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

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, EXT 1 and EXT 2 , including mutation screening by direct sequence analysis and multiplex ligation‐dependent probe amplification. Whole transcriptome sequencing identified a SAMD 12‐ EXT 1 fusion transcript that could have resulted from a chromosomal deletion, leading to the loss of EXT 1 function. Re‐review of the clinical array comparative genomic hybridization results indicated a possible unreported mosaic deletion affecting the SAMD 12 and EXT 1 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 EXT 1 and EXT 2 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.

Glycogene Expression Profiling of Hepatic Cells by RNA-Seq Analysis for Glyco-Biomarker Identification

“…In fact, RNA-Seq of human colon cancer LSC confirmed a non-sense mutation in N-terminal area of C1GALT1C1 (COSMC) as we previously reported [(35), data not shown]. This suggests that RNA-Seq can avoid errors in counting transcripts with mutations, which causes no or low enzymatic activity that is consistent with the recent reports (36,37).…”

Identification of gene fusions associated with amyotrophic lateral sclerosis

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A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease

“…Patient 37 is a male child who presented with a phenotype including pachygyria, epilepsy, developmental delay, short stature, failure to thrive, facial dysmorphisms, and multiple exostoses [45]. Trio-based clinical exome sequencing identified a maternally inherited, X-linked loss-of-function variant in Doublecortin ( DCX ), which was classified as pathogenic and diagnostic of the patient’s neurological phenotype.…”

“…Agilent 44k and 180k array comparative genome hybridization (aCGH), fluorescence in-situ hybridization (FISH), multiplex-ligation probe analysis (MLPA) and Molecular Inversion Probe (MIP) Analysis were performed as previously described by Oliver et al . [45]. Flow cytometry, long range PCR, Pacific Biosciences (PacBio) sequencing, targeted PCR and Sanger sequencing were performed as previously described by Cousin et al .…”