Evaluating NGS variant callers in a challenging genomic context with a focus on the PRSS1-PRSS2 locus for hereditary pancreatitis
Date
2025
Authors
Kusay, Y.
Wu, D.
De Sousa, S.M.C.
Drogemuller, C.J.
Coates, P.T.
Kok, C.H.
Scott, H.S.
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Journal article
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Gut, online, 2025; online:1-3
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Abstract
Hereditary pancreatitis is frequently associated with pathogenic variants in PRSS1. However, the PRSS1 and PRSS2 loci reside within a genomic region with extensive sequence homology to multiple pseudogenes (ie, PRSS3P2 and TRY7) with reads misaligning to PRSS1/2, causing erroneous variant calling in conventional pipelines. Therefore, accurate identification of PRSS1/2 variants with high sensitivity and specificity is essential for reliable clinical diagnosis and genetic risk assessment. To address these challenges, Lou et al recently developed NGS.PRSS1-2caller, which improves variant calling accuracy by using an alternative contig of chromosome 7 from GRCh38 with all relevant pseudogenes.
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Copyright 2025 Author(s) (or their employer(s)). No commercial re- use.