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Genome Database of Latvian population - National Biobank Latvia (LGDB)
Identification
Hosting Legal Entity
Self-standing RI
Legal Status
Research organisation
Location
Ratsupites Str. 1 k-1, Latvian Biomedical Research and Study centre, Riga, PO: LV1067 (Latvia)
Structure
Type Of RI
Single-sited
Coordinating Country
Latvia
Status
Status
Current Status:
Operational since 2006
Timeline
Design/planning since 2003 to 2007
Operational since 2003
Scientific Description
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. Since its start in 2006 the LGDB is comprised of biosamples, associated phenotypic and clinical information from over 32,000 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 complemented by cancer biopsies, microbiome and urine samples. Sample associated information stored contains health and heredity information questionnaire data, diagnosis status of participant, blood biochemistry and genotypes. Additional information from State Health registries about the participants can be obtained on project specific basis. The LGDB acts as a core structure for the Latvian Biomedical Research and Study Centre, representing the national node of Latvia in Biobanking and BioMolecular resources Research Infrastructure – European Research Infrastructure Consortium (BBMRI-ERIC). LGDB receives small basic funding from the Ministry of Health of the Republic of Latvia, and attracts additional funding from research project specific resources.

RI Keywords
Access to biological collection data, Genomics, DNA, Biobank, Genetics, Personalized medicine, Biological samples, Health registry access, Biomolecular research, Biological collection data, Public health
Classifications
RI Category
Collections of Biological Resources (e.g. Microorganisms, Biobanks and Seed Banks)
Scientific Domain
Biological and Medical Sciences
ESFRI Domain
Health and Food
Services
DNA isolation

LGDB uses phenol extraction method with specific modifications for fresh of frozen blood extraction, isolated frozen buffy coat DNA extraction. The procedure for DNA isolation has been tested in quality assurance scheme for Biospecimen Proficiency Testing 2017/2018. year cycle at IBBL with highest possible evaluation mark. Laboratory provides DNA extraction from various biological material as a service.

Sample and data access

LGDB stores collection of biological material of over 32 000 donors from Latvian population, this includes population and disease based cohorts. The standard set of biosamples stored in the LGDB consists of DNA, plasma, serum and white blood cells, in some cohorts complemented by cancer biopsies, microbiome and urine samples. The data stored at LGDB includes core health heredity questionnaire, diagnosis (ICD10), biochemistry test results and genotypes. The additional data about donors could be obtained from state health system on project based purposes. The samples and data can be accessed for research. For detailed information about biobank design, available samples and data see: Rovite et al. J Epidemiol. 2018.

Genetic analysis

Targeted genotyping using RT-systems, Sanger sequencing or Next-Generation Sequencing using IonTorrent PGM and IonProton platforms. Services include experimental design, library preparation, sequencing and bioinformatics analysis. Most frequently used analysis includes TaqMan genotyping, Sanger sequencing, AmpliSeq targeted gene sequencing, exome sequencing, 16S RNA sequencing, transcriptome sequencing, metagenome sequencing, whole small genome analysis.

Biospecimen storage

LGDB is equipped with liquid handling robots (for DNA dilution aliquoting, plate preparation), low temperature freezers, liquid nitrogen containers, for storage of biological materials. The storage of biological materials is available as a service.

Equipment
ABI PRISM 3130xl Genetic Analyzer (ThermoFisher Scientific)
Agilent 2100 Bioanalyser (Agilent)
ULTF 420® ultra low temperature freezer (ARCTIKO)
RX Imola, an Automated clinical chemistry analyser (Randox)
ViiA7 Real-Time PCR System (ThermoFisher Scientific)
KingFisher Duo Magnetic Purification System (ThermoFisher Scientific)
AutoFlex™ MALDI-TOF Mass Spectrometer (Bruker Daltocnics)
IonProton System for Next-Generation Sequencing (ThermoFisher Scientific)
Veriti™ 96-Well Thermal Cycler (Applied Biosystems)
Freedom EVO Liquid Handling System (Tecan)
IonTorrent PGM System for Next-Generation Sequencing (ThermoFisher Scientific)
BluePippin Automated DNA Size Selection System (Sage Science)
GeneAmp® PCR System 9700 (Applied Biosystems)
S220 Focused-ultrasonicator (Covaris)
Access
Access Type
For research purposes
Access Mode
Excellence Driven, Wide
Access Webpage
Users
Users Definition
Institutions
Date of last update: 12/09/2018
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