| Types of Genetic Variation Databases | -Population variation databases
-Disease-related variation databases |
| Sources of Variation Data? | • Various genome sequencing projects (e.g., 1000 Genomes Project, Japanese population sequencing project, etc.)
• Exome sequencing projects (e.g., NHLBI GO Exome Sequencing Project, etc.)
• Genome-Wide Association Studies (GWAS) |
| Parts of the Entrez databases? | -Database of Short Genetic Variations (dbSNP)
-Database of Genomic Structural Variation (dbVar)
-Database of Genotypes and Phenotypes (dbGaP)
-ClinVar |
| Human Genetic Variation Database (Japan) | • A central resource to archive and display Japanese genetic variation
• Currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals
• The HGVD browser can be used to view allele and genotype frequencies, number of samples, coverages, and expression QTL (eQTL) significances |
| What is PGG | A suite of databases and toolkit focusing on the diverse research fields of human Population Genomics and Genetics (PGG)
Currently, the suite includes 2 databases (PGG.Population and PGG.SNV) and 1 web toolkit (PGG.Tools, under construction)
PGG.Population is a database for understanding genomic diversity and genetic ancestry of human populations.
PGG.SNV is database for understanding evolutionary and medical implications of human single nucleotide variation (SNV) on population levels |
| What is Genome Aggregation Database (gnomAD) | Includes about 85,000 genome sequences and about 126,000 exome sequences
Aggregates and harmonizes both exome and genome sequencing data from a wide variety of large-scale sequencing projects
Makes summary data available for the wider scientific community |
| How to access the databases? | -Access to aggregated data (population allele frequencies) is free and uncontrolled
-Access to the individual genotype data can be either uncontrolled or controlled, particularly to the clinically related data |
| What is LOVD v.3.0? | Leiden Open Variation Database |
| List the human variation databases? | - Entrez Databases
-Ensembl
-Human Genetic Variation Database (Japan)
-PGG
-Genome Aggregation Database (gnomAD)
-Database of Genomic Variants
-LOVD v.3.0 - Leiden Open Variation Database
-DECIPHER - NHLBI Exome sequencing project - Saudi genome program |
| Advantages of human variation databases? | - Data from many studies are aggregated in one place
-GUI and easy navigation through the data
-good visualization via browsers
-analytic tools (albeit limited) |
| Disadvantages of human variation databases? | Some databases are obsolete or defunct
Most databases do not provide access to the individual genotype data (necessary for many analyses)
Smaller databases often lack comprehensive help
Some databases provide an access to data only via ftp |
| What is the database of genomic variants (DGV)? | A database of the human structural variation
Stores data of the human genetic variants >50 bp
Continuously updated |
