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

12 Citations (Scopus)

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

Fingerprint

Exome
Molecular Pathology
Rare Diseases
Phenotype
Systemic Hyalinosis
Neuroaxonal Dystrophies
Leukoencephalopathies
High-Throughput Nucleotide Sequencing
Ataxia
Base Pairing
Genes
Atrophy
Exons
Magnetic Resonance Spectroscopy
Software

Keywords

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

ASJC Scopus subject areas

  • Genetics(clinical)

Cite this

Looking beyond the exome : A phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases. / Undiagnosed Diseases Network Members.

In: Genetics in Medicine, Vol. 20, No. 4, 01.04.2018, p. 464-469.

Research output: Contribution to journalArticle

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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.",
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AU - El-Dairi, Mays

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AU - Jasien, Joan

AU - Kranz, Peter G.

AU - Noel, Richard

AU - Nagaraj, Shashi K.

AU - Lark, Robert K.

AU - Wechsler, Daniel S.G.

AU - Del Gaudio, Daniela

AU - Leung, Marco L.

AU - Hendon, Laura G.

AU - Parker, Collette C.

AU - Jones, Kelly L.

AU - Goldstein, David B.

AU - Shashi, Vandana

AU - Alejandro, Mercedes E.

AU - Bacino, Carlos A.

AU - Balasubramanyam, Ashok

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AU - Chen, Shan

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AU - Emrick, Lisa T.

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AU - Hanchard, Neil A.

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AU - Lewis, Richard A.

AU - Azamian, Mashid S.

AU - Moretti, Paolo M.

AU - Nicholas, Sarah K.

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N2 - 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.

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KW - Undiagnosed Diseases Network

KW - whole-exome sequencing

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