SNPlice

SNPlice identifies cis-acting splice-modulating single-nucleotide variants (SNVs) by mining whole-transcriptome RNA sequencing (RNA-seq) splice profiles to detect co-occurrence of variants with altered splicing at exon-intron boundaries.

Key Features:

• Identification of Splice-Modulating Variants: Mines RNA-seq reads that span SNV loci and adjacent splice junctions to highlight intron-containing molecules potentially affected by altered splicing.
• Allele-Specific Sequencing: Employs allele-specific sequencing to link variant nucleotides to exon-intron boundary retention and splicing alterations.
• Consistency with Splice-Prediction Tools: Produces results generally consistent with existing splice-prediction tools while detecting additional splice-modulating elements not identified by those predictors.
• Evaluation of Canonical Splice-Site SNVs: Identifies variants associated with unexpected splicing events and evaluates the splice-modulating potential of canonical splice-site SNVs.

Scientific Applications:

• Variant discovery in splicing studies: Identifies SNVs that co-occur with altered splice junction usage in RNA-seq datasets.
• Assessment of canonical splice-site SNVs: Evaluates the splice-modulating potential of known splice-site SNVs using transcriptome evidence.
• Investigation of splicing-related biology and disease: Facilitates study of how cis-acting variants contribute to unexpected splicing events and their implications in biological processes and disease.

Methodology:

Analyzes RNA-seq datasets to find reads that intersect SNV loci and nearby splice junctions, assesses co-occurrence with molecules that remain unspliced at exon-intron boundaries, and incorporates allele-specific sequencing to associate variant nucleotides with splicing alterations.