Interpretable prioritization of splice variants in diagnostic next-generation sequencing

Daniel Danis, Julius O.B. Jacobsen, Leigh C. Carmody, Michael A. Gargano, Julie A. McMurry, Ayushi Hegde, Melissa A. Haendel, Giorgio Valentini, Damian Smedley, Peter N. Robinson

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

A critical challenge in genetic diagnostics is the computational assessment of candidate splice variants, specifically the interpretation of nucleotide changes located outside of the highly conserved dinucleotide sequences at the 5′ and 3′ ends of introns. To address this gap, we developed the Super Quick Information-content Random-forest Learning of Splice variants (SQUIRLS) algorithm. SQUIRLS generates a small set of interpretable features for machine learning by calculating the information-content of wild-type and variant sequences of canonical and cryptic splice sites, assessing changes in candidate splicing regulatory sequences, and incorporating characteristics of the sequence such as exon length, disruptions of the AG exclusion zone, and conservation. We curated a comprehensive collection of disease-associated splice-altering variants at positions outside of the highly conserved AG/GT dinucleotides at the termini of introns. SQUIRLS trains two random-forest classifiers for the donor and for the acceptor and combines their outputs by logistic regression to yield a final score. We show that SQUIRLS transcends previous state-of-the-art accuracy in classifying splice variants as assessed by rank analysis in simulated exomes, and is significantly faster than competing methods. SQUIRLS provides tabular output files for incorporation into diagnostic pipelines for exome and genome analysis, as well as visualizations that contextualize predicted effects of variants on splicing to make it easier to interpret splice variants in diagnostic settings.

Original languageEnglish (US)
Pages (from-to)1564-1577
Number of pages14
JournalAmerican Journal of Human Genetics
Volume108
Issue number9
DOIs
StatePublished - Sep 2 2021
Externally publishedYes

Keywords

  • Mendelian genetics
  • bioinformatics
  • cryptic splicing
  • exome sequencing
  • genome sequencing
  • machine learning
  • random forest
  • sequence logo
  • splice mutation
  • splice variant
  • splicing

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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