title: Significant contribution of genomic rearrangements in SLC3A1 and SLC7A9 to the etiology of cystinuria.
abstract: BACKGROUND
  Cystinuria is an inherited disorder of defective renal reabsorption of cystine and the dibasic amino acids. Recently, SLC3A1 and SLC7A9 have been identified as responsible genes. While point mutations in the two genes are well known to cause cystinuria, only a few studies are aimed on the identification of gross genomic alterations. Here, we report our results of a systematic screening for deletions and duplications in SLC3A1 and SLC7A9 by quantitative real-time polymerase chain reaction (PCR).
  
  
  METHODS
  We screened a cohort of 49 cystinurics for copy number deviations in the genes SLC3A1 and SLC7A9 by quantitative real-time PCR assays using fluorogenic 5' nuclease chemistry. The detected duplication in SLC3A1 was analyzed in detail by further real-time assays, reverse transcription (RT)-PCR and direct sequencing.
  
  
  RESULTS
  In seven patients, we could identify a large duplication in SLC3A1 spanning from intron 4 to intron 9. This tandem duplication was accompanied by a small inversion of 25 bp and a 2 bp deletion in intron 9. As a formation mechanism, we presume that the inversion in intron 9 and several Alu sequences neighbored to the affected region provoke a chromatin structure that stimulates the duplication event. In addition to the SLC3A1 duplication, we observed deletions in SLC7A9 in three patients.
  
  
  CONCLUSIONS
  The frequency of genomic rearrangements in our patient population illustrates the significant contribution of large genomic alterations to the mutation spectrum in cystinuria. As we could show, quantitative real-time PCR is a reliable and effective tool for the identification of unbalanced genomic rearrangements.
authors.affiliation: Institute of Human Genetics, Technical University of Aachen, Aachen, Germany. cschmidt@ujaachen.de
authors.forename: Christa
authors.initials: C
authors.lastname: Schmidt
authors.forename: Udo
authors.initials: U
authors.lastname: Vester
authors.forename: Carsten A
authors.initials: CA
authors.lastname: Wagner
authors.forename: Sven
authors.initials: S
authors.lastname: Lahme
authors.forename: Albrecht
authors.initials: A
authors.lastname: Hesse
authors.forename: Peter
authors.initials: P
authors.lastname: Hoyer
authors.forename: Florian
authors.initials: F
authors.lastname: Lang
authors.forename: Klaus
authors.initials: K
authors.lastname: Zerres
authors.forename: Thomas
authors.initials: T
authors.lastname: Eggermann
mesh_terms: D026923:Amino Acid Transport Systems, Basic; D001483:Base Sequence; D002352:Carrier Proteins / Q000235:genetics*; D003555:Cystinuria / Q000209:etiology / Q000235:genetics*; D017353:Gene Deletion; D020440:Gene Duplication; D015321:Gene Rearrangement; D005838:Genotype; D006801:Humans; D007438:Introns / Q000235:genetics; D008562:Membrane Glycoproteins / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction / Q000592:standards; D015203:Reproducibility of Results
chemical_list: D026923:Amino Acid Transport Systems, Basic; D002352:Carrier Proteins; D008562:Membrane Glycoproteins; C499489:SLC7A9 protein, human