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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Pena, LDM; Jiang, Y-H; Schoch, K; Spillmann, RC; Walley, N; Stong, N; Rapisardo Horn, S; Sullivan, JA; McConkie-Rosell, A; Kansagra, S; Smith, EC; El-Dairi, M; Bellet, J; Keels, MA; Jasien, J; Kranz, PG; Noel, R; Nagaraj, SK; Lark, RK; Wechsler, DSG; Del Gaudio, D; Leung, ML; Hendon, LG; Parker, CC; Jones, KL; Undiagnosed Diseases Network Members, ; Goldstein, DB; Shashi, V

Published Date

  • April 2018

Published In

Volume / Issue

  • 20 / 4

Start / End Page

  • 464 - 469

PubMed ID

  • 28914269

Pubmed Central ID

  • PMC5851806

Electronic International Standard Serial Number (EISSN)

  • 1530-0366

Digital Object Identifier (DOI)

  • 10.1038/gim.2017.128


  • eng

Conference Location

  • United States