Mapping translocation breakpoints by next-generation sequencing.
Balanced chromosome rearrangements (BCRs) can cause genetic diseases by disrupting or inactivating specific genes, and the characterization of breakpoints in disease-associated BCRs has been instrumental in the molecular elucidation of a wide variety of genetic disorders. However, mapping chromosome breakpoints using traditional methods, such as in situ hybridization with fluorescent dye-labeled bacterial artificial chromosome clones (BAC-FISH), is rather laborious and time-consuming. In addition, the resolution of BAC-FISH is often insufficient to unequivocally identify the disrupted gene. To overcome these limitations, we have performed shotgun sequencing of flow-sorted derivative chromosomes using "next-generation" (Illumina/Solexa) multiplex sequencing-by-synthesis technology. As shown here for three different disease-associated BCRs, the coverage attained by this platform is sufficient to bridge the breakpoints by PCR amplification, and this procedure allows the determination of their exact nucleotide positions within a few weeks. Its implementation will greatly facilitate large-scale breakpoint mapping and gene finding in patients with disease-associated balanced translocations.
Chen
Wei
W
Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. wei@molgen.mpg.de
Kalscheuer
Vera
V
Tzschach
Andreas
A
Menzel
Corinna
C
Ullmann
Reinhard
R
Schulz
Marcel Holger
MH
Erdogan
Fikret
F
Li
Na
N
Kijas
Zofia
Z
Arkesteijn
Ger
G
Pajares
Isidora Lopez
IL
Goetz-Sothmann
Margret
M
Heinrich
Uwe
U
Rost
Imma
I
Dufke
Andreas
A
Grasshoff
Ute
U
Glaeser
Birgitta
B
Vingron
Martin
M
Ropers
H Hilger
HH
D000293:Adolescent; D001483:Base Sequence; D002648:Child; D019457:Chromosome Breakage; D002874:Chromosome Mapping / Q000379:methods; D005260:Female; D006801:Humans; D008607:Intellectual Disability / Q000235:genetics; D008297:Male; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D014178:Translocation, Genetic