ED Web API for mutational signature

#Design : Web API for mutational-signature Date Accepted: 2016-11-23

Abstract: A Web API endpoint at {appname}/api-legacy/mutation-signature would return per-sample mutational-signature values. These values are a set of counts of single nucleotide substitution mutations across all genes grouped by the type of transition (such as C->A : adenine replacement of Cytosine). Type of transition grouping can also include some amount of flanking context (a requested number of upstream nucleotides and downstream nucleotides downstream). Samples are selected by study_id, and can be further filtered by providing a list of stable sample identifiers.

Uses: The distribution of relative count sizes can indicate exposure to particular known mutagenic environmental factors, such as overexposure to Ultraviolet light causing many C -> T and C->A substitutions. Other patterns may indicate exposure to cigarette smoke or malfunction in particular DNA maintenance pathways. This Api will deliver the full distribution of counts, and categorization of likely mutagenic drivers will be accomplished in the front end code. One visualization will be as a Clinical Annotation Track above the OncoPrint:

Summary points:

• return type would be one object per sample
• the representation would define (within the response) the mapping of count values to type of substitution (such as C->A)
• when sample lists are not provided, mutation-signatures for all samples in the profile would be returned.
• If unrecognized study identifiers or sample identifiers are encountered, an error code is returned.