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Detection of a novel intragenic rearrangement in the creatine transporter gene by next generation sequencing.

Abstract
Deficiency caused by mutations in the creatine transporter gene (SLC6A8/CT1) is an X-linked form of intellectual disability. The presence of highly homologous pseudogenes and high GC content of SLC6A8 genomic sequence complicates the molecular diagnosis of this disorder. To minimize the pseudogene interference, exons 2 to 13 of SLC6A8 were amplified as a single PCR product using gene-specific long-range PCR (LR-PCR) primers. The GC-rich exon 1 and its flanking intronic sequences were amplified separately in a short fragment under GC-rich conditions and a touchdown PCR program. Traditional Sanger sequence analysis of all coding exons of SLC6A8 from a 3-year-old boy with creatine transporter deficiency did not detect deleterious mutations. The long-range PCR product was used as template followed by massively parallel sequencing (MPS) on HiSeq2000. We were able to detect a tandem duplication involving part of exons 11 and 12 in the SLC6A8 gene. The deduced c.1592_1639dup133 mutation was confirmed to be a hemizygous insertion by targeted genomic DNA and cDNA Sanger sequencing. Combination of deep sequencing technology with long-range PCR revealed a novel intragenic duplication in the SLC6A8 gene, providing a definitive molecular diagnosis of creatine transporter deficiency in a male patient.
AuthorsHui Yu, Clara van Karnebeek, Graham Sinclair, Alan Hill, Hong Cui, Victor Wei Zhang, Lee-Jun Wong
JournalMolecular genetics and metabolism (Mol Genet Metab) Vol. 110 Issue 4 Pg. 465-71 (Dec 2013) ISSN: 1096-7206 [Electronic] United States
PMID24140398 (Publication Type: Journal Article)
Copyright© 2013 Elsevier Inc. All rights reserved.
Chemical References
  • Nerve Tissue Proteins
  • Plasma Membrane Neurotransmitter Transport Proteins
  • SLC6A8 protein, human
  • Creatine
Topics
  • Brain Diseases, Metabolic, Inborn (diagnosis, genetics)
  • Child, Preschool
  • Creatine (deficiency, genetics)
  • Exons
  • Gene Duplication
  • Genetic Diseases, X-Linked (diagnosis, genetics)
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Intellectual Disability (genetics)
  • Male
  • Mental Retardation, X-Linked (diagnosis, genetics)
  • Models, Structural
  • Molecular Sequence Data
  • Mutation
  • Nerve Tissue Proteins (genetics)
  • Pathology, Molecular (methods)
  • Pedigree
  • Plasma Membrane Neurotransmitter Transport Proteins (deficiency, genetics)
  • Pseudogenes (genetics)

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