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

Undiagnosed Diseases Network Members

Research output: Contribution to journalArticle

18 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)464-469
Number of pages6
JournalGenetics in Medicine
Volume20
Issue number4
DOIs
StatePublished - Apr 1 2018
Externally publishedYes

Keywords

  • Undiagnosed Diseases Network
  • infantile neuroaxonal dystrophy
  • infantile systemic hyalinosis
  • leukoencephalopathy with vanishing white matter
  • whole-exome sequencing

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