SUsPECT – a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation

Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular if they affect transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. Researchers at Radboud University Medical Center have developed SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. This pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. The researchers demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are not predicted to be pathogenic using the reference transcript annotation. In further support of SUsPECT’s utility, they identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. This pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.

Premise for the creation of SUsPECT

Fig. 1

(A) Some pathogenic variants may be missed without actual information about all alternative transcripts expressed in a relevant sample. A variant in a particular genomic position may be incorrectly predicted to be non-deleterious. (B) A variant at the same genomic position may cause a different missense variant in different transcript structures due to varying open reading frames per transcript

Availability – SUsPECT is open source and freely available for download on GitHub (

Salz R, Saraiva-Agostinho N, Vorsteveld E, van der Made CI, Kersten S, Stemerdink M, Allen J, Volders PJ, Hunt SE, Hoischen A, ‘t Hoen PAC. (2023) SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation. BMC Genomics 24(1):305. [article]

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