Genome Database of the Latvian Population (LGDB): Design, Goals, and Primary Results

Background The Genome Database of the Latvian Population (LGDB) is a national biobank that collects, maintains, and processes health information, data, and biospecimens collected from representatives of the Latvian population. These specimens serve as a foundation for epidemiological research and prophylactic and therapeutic purposes. Methods Participant recruitment and biomaterial and data processing were performed according to specifically designed standard protocols, taking into consideration international quality requirements. Legal and ethical aspects, including broad informed consent and personal data protection, were applied according to legal norms of the Republic of Latvia. Results Since its start in 2006, the LGDB is comprised of biosamples and associated phenotypic and clinical information from over 31,504 participants, constituting approximately 1.5% of the Latvian population. The LGDB represents a mixed-design biobank and includes participants from the general population as well as disease-based cohorts. The standard set of biosamples stored in the LGDB consists of DNA, plasma, serum, and white blood cells; in some cohorts, these samples are complemented by cancer biopsies and microbiome and urine samples. The LGDB acts as a core structure for the Latvian Biomedical Research and Study Centre (BMC), representing the national node of Latvia in Biobanking and BioMolecular resources Research Infrastructure – European Research Infrastructure Consortium (BBMRI-ERIC). Conclusions The development of the LGDB has enabled resources for biomedical research and promoted genetic testing in Latvia. Further challenges of the LGDB are the enrichment and harmonization of collected biosamples and data, the follow-up of selected participant groups, and continued networking and participation in collaboration projects.


Information about the Genome Database of the Latvian population
Dear Sir or Madam! We invite you to participate in the project of the development of the Genome Database of Latvian population in collaboration with Latvian Biomedical Research and Study centre. We kindly ask you read the following information carefully before signing the consent form.

The aim of the project:
Scientists have discovered that almost all disease development is facilitated by the interaction between heredity and harmful environmental factors. The aim of the project is to collect information about the heredity and genes of the population of Latvia, and environmental factor which might affect disease development, and store this information in a united database. These genetic studies would allow us to obtain new information about disease development and make steps for prophylaxis to attain or prevent these diseases. During the development of the Genome Database of Latvian population several scientific groups are participating to study gene influence on disease development. These researches will receive anonymized samples of your biological material and information about your health status from the Genome Database of Latvian population.

Description of enrolment procedures:
A certified medical specialist will draw a sample of your venous blood. Afterwards, a trained interviewer will help you to fill in the health and hereditary questionnaire, in which you will be asked to answer questions about you and your relatives regarding hereditary and environmental factors, which might affect disease development. Your health and hereditary information, and blood samples will be coded to ensure confidentiality. Coded blood samples will be transported to Latvian Biomedical Research and Study centre and processed, to make sure your genetic information could be suitable for genetic analysis and long term storage in specifically designed restricted authorization area. Only project participants and persons with specific permissions will be allowed to use this coded information for scientific research only. Your personal data and other information that is acquired during enrolment and research process will not be accessible, with exclusion of cases provided in the legal regulation of the Republic of Latvia, these examples are described further in this form. The informed consent, sample and data identification code will be stored at State Genome Registry.

Duration of the project:
Genome Database of Latvian population is developed and maintained at Latvian Biomedical Research and Study centre for an unlimited period of time. Your consent form will be stored at State Genome Registry for 75 years after the last revisions made.

Potential risks:
The participation in genome research will not harm your health. You will be required to provide a blood sample the same way as in case of a regular blood test. In rare cases a local hemorrhage or in very rare cases local skin inflammation can develop at the site of venipuncture.

Data confidentiality and the rights of the project participant:
Confidentiality of your personal data, health and hereditary information, genetic research results are ensured by "Human Genome Research Law" and "Personal Data Protection Law" of the Republic of Latvia. This information will be stored in a restricted access area and will not be provided to your relatives, insurance companies, or employers. Obtained data and tissue materials will not be used for commercial purposes and will not be illegally given to third parties. The data collected about you in Genome Database of Latvian population will be given to the requesting parties only in cases that are provided to State Genome Registry, in cases described in "Human Genome Research Law", and to you personally based on a submitted written application. Information about your health and results of genetic research (not your personal information!) will be accessible to researchers, who's projects are approved by the Genome Research council and the Central Medical Ethics committee. With your written consent (with exclusion of emergency medical help) your health information will be accessible for your doctor in case of reasonably grounded request. You have rights to access your data that are stored at Genome Database of Latvian population and supplement new data. You also have rights to prohibit supplementation, renewal and control of your data stored at Genome Database of Latvian population or limit the extent of your genome research. You have rights at any moment to withdraw your participation in the genome research project, in this case your tissue material, health status and hereditary information will be destroyed in Genome Database of Latvian population and in State Genome Registry.

