How to narrow down chromosomal breakpoints in small and large derivative chromosomes--a new probe set

J Appl Genet. 2012 Aug;53(3):259-69. doi: 10.1007/s13353-012-0098-9. Epub 2012 Apr 29.


Here a new fluorescence in situ hybridization (FISH-) based probe set is presented and its possible applications are highlighted in 34 exemplary clinical cases. The so-called pericentric-ladder-FISH (PCL-FISH) probe set enables a characterization of chromosomal breakpoints especially in small supernumerary marker chromosomes (sSMC), but can also be applied successfully in large inborn or acquired derivative chromosomes. PCL-FISH was established as 24 different chromosome-specific probe sets and can be used in two- up multicolor-FISH approaches. PCL-FISH enables the determination of a chromosomal breakpoint with a resolution between 1 and ∼10 megabasepairs and is based on locus-specific bacterial artificial chromosome (BAC) probes. Results obtained on 29 sSMC cases and five larger derivative chromosomes are presented and discussed. To confirm the reliability of PCL-FISH, eight of the 29 sSMC cases were studied by array-comparative genomic hybridization (aCGH); the used sSMC-specific DNA was obtained by glass-needle based microdissection and DOP-PCR-amplification. Overall, PCL-FISH leads to a better resolution than most FISH-banding approaches and is a good tool to narrow down chromosomal breakpoints.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Breakpoints*
  • Chromosomes, Artificial, Bacterial / genetics
  • Chromosomes, Human / genetics*
  • DNA Probes / metabolism*
  • Humans
  • In Situ Hybridization, Fluorescence
  • Karyotyping


  • DNA Probes