title: Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing.
abstract: Characterisation of breakpoints in disease-associated balanced chromosome rearrangements (DBCRs), which disrupt or inactivate specific genes, has facilitated the molecular elucidation of a wide variety of genetic disorders. However, conventional methods for mapping chromosome breakpoints, such as in situ hybridisation with fluorescent dye-labelled bacterial artificial chromosome clones (BAC-FISH), are laborious, time consuming and often with insufficient resolution to unequivocally identify the disrupted gene. By combining DNA array hybridisation with chromosome sorting, the efficiency of breakpoint mapping has dramatically improved. However, this can only be applied when the physical properties of the derivative chromosomes allow them to be flow sorted. To characterise the breakpoints in all types of balanced chromosome rearrangements more efficiently and more accurately, we performed massively parallel sequencing using Illumina 1G analyser and ABI SOLiD systems to generate short sequencing reads from both ends of DNA fragments. We applied this method to four different DBCRs, including two reciprocal translocations and two inversions. By identifying read pairs spanning the breakpoints, we were able to map the breakpoints to a region of a few hundred base pairs that could be confirmed by subsequent PCR amplification and Sanger sequencing of the junction fragments. Our results show the feasibility of paired-end sequencing of systematic breakpoint mapping and gene finding in patients with disease-associated chromosome rearrangements.
authors: Max Planck Institute for Molecular Genetics, Berlin, Germany. wei.chen@mdc-berlin.de
authors: Wei
authors: W
authors: Chen
authors: Reinhard
authors: R
authors: Ullmann
authors: Claudia
authors: C
authors: Langnick
authors: Corinna
authors: C
authors: Menzel
authors: Zofia
authors: Z
authors: Wotschofsky
authors: Hao
authors: H
authors: Hu
authors: Andreas
authors: A
authors: Döring
authors: Yuhui
authors: Y
authors: Hu
authors: Hui
authors: H
authors: Kang
authors: Andreas
authors: A
authors: Tzschach
authors: Maria
authors: M
authors: Hoeltzenbein
authors: Heidemarie
authors: H
authors: Neitzel
authors: Susanne
authors: S
authors: Markus
authors: Eberhard
authors: E
authors: Wiedersberg
authors: Gerd
authors: G
authors: Kistner
authors: Conny M A
authors: CM
authors: van Ravenswaaij-Arts
authors: Tjitske
authors: T
authors: Kleefstra
authors: Vera M
authors: VM
authors: Kalscheuer
authors: Hans-Hilger
authors: HH
authors: Ropers
mesh_terms: D001483:Base Sequence; D002675:Child, Preschool; D002869:Chromosome Aberrations; D019457:Chromosome Breakage; D005260:Female; D015321:Gene Rearrangement / Q000235:genetics*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D008969:Molecular Sequence Data; D011247:Pregnancy; D017422:Sequence Analysis, DNA / Q000379:methods*