Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server

Methods

Below we provide a basic description of the annotations, delineated by class, provided by SG-ADVISER. The relevant annotations refer to the annotation columns presented in the output file. See Results Description for a more detailed description of the specific annotation columns, the implemented tools, and their output formats.

Physical and Gene-Relative Mapping and Characteristics

The most basic level of annotation including user provided information about the type and location of variants, the nearest gene and location and distance from that gene, as well as variant identifiers. These annotations include:

Coding Gene Impact, Inferred and Predicted

The impact of variants on protein coding genes - including a basic impact inferred from the reading frame and the predicted functional impact based on a variety of tools. These annotations include:

Splicing Impact, Inferred and Predicted

The impact of variants on splicing of genes - including a basic impact inferred from canonical splice site donors/acceptor sequences and the predicted functional impact of variants. These annotations include:

Regional Information

Information about the genomic region in which the variant resides. These annotations include:

Population-Based Information

Population genetics annotations. These annotations include:

Regulatory Variants

Known and predicted impacts of variants on gene regulation. These annotations include:

Disease-based, Drug-based and other Clinical Annotations

Gene and variant based information that is relevant to diseases and/or drugs. These annotations include.

Gene Networks, Pathways, Biological Process and Molecular Functions

Annotations that link genes to one another based upon shared participation in biological pathways, processes, or molecular functions.

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Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server