocols
DNA handling and storage DNA diluent
  • Yes TE
  • No H2O
  • No Others
DNA concentration (ng/µl)
Storage conditions
  • No 4°C
  • No -20°C
  • No -40°C
  • No -80°C
  • No Dried
  • Yes Others (CBS™ storage straws, from -150 to –196 ºC in liquid nitrogen)
Protocols
DNA quantification Methods
  • Yes A260/A280
  • No Picogreen
  • No Nanodrop
  • No Others
Technical quality
  • No Automated
  • No Manual
  • No Reproducibility
Protocols
DNA quality control Percentage of samples that are tested
DNA quality method
  • Yes Agarose gel
  • Yes PCR
  • Yes A260/A280 ratio
  • No Others
Protocols

General Information

Name Information Technologies
Study name Estonian Genome Center of University of Tartu [EGC]
Last update 10/28/2009

Contact

Erkki Leego
Estonian Genome Project, University of Tartu
Tartu 50410
Phone: +372 5332 9211
Email: erkki.leego@geenivaramu.eeMail

Software

Legend Yes No

Software overview

Biobanking areas covered QureServer3.5.2 MAPI LIMS 4.1 Kodeerimiskeskus GenoByte DataCollector 2.6.1.433
Participant recruitment (ex: CATI, CRM) Yes
Data collection
Sample collection, storage and processing Yes Yes
Data repository Yes
Other Yes Yes
 
Programming language QureServer3.5.2 MAPI LIMS 4.1 Kodeerimiskeskus GenoByte DataCollector 2.6.1.433
Name and version of programming language Java 1.6 Java 1.6 Java Java
 
Internal/external development QureServer3.5.2 MAPI LIMS 4.1 Kodeerimiskeskus GenoByte DataCollector 2.6.1.433
In-house by IT department
By an external company Yes Yes Yes Yes Yes Yes
 
Shareability QureServer3.5.2 MAPI LIMS 4.1 Kodeerimiskeskus GenoByte DataCollector 2.6.1.433
Freely available Yes
Purchaseable Yes
Needs extensive work Yes Yes Yes Yes
Not for share

Software details

Biobanking areas covered

  • No Participant recruitment (ex: CATI, CRM)
  • No Data collection
  • No Questionnaires (ex: CAPI)
  • No Physical and cognitive measures
  • No Sample collection, storage and processing
  • No Collection
  • No Sample bio-repository management system (ex: sample storage management software)
  • No LIMS (ex: biochemical analysis, DNA extraction, genotyping)
  • Yes Data repository
  • Yes Data warehousing
  • No Study monitoring (ex: quality control)
  • No User data / sample request management

Name and version of programming language

Java 1.6

Internal/external development

  • No In-house by IT department
  • Yes By an external company (QureTec)

Shareability

  • No Freely available
  • No Purchaseable
  • Yes Needs extensive work
  • No Not for share

Biobanking areas covered

  • No Participant recruitment (ex: CATI, CRM)
  • No Data collection
  • No Questionnaires (ex: CAPI)
  • No Physical and cognitive measures
  • Yes Sample collection, storage and processing
  • No Collection
  • Yes Sample bio-repository management system (ex: sample storage management software)
  • No LIMS (ex: biochemical analysis, DNA extraction, genotyping)
  • No Data repository
  • No Data warehousing
  • No Study monitoring (ex: quality control)
  • No User data / sample request management

Internal/external development

  • No In-house by IT department
  • Yes By an external company (Cryo Bio System)

Shareability

  • No Freely available
  • Yes Purchaseable
  • No Needs extensive work
  • No Not for share

Biobanking areas covered

  • No Participant recruitment (ex: CATI, CRM)
  • No Data collection
  • No Questionnaires (ex: CAPI)
  • No Physical and cognitive measures
  • Yes Sample collection, storage and processing
  • No Collection
  • No Sample bio-repository management system (ex: sample storage management software)
  • Yes LIMS (ex: biochemical analysis, DNA extraction, genotyping)
  • No Data repository
  • No Data warehousing
  • No Study monitoring (ex: quality control)
  • No User data / sample request management

Name and version of programming language

Java 1.6

Internal/external development

  • No In-house by IT department
  • Yes By an external company (Trillian)

Shareability

  • No Freely available
  • No Purchaseable
  • Yes Needs extensive work
  • No Not for share

Biobanking areas covered

  • No Participant recruitment (ex: CATI, CRM)
  • No Data collection
  • No Questionnaires (ex: CAPI)
  • No Physical and cognitive measures
  • No Sample collection, storage and processing
  • No Collection
  • No Sample bio-repository management system (ex: sample storage management software)
  • No LIMS (ex: biochemical analysis, DNA extraction, genotyping)
  • No Data repository
  • No Data warehousing
  • No Study monitoring (ex: quality control)
  • No User data / sample request management
  • Yes Other (Consent forms management, coding management)

Name and version of programming language

Java

Internal/external development

  • No In-house by IT department
  • Yes By an external company (Fujitsu)

Shareability

  • No Freely available
  • No Purchaseable
  • Yes Needs extensive work
  • No Not for share

Biobanking areas covered

  • No Participant recruitment (ex: CATI, CRM)
  • No Data collection
  • No Questionnaires (ex: CAPI)
  • No Physical and cognitive measures
  • No Sample collection, storage and processing
  • No Collection
  • No Sample bio-repository management system (ex: sample storage management software)
  • No LIMS (ex: biochemical analysis, DNA extraction, genotyping)
  • No Data repository
  • No Data warehousing
  • No Study monitoring (ex: quality control)
  • No User data / sample request management
  • Yes Other (Storing and querying data resulting from the aggregation of high-throughput genotyping experiments across many subjects.
    http://www.obiba.org/home/projects/genobyte)

Internal/external development

  • No In-house by IT department
  • Yes By an external company (Genome Quebec)

Shareability

  • Yes Freely available
  • No Purchaseable
  • No Needs extensive work
  • No Not for share

Biobanking areas covered

  • Yes Participant recruitment (ex: CATI, CRM)
  • No Data collection
  • No Questionnaires (ex: CAPI)
  • No Physical and cognitive measures
  • No Sample collection, storage and processing
  • No Collection
  • No Sample bio-repository management system (ex: sample storage management software)
  • No LIMS (ex: biochemical analysis, DNA extraction, genotyping)
  • No Data repository
  • No Data warehousing
  • No Study monitoring (ex: quality control)
  • No User data / sample request management

Name and version of programming language

Java

Internal/external development

  • No In-house by IT department
  • Yes By an external company (Quretec)

Shareability

  • No Freely available
  • No Purchaseable
  • Yes Needs extensive work
  • No Not for share

Comments

No information available

© 2005 Public Population Project in Genomics.
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