Voluntary participation:
Your participation is voluntary. Your refusal to participate in this project will not harm you by any means.

Potential benefits:
Participation in this project will not give you any immediate benefit, but will serve for the generation of novel knowledge about diseases and heritability, that in future might help you, your relatives or the general society. In accordance with "Human Genome Research Law" you do not have the rights to demand charge for your biomaterial, health and hereditary information, as well as for the use of the genetic research results.  agree that this information is communicated to me  agree, that this information is communicated to me in cases if the risk for the health is preventable  do not want this information to be communicated to me 7. I agree to be a gene donor in the genome research project voluntary, without any charge. I agree that for the purposes of the genetic research my tissue samples will be taken and health status and (or) genealogy can be recorded. I understand that at any time I have the right to withdraw my participation without providing any explanations. In this case my tissue sample, health status and any personal information will be destroyed. Place of consent completion *"gene donor"term used in "Human Genome Research Law" of the Republic of Latvia to describe a participant consenting to the research of his/her genetic material. Therefore, "gene donor" is a historical term, however, overtime biobank has evolved having much broader sense of patient recruitment and biosample application. 2) Blood sample in collection tube is centrifuged for 15 min at +4˚C and 4000 rpm (centrifuge must be cooled to +4˚C).

Gene donor
3) Plasma is removed by pipetting, leaving 0.5 -1 cm plasma level over buffy coat and red blood cell fraction.

4)
Carefully, with sterile cut-off tip, all buffy coat is removed, containing small portion of the plasma, but avoiding the transfer of blood cells from the red fraction, cells are transferred to empty 15 mL tube.

Note: If by accident buffy coat fraction is contaminated with red blood cell fraction, this tube
can be repeatedly centrifuged for 15 min at +4˚C and 4000 rpm, and repeated buffy coat collection carried out.
5) The rest of the blood is discarded in biological waste.

Lysis of red blood cells
6) 10 mL of RBC Lysis solution is added to 15 mL centrifuge tube containing white blood cells and the tube inverted three times (without use of vortex and avoiding vigorous shaking).

7)
Mixture is incubated for 15 min at +4˚C.

8)
After incubation 15 mL tubes are centrifuged for 15 min at +4˚C and 4000 rpm.
9) The supernatant is removed by decanting to biologic waste container and the white blood cell pellet is kept.
10) The cells are washed with 5 mL Cell Suspension solution by inverting the tube (avoiding vigorous shaking or vortexing) and centrifuged for 5 min at +4˚C and 4000 rpm. The supernatant is removed.

3.Lysis of white blood cells
11) 5 mL of Cell Suspention solution is added to the pellet.

12)
Tube is mixed on rotator until cells are suspended, no longer than 5 min. 13) 0.4 mL 10% SDS solution is added and mixed by inverting the tube 3 times.
14) 5 µl of Proteinase K is added and mixed by inverting the tube 3 times.
15) Mixture is incubated overnight at +50 ˚C, by mixing the tube several times at the start of incubation.

DNA isolation
16) 5 mL of phenol is added to lysed white blood cells and mixed on rotator for 15 min.  22) Slowly, on the inner side of the tube, 5 mL isopropanol is added to transferred fraction and mixed by inverting tube several times (avoiding shaking), until DNA precipitates (appears medusa).

Note. In case if DNA precipitate do not form, sample with isopropanol is left overnight at -18
˚C 23) Mixture is centrifuged for 10 min at +20 ˚C, 4000 rpm. 24) All supernatant is discarded and 5mL of 70% ethanol added, mixture is vortexed thoroughly and mixed on rotator for 2 min. 25) Mixture is centrifuged for 10 min at +20 ˚C, 4000 rpm.

26)
The supernatant is carefully removed by decanting, making sure that sediment stays on walls of the tube. Tube is turned upside down and sediment dried for 10 min at room temperature or until it is completely dry. 27) 0,5 mL or 1 mL of DNA Hydration Solution is added to the sediment, depending on size of precipitated DNA, and tube placed on rotator on slow rate over the night.
28) Isolated DNA is stored for a week at +4 ˚C to completely dissolve. Total yield and quality of DNA is measured by NanoDrop 1000 Spectrophotometer. eMaterial 4. Categories of collected data on participants of Genome Database of Latvian population