Scripps Genome Annotation and Distributed Variant Interpretation Server (SG-ADVISER) is a web-server developed at The Scripps Research Translational Institute for the interpretation of genetic variant data. Downstream applications of variant annotation include:
- Clinical sequencing applications including: carrier testing, or identification of causal variants in molecular diagnosis, tumor sequencing, or diagnostic odyssey.
- Prioritization of variants prior to statistical analysis of sequence based disease association studies, especially for automated set-generation and enrichment of likely functional variants within sets.
- Identification of causal variants in post-GWAS/linkage sequencing studies.
- Identification of causal variants in forward genetic screens (stay tuned for non-human annotation).
SG-ADVISER provides known and predicted information about genetic variants - otherwise known as variant annotations - to place genetic variants in the appropriate context for downstream analysis.
These annotations fall broadly into four categories:
- Determination of the known or inferred genomic elements within which variants reside (e.g., exons, promoters, conserved elements, transcription factor binding sites, protein domains etc.).
- Prediction of the functional impact of variants on genomic elements (prediction of impact on protein function, changes in transcription factor binding strength, splicing efficiency, microRNA binding, etc.).
- Annotation of molecular and biological processes which link variants across genes and/or genomic elements with one another.
- 4. Annotation of known or predicted population-based, clinical, and/or molecular characteristics of the gene or variant (e.g. population frequency, pharmacogenetic variants, disease associations, eQTLs etc.).
See Methods for a detailed description of the annotations provided by SG-ADVISER.