RNA-Seq detects a SAMD12-EXT1 fusion transcript and leads to the discovery of an EXT1 deletion in a child with multiple osteochondromas

Gavin R. Oliver, Patrick R. Blackburn, Marissa S. Ellingson, Erin Conboy, Filippo Pinto e Vairo, Matthew Webley, Erik C Thorland, Matthew Ferber, Els Van Hul, Ilse M. van der Werf, Wim Wuyts, Dusica Babovic-Vuksanovic, Eric W Klee

Research output: Contribution to journalArticle

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Abstract

Background: We describe a patient presenting with pachygyria, epilepsy, developmental delay, short stature, failure to thrive, facial dysmorphisms, and multiple osteochondromas. Methods: The patient underwent extensive genetic testing and analysis in an attempt to diagnose the cause of his condition. Clinical testing included metaphase karyotyping, array comparative genomic hybridization, direct sequencing and multiplex ligation-dependent probe amplification and trio-based exome sequencing. Subsequently, research-based whole transcriptome sequencing was conducted to determine whether it might shed light on the undiagnosed phenotype. Results: Clinical exome sequencing of patient and parent samples revealed a maternally inherited splice-site variant in the doublecortin (DCX) gene that was classified as likely pathogenic and diagnostic of the patient's neurological phenotype. Clinical array comparative genome hybridization analysis revealed a 16p13.3 deletion that could not be linked to the patient phenotype based on affected genes. Further clinical testing to determine the cause of the patient's multiple osteochondromas was unrevealing despite extensive profiling of the most likely causative genes, EXT1 and EXT2, including mutation screening by direct sequence analysis and multiplex ligation-dependent probe amplification. Whole transcriptome sequencing identified a SAMD12-EXT1 fusion transcript that could have resulted from a chromosomal deletion, leading to the loss of EXT1 function. Re-review of the clinical array comparative genomic hybridization results indicated a possible unreported mosaic deletion affecting the SAMD12 and EXT1 genes that corresponded precisely to the introns predicted to be affected by a fusion-causing deletion. The existence of the mosaic deletion was subsequently confirmed clinically by an increased density copy number array and orthogonal methodologies. Conclusions: While mosaic mutations and deletions of EXT1 and EXT2 have been reported in the context of multiple osteochondromas, to our knowledge, this is the first time that transcriptomics technologies have been used to diagnose a patient via fusion transcript analysis in the congenital disease setting.

Original languageEnglish (US)
Article numbere00560
JournalMolecular Genetics and Genomic Medicine
Volume7
Issue number3
DOIs
StatePublished - Mar 1 2019

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Multiple Hereditary Exostoses
RNA
Comparative Genomic Hybridization
Exome
Multiplex Polymerase Chain Reaction
Phenotype
Transcriptome
Genes
Lissencephaly
Karyotyping
Failure to Thrive
Sequence Deletion
Genetic Testing
Metaphase
Introns
Sequence Analysis
Epilepsy
Technology
Mutation

Keywords

  • exostoses
  • gene fusion
  • multiple hereditary
  • osteochondroma

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

RNA-Seq detects a SAMD12-EXT1 fusion transcript and leads to the discovery of an EXT1 deletion in a child with multiple osteochondromas. / Oliver, Gavin R.; Blackburn, Patrick R.; Ellingson, Marissa S.; Conboy, Erin; Pinto e Vairo, Filippo; Webley, Matthew; Thorland, Erik C; Ferber, Matthew; Van Hul, Els; van der Werf, Ilse M.; Wuyts, Wim; Babovic-Vuksanovic, Dusica; Klee, Eric W.

In: Molecular Genetics and Genomic Medicine, Vol. 7, No. 3, e00560, 01.03.2019.

Research output: Contribution to journalArticle

Oliver, Gavin R. ; Blackburn, Patrick R. ; Ellingson, Marissa S. ; Conboy, Erin ; Pinto e Vairo, Filippo ; Webley, Matthew ; Thorland, Erik C ; Ferber, Matthew ; Van Hul, Els ; van der Werf, Ilse M. ; Wuyts, Wim ; Babovic-Vuksanovic, Dusica ; Klee, Eric W. / RNA-Seq detects a SAMD12-EXT1 fusion transcript and leads to the discovery of an EXT1 deletion in a child with multiple osteochondromas. In: Molecular Genetics and Genomic Medicine. 2019 ; Vol. 7, No. 3.
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T1 - RNA-Seq detects a SAMD12-EXT1 fusion transcript and leads to the discovery of an EXT1 deletion in a child with multiple osteochondromas

AU - Oliver, Gavin R.

