title: Breakpoint mapping by next generation sequencing reveals causative gene disruption in patients carrying apparently balanced chromosome rearrangements with intellectual deficiency and/or congenital malformations.
abstract: BACKGROUND
  Apparently balanced chromosomal rearrangements (ABCR) are associated with an abnormal phenotype in 6% of cases. This may be due to cryptic genomic imbalances or to the disruption of genes at the breakpoint. However, breakpoint cloning using conventional methods (ie, fluorescent in situ hybridisation (FISH), Southern blot) is often laborious and time consuming. In this work, we used next generation sequencing (NGS) to locate breakpoints at the molecular level in four patients with multiple congenital abnormalities and/or intellectual deficiency (MCA/ID) who were carrying ABCR (one translocation, one complex chromosomal rearrangement and two inversions), which corresponded to nine breakpoints.
  
  
  METHODS
  Genomic imbalance was previously excluded by array comparative genomic hybridisation (CGH) in all four patients. Whole genome paired-end protocol was used to identify breakpoints. The results were verified by FISH and by PCR with Sanger sequencing.
  
  
  RESULTS
  We were able to map all nine breakpoints. NGS revealed an additional breakpoint due to a cryptic inversion at a breakpoint junction in one patient. Nine of 10 breakpoints occurred in repetitive elements and five genes were disrupted in their intronic sequence (TCF4, SHANK2, PPFIA1, RAB19, KCNQ1).
  
  
  CONCLUSIONS
  NGS is a powerful tool allowing rapid breakpoint cloning of ABCR at the molecular level. We showed that in three out of four patients, gene disruption could account for the phenotype, allowing adapted genetic counselling and stopping unnecessary investigations. We propose that patients carrying ABCR with an abnormal phenotype should be explored systematically by NGS once a genomic imbalance has been excluded by array CGH.
authors: Laboratoire de Cytogénétique Constitutionnelle, Service de Génétique, Centre de Biologie et de Pathologie Est, 59, boulevard Pinel, BRON 69677 Cedex, France. caroline.schluth-bolard@chu-lyon.fr
authors: Caroline
authors: C
authors: Schluth-Bolard
authors: Audrey
authors: A
authors: Labalme
authors: Marie-Pierre
authors: MP
authors: Cordier
authors: Marianne
authors: M
authors: Till
authors: Gwenaël
authors: G
authors: Nadeau
authors: Hélène
authors: H
authors: Tevissen
authors: Gaétan
authors: G
authors: Lesca
authors: Nadia
authors: N
authors: Boutry-Kryza
authors: Sylvie
authors: S
authors: Rossignol
authors: Delphine
authors: D
authors: Rocas
authors: Estelle
authors: E
authors: Dubruc
authors: Patrick
authors: P
authors: Edery
authors: Damien
authors: D
authors: Sanlaville
mesh_terms: D000015:Abnormalities, Multiple / Q000235:genetics*; D000328:Adult; D001483:Base Sequence; D002675:Child, Preschool; D056905:Chromosome Breakpoints; D002874:Chromosome Mapping / Q000379:methods*; D055028:Comparative Genomic Hybridization; D005260:Female; D015321:Gene Rearrangement; D006801:Humans; D007223:Infant; D008607:Intellectual Disability / Q000235:genetics*; D008297:Male; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011247:Pregnancy; D017422:Sequence Analysis, DNA / Q000379:methods*