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

Genet Med. 2018 Apr;20(4):464-469. doi: 10.1038/gim.2017.128. Epub 2017 Sep 14.

Abstract

PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 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.ConclusionThese cases illustrate potential pitfalls of WES/NGS testing and the importance of phenotype-guided molecular testing in yielding diagnoses.

Publication types

  • Case Reports
  • Research Support, N.I.H., Extramural

MeSH terms

  • Alleles
  • Biopsy
  • Child
  • Child, Preschool
  • Exome*
  • Female
  • Genetic Association Studies* / methods
  • Genetic Diseases, Inborn / diagnosis
  • Genetic Diseases, Inborn / genetics
  • Genetic Predisposition to Disease*
  • Genotype
  • Humans
  • Infant
  • Molecular Diagnostic Techniques* / methods
  • Molecular Diagnostic Techniques* / standards
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Rare Diseases / diagnosis
  • Rare Diseases / genetics
  • Whole Exome Sequencing
  • Whole Genome Sequencing