title: Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing.
abstract: Translocations are a common class of chromosomal aberrations and can cause disease by physically disrupting genes or altering their regulatory environment. Some translocations, apparently balanced at the microscopic level, include deletions, duplications, insertions, or inversions at the molecular level. Traditionally, chromosomal rearrangements have been investigated with a conventional banded karyotype followed by arduous positional cloning projects. More recently, molecular cytogenetic approaches using fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH), or whole-genome SNP genotyping together with molecular methods such as inverse PCR and quantitative PCR have allowed more precise evaluation of the breakpoints. These methods suffer, however, from being experimentally intensive and time-consuming and of less than single base pair resolution. Here we describe targeted breakpoint capture followed by next-generation sequencing (TBCS) as a new approach to the general problem of determining the precise structural characterization of translocation breakpoints and related chromosomal aberrations. We tested this approach in three patients with complex chromosomal translocations: The first had craniofacial abnormalities and an apparently balanced t(2;3)(p15;q12) translocation; the second has cleidocranial dysplasia (OMIM 119600) associated with a t(2;6)(q22;p12.3) translocation and a breakpoint in RUNX2 on chromosome 6p; and the third has acampomelic campomelic dysplasia (OMIM 114290) associated with a t(5;17)(q23.2;q24) translocation, with a breakpoint upstream of SOX9 on chromosome 17q. Preliminary studies indicated complex rearrangements in patients 1 and 3 with a total of 10 predicted breakpoints in the three patients. By using TBCS, we quickly and precisely defined eight of the 10 breakpoints.
authors: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors: Nara L M
authors: NL
authors: Sobreira
authors: Veena
authors: V
authors: Gnanakkan
authors: Michael
authors: M
authors: Walsh
authors: Beth
authors: B
authors: Marosy
authors: Elizabeth
authors: E
authors: Wohler
authors: George
authors: G
authors: Thomas
authors: Julie E
authors: JE
authors: Hoover-Fong
authors: Ada
authors: A
authors: Hamosh
authors: Sarah J
authors: SJ
authors: Wheelan
authors: David
authors: D
authors: Valle
mesh_terms: D000328:Adult; D001483:Base Sequence; D055036:Campomelic Dysplasia / Q000235:genetics; D056905:Chromosome Breakpoints; D002874:Chromosome Mapping; D002877:Chromosomes, Human; D002973:Cleidocranial Dysplasia / Q000235:genetics; D050659:Core Binding Factor Alpha 1 Subunit / Q000235:genetics; D019465:Craniofacial Abnormalities / Q000235:genetics; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010375:Pedigree; D055758:SOX9 Transcription Factor / Q000235:genetics; D014178:Translocation, Genetic
chemical_list: D050659:Core Binding Factor Alpha 1 Subunit; C493709:RUNX2 protein, human; D055758:SOX9 Transcription Factor; C527932:SOX9 protein, human