ArticleHuman heredity2025
Easy-PSAP: An Integrated Workflow to Prioritize Pathogenic Variants in Sequence Data from a Single Individual.
Article in Human heredity, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
introductionNext-generation sequencing (NGS) data analysis has become an integral part of clinical genetic diagnosis, raising the question of variant prioritization. The Population Sampling Probability (PSAP) method has been developed to tackle the issue of variant prioritization in the exome of a single patient, by leveraging allele frequencies from population databases and a variant pathogenicity score.
methodsHere, we present Easy-PSAP, a completely new implementation of the PSAP method comprising two user-friendly and highly adaptable pipelines. Easy-PSAP allows the gene-based recalibration of any in silico pathogenicity prediction score compared to scores of variants seen in the general population, including popular scores like CADD or AlphaMissense. Easy-PSAP can evaluate genetic variants at the scale of a whole exome or a whole genome using information from the latest population and annotation databases.
resultsThrough simulations on synthetic disease exomes, we show that Easy-PSAP is able to rank more than 50% of causal pathogenic variants in the top 10 variants for an autosomal dominant model of transmission and in top 1 for an autosomal recessive model of transmission. DISCUSSION: These findings, along with the accessibility of the pipeline to both researchers and clinicians, make Easy-PSAP a state-of-the-art tool for variant prioritization in NGS data that can continue to evolve as new frameworks and databases become available. Easy-PSAP is implemented in R and bash within an open-source Snakemake framework. It is available on GitHub alongside conda environments containing the required dependencies (<ext-link ext-link-type="uri" xlink:href="https://github.com/msogloblinsky/Easy-PSAP" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/msogloblinsky/Easy-PSAP</ext-link>).
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