Assay facts¶
MaveDB captures key facts about the experimental assay used to generate variant effect measurements from controlled keywords based on a controlled vocabulary. This information is then used to generate a concise summary of assay facts that is displayed on the score set page.
Fig. 2 Example of the assay facts section from a score set¶
This figure shows the assay facts section from urn:mavedb:00000097-0-2, which describes saturation genome editing of BRCA1.
Assay fact sheet properties¶
- Gene Symbol
The HGNC gene symbol for the target gene being assayed.
- Assay type
The type of functional assay used to measure variant effects. This corresponds to the phenotypic assay method controlled vocabulary term.
- Molecular mechanism
The molecular mechanism by which the assay measures variant effects. This corresponds to the molecular mechanism controlled vocabulary term.
- Variant consequences detected
The types of variant consequences that the assay is capable of detecting. This corresponds to the phenotypic assay mechanism controlled vocabulary term.
- Model system
The biological system in which the assay was performed. This corresponds to the model system controlled vocabulary term.
- Detects splicing variants
Whether the assay is capable of detecting splicing variants. Based on assay design, and inferred based on a combination of the variant library creation method and other terms.
- Detects nonsense-mediated decay (NMD) variants
Whether the assay is capable of detecting NMD variants. Based on assay design, and inferred based on a combination of the variant library creation method and other terms.
- OddsPaths
The Odds of Pathogenicity score calculated for abnormal and normal functional readouts, if applicable. These OddsPaths are based on the framework described in Brnich et al., 2019.
Note
OddsPath calculations are provided when available.
For some assays, MaveDB maintainers may have selected OddsPaths other than those submitted by the data contributor, based on updated calibrations or reanalyses of the data. In these cases, the source of the OddsPath scores will be indicated on the score set page.