AU - Blackburn, Patrick R.

AU - Ellingson, Marissa S.

AU - Conboy, Erin

AU - Pinto e Vairo, Filippo

AU - Webley, Matthew

AU - Thorland, Erik C

AU - Ferber, Matthew

AU - Van Hul, Els

AU - van der Werf, Ilse M.

AU - Wuyts, Wim

AU - Babovic-Vuksanovic, Dusica

AU - Klee, Eric W

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N2 - Background: We describe a patient presenting with pachygyria, epilepsy, developmental delay, short stature, failure to thrive, facial dysmorphisms, and multiple osteochondromas. Methods: The patient underwent extensive genetic testing and analysis in an attempt to diagnose the cause of his condition. Clinical testing included metaphase karyotyping, array comparative genomic hybridization, direct sequencing and multiplex ligation-dependent probe amplification and trio-based exome sequencing. Subsequently, research-based whole transcriptome sequencing was conducted to determine whether it might shed light on the undiagnosed phenotype. Results: Clinical exome sequencing of patient and parent samples revealed a maternally inherited splice-site variant in the doublecortin (DCX) gene that was classified as likely pathogenic and diagnostic of the patient's neurological phenotype. Clinical array comparative genome hybridization analysis revealed a 16p13.3 deletion that could not be linked to the patient phenotype based on affected genes. Further clinical testing to determine the cause of the patient's multiple osteochondromas was unrevealing despite extensive profiling of the most likely causative genes, EXT1 and EXT2, including mutation screening by direct sequence analysis and multiplex ligation-dependent probe amplification. Whole transcriptome sequencing identified a SAMD12-EXT1 fusion transcript that could have resulted from a chromosomal deletion, leading to the loss of EXT1 function. Re-review of the clinical array comparative genomic hybridization results indicated a possible unreported mosaic deletion affecting the SAMD12 and EXT1 genes that corresponded precisely to the introns predicted to be affected by a fusion-causing deletion. The existence of the mosaic deletion was subsequently confirmed clinically by an increased density copy number array and orthogonal methodologies. Conclusions: While mosaic mutations and deletions of EXT1 and EXT2 have been reported in the context of multiple osteochondromas, to our knowledge, this is the first time that transcriptomics technologies have been used to diagnose a patient via fusion transcript analysis in the congenital disease setting.

AB - Background: We describe a patient presenting with pachygyria, epilepsy, developmental delay, short stature, failure to thrive, facial dysmorphisms, and multiple osteochondromas. Methods: The patient underwent extensive genetic testing and analysis in an attempt to diagnose the cause of his condition. Clinical testing included metaphase karyotyping, array comparative genomic hybridization, direct sequencing and multiplex ligation-dependent probe amplification and trio-based exome sequencing. Subsequently, research-based whole transcriptome sequencing was conducted to determine whether it might shed light on the undiagnosed phenotype. Results: Clinical exome sequencing of patient and parent samples revealed a maternally inherited splice-site variant in the doublecortin (DCX) gene that was classified as likely pathogenic and diagnostic of the patient's neurological phenotype. Clinical array comparative genome hybridization analysis revealed a 16p13.3 deletion that could not be linked to the patient phenotype based on affected genes. Further clinical testing to determine the cause of the patient's multiple osteochondromas was unrevealing despite extensive profiling of the most likely causative genes, EXT1 and EXT2, including mutation screening by direct sequence analysis and multiplex ligation-dependent probe amplification. Whole transcriptome sequencing identified a SAMD12-EXT1 fusion transcript that could have resulted from a chromosomal deletion, leading to the loss of EXT1 function. Re-review of the clinical array comparative genomic hybridization results indicated a possible unreported mosaic deletion affecting the SAMD12 and EXT1 genes that corresponded precisely to the introns predicted to be affected by a fusion-causing deletion. The existence of the mosaic deletion was subsequently confirmed clinically by an increased density copy number array and orthogonal methodologies. Conclusions: While mosaic mutations and deletions of EXT1 and EXT2 have been reported in the context of multiple osteochondromas, to our knowledge, this is the first time that transcriptomics technologies have been used to diagnose a patient via fusion transcript analysis in the congenital disease setting.

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