Looking beyond the exome: A phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases

Academic Article


  • Purpose: To describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing. Methods: Guided by phenotypic information, three children with negative WES underwent targeted single-gene testing. Results: Individual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software. Individual 2 had neurodevelopmental regression and cerebellar atrophy, with no diagnosis on WES. New clinical findings prompted Sanger sequencing and copy number testing of PLA2G6. A novel homozygous deletion of the noncoding exon 1 (not included in the WES capture kit) was detected, with extension into the promoter, confirming the clinical suspicion of infantile neuroaxonal dystrophy. Individual 3 had progressive ataxia, spasticity, and magnetic resonance image changes of vanishing white matter leukoencephalopathy. An NGS leukodystrophy gene panel and WES showed a heterozygous pathogenic variant in EIF2B5; no deletions/duplications were detected. Sanger sequencing of EIF2B5 showed a frameshift indel, probably missed owing to failure of alignment. Conclusion: These cases illustrate potential pitfalls of WES/NGS testing and the importance of phenotype-guided molecular testing in yielding diagnoses.
  • Published In

    Digital Object Identifier (doi)

    Author List

  • Pena LDM; Jiang YH; Schoch K; Spillmann RC; Walley N; Stong N; Horn SR; Sullivan JA; McConkie-Rosell A; Kansagra S
  • Start Page

  • 464
  • End Page

  • 469
  • Volume

  • 20
  • Issue

  • 4