Methods and systems for detecting alternative splicing in sequencing data

A computer system comprising:

• one or more processors;
• and
• a non-transitory computer-readable medium including computer-executable instructions that, when executed by the one or more processors, cause the processors to perform a method for mapping splicing events in a test subject, the method comprising:
• A) obtaining, for each respective gene in a first set of one or more genes, a respective set of splice site coordinates for respective aligned sequence reads, in a plurality of aligned sequence reads for mRNA in a biological sample from a test subject, mapping to the respective gene, wherein each respective splice site coordinate in the respective splice site coordinates corresponds to a respective donor splice site and a respective acceptor splice site in the respective gene, to obtain a respective plurality of splice site coordinates for the respective gene in the plurality of sequence reads;
• B) comparing, for each respective gene in the first set of one or more genes, the respective plurality of splice site coordinates to reference splice site coordinates in a respective principal mRNA isoform for the respective gene, to identify (i) a respective first subset of the respective plurality of splice site coordinates that correspond to a splice site coordinate in the principal mRNA isoform, representative of constitutional splicing events in common with the respective principal mRNA isoform, and (ii) a respective second subset of the respective plurality of splice site coordinates that do not correspond to a splice site coordinate in the principal mRNA isoform, representative of alternative splicing events not in common with the respective principal mRNA isoform;
• C) determining, for each respective gene in the set of one or more genes, for each respective splice site coordinate in the respective second subset of splice site coordinates, whether the respective splice site coordinate satisfies a first criteria, wherein the first criteria is satisfied when both the respective donor site and the respective acceptor site corresponding to the respective splice site coordinate are represented in the reference splice site coordinates for the respective principal mRNA isoform for the respective gene, to identify (i) a respective third subset of the respective plurality of splice site coordinates that satisfy the first criteria, representative of alternative splicing events between donor splice sites and acceptor splice sites in common with the respective principal mRNA isoform, and (ii) a respective fourth subset of the respective plurality of splice site coordinates that do not satisfy the first criteria, representative of alternative splicing events occurring between a donor site or an acceptor site not in common with the respective principal mRNA isoform,
• thereby mapping splicing events in the subject for the set of one or more respective genes.

A non-transitory computer-readable storage medium having stored thereon program code instructions that, when executed by a processor, cause the processor to perform a method for mapping splicing events in a test subject, the method comprising:

• A) obtaining, for each respective gene in a first set of one or more genes, a respective set of splice site coordinates for respective aligned sequence reads, in a plurality of aligned sequence reads for mRNA in a biological sample from a test subject, mapping to the respective gene, wherein each respective splice site coordinate in the respective splice site coordinates corresponds to a respective donor splice site and a respective acceptor splice site in the respective gene, to obtain a respective plurality of splice site coordinates for the respective gene in the plurality of sequence reads;
• B) comparing, for each respective gene in the first set of one or more genes, the respective plurality of splice site coordinates to reference splice site coordinates in a respective principal mRNA isoform for the respective gene, to identify (i) a respective first subset of the respective plurality of splice site coordinates that correspond to a splice site coordinate in the principal mRNA isoform, representative of constitutional splicing events in common with the respective principal mRNA isoform, and (ii) a respective second subset of the respective plurality of splice site coordinates that do not correspond to a splice site coordinate in the principal mRNA isoform, representative of alternative splicing events not in common with the respective principal mRNA isoform;
• C) determining, for each respective gene in the set of one or more genes, for each respective splice site coordinate in the respective second subset of splice site coordinates, whether the respective splice site coordinate satisfies a first criteria, wherein the first criteria is satisfied when both the respective donor site and the respective acceptor site corresponding to the respective splice site coordinate are represented in the reference splice site coordinates for the respective principal mRNA isoform for the respective gene, to identify (i) a respective third subset of the respective plurality of splice site coordinates that satisfy the first criteria, representative of alternative splicing events between donor splice sites and acceptor splice sites in common with the respective principal mRNA isoform, and (ii) a respective fourth subset of the respective plurality of splice site coordinates that do not satisfy the first criteria, representative of alternative splicing events occurring between a donor site or an acceptor site not in common with the respective principal mRNA isoform,
• thereby mapping splicing events in the subject for the set of one or more respective genes.