Table 3.
Overview of Free Online Databases of CNVs in Controls (DGV) or Patients with Genotype–Phenotype Information
| DGV | DECIPHER | ECARUCA | ISCA | |
|---|---|---|---|---|
| Account holders | No accounts are created, freely accessible to all users. | Professionals in medical genetics only. | Professionals in medical genetics and families (patient portal; access to own data only). | ISCA Members |
| Access | No restrictions | Free public access to anonymized, consented data. Login upon registration for data entry and curation. |
Login upon registration. | Login upon registration. |
| Costs involved? | No | No | No | No |
| Number of account holders | 0 | 1,135 | >1,500 | >900 |
| Objectives of the database | To provide a comprehensive summary of structural variation in the human genome. The DGV provides a useful catalogue of control data for studies aiming to correlate genomic variation with phenotypic data. | Catalogue of pathogenic submicroscopic copy number variants and associated phenotype. | Reliable information on rare chromosome anomalies. | Leveraging high-quality clinical copy number data to create a CNV Atlas of the human genome. |
| Number cases | ||||
| Total | 11,941 controls | >11,300 | > 4,600 | >28,000 deidentified “calls-only” cases; approximately 8,000 of these cases have been collected under the opt-out method of consent and have associated raw data files available in dbGaP. |
| Consented | 11,941 | >5,300 (for free public access and browser display) | > 4,600 | |
| Number cases | ||||
| Prenatal cases | 0 | 0 | ~200 | ~4,000a |
| Postnatal cases | 11,941 | >11,300 | >4,400 | >28,000 postnatal |
| Number of aberrations | 101,923 (66,741 CNV; 34,229 InDels; 953 inversions | 31,148 | >6,200 | >13,000 |
| Aberrations | Primarily submicroscopic variants are included. Maximum size for CNVs is 3 Mb, while inversions up to 10 Mb are included and may be cytogenetically visible. | Some cases have benign CNVs listed as well. | Cytogenetically visible and submicroscopic imbalances. | Copy number variants identified via clinical constitutional microarray testing. |
| Karyotyping | 394 | Only clinically relevant findings are registered. | ||
| FISH | 2,457 | |||
| MLPA | 475 | |||
| QF-PCR | 1,271 | |||
| GW array | 31,148 | |||
| Number of cases with clinical features | 0 | 4,054 | >4,600; based on LDDB | >5,000 cases with ≥ one HPO term |
| Gender | Yes | Yes | Yes | |
| Age | At examination | At last examination | At time of testing | |
| Ethnicity | No | No | No | |
| Data curation | Peer reviewed data submitted, with additional data curation provided by DGV staff prior to data entry. | Account holders responsibility. | Quality control upon entry by the Database Management Team. | Submitting laboratories have the opportunity to curate their data against their own previous submissions and the ISCA curated dataset; expert curation committee periodically curates the entire dataset. |
| Visualization of database content in genome browser? | UCSC | UCSC | UCSC | UCSC |
| DGV genome browser | Ensembl DECIPHER | Ensembl | dbVar | |
a
To be submitted at end of prenatal grant.
DGV, Database of Genomic Variants; DECIPHER, DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources ECARUCA, European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations; ISCA, International Standards for Cytogenomic Arrays.