Limits...
Mapping of balanced chromosome translocation breakpoints to the basepair level from microdissected chromosomes.

Obenauf AC, Schwarzbraun T, Auer M, Hoffmann EM, Waldispuehl-Geigl J, Ulz P, Günther B, Duba HC, Speicher MR, Geigl JB - J. Cell. Mol. Med. (2010)

Bottom Line: The analysis of structural variants associated with specific phenotypic features is promising for the elucidation of the function of involved genes.There is, however, at present no approach allowing the rapid mapping of chromosomal translocation breakpoints to the basepair level from a single chromosome.The amplification products of the der(7) and of the der(13) were hybridized to custom-made arrays, enabling us to define primers at flanking breakpoint regions and thus to fine-map the breakpoints to the basepair level.

View Article: PubMed Central - PubMed

Affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.

ABSTRACT
The analysis of structural variants associated with specific phenotypic features is promising for the elucidation of the function of involved genes. There is, however, at present no approach allowing the rapid mapping of chromosomal translocation breakpoints to the basepair level from a single chromosome. Here we demonstrate that we have advanced both the microdissection and the subsequent unbiased amplification to an extent that breakpoint mapping to the basepair level has become possible. As a case in point we analysed the two breakpoints of a t(7;13) translocation observed in a patient with split hand/foot malformation (SHFM1). The amplification products of the der(7) and of the der(13) were hybridized to custom-made arrays, enabling us to define primers at flanking breakpoint regions and thus to fine-map the breakpoints to the basepair level. Consequently, our results will also contribute to a further delineation of causative mechanisms underlying SHFM1 which are currently unknown.

Show MeSH

Related in: MedlinePlus

Hybridization of the der(7) and der(13) chromosomes to custom made arrays of the respective breakpoint region with a probe spacing of one oligonucleotide every 125 bp.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3822999&req=5

fig03: Hybridization of the der(7) and der(13) chromosomes to custom made arrays of the respective breakpoint region with a probe spacing of one oligonucleotide every 125 bp.

Mentions: This enabled us to select the best six laser-microdissected chromosomes of each derivative chromosome. These were pooled and hybridized on a 244K array (Fig. 2). Based on the obtained hybridization pattern, we could already locate the chromosome 7 breakpoint to chromosomal region 96350310–96498328 and the chromosome 13 breakpoint to 98146050–98213431. We used this information to design an extremely high-resolution tiling oligoarray where each breakpoint region was covered with a probe density of one probe/125 bp. This high-density custom-made array enabled us to pinpoint the breakpoint on the derivative chromosome 7 to a 3.3 kb region (Chr7: 96463274–96466595) and the breakpoint on the derivative chromosome 13 even to a 130 bp region (Chr13: 98184265–98184394 (Fig. 3).


Mapping of balanced chromosome translocation breakpoints to the basepair level from microdissected chromosomes.

Obenauf AC, Schwarzbraun T, Auer M, Hoffmann EM, Waldispuehl-Geigl J, Ulz P, Günther B, Duba HC, Speicher MR, Geigl JB - J. Cell. Mol. Med. (2010)

Hybridization of the der(7) and der(13) chromosomes to custom made arrays of the respective breakpoint region with a probe spacing of one oligonucleotide every 125 bp.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3822999&req=5

fig03: Hybridization of the der(7) and der(13) chromosomes to custom made arrays of the respective breakpoint region with a probe spacing of one oligonucleotide every 125 bp.
Mentions: This enabled us to select the best six laser-microdissected chromosomes of each derivative chromosome. These were pooled and hybridized on a 244K array (Fig. 2). Based on the obtained hybridization pattern, we could already locate the chromosome 7 breakpoint to chromosomal region 96350310–96498328 and the chromosome 13 breakpoint to 98146050–98213431. We used this information to design an extremely high-resolution tiling oligoarray where each breakpoint region was covered with a probe density of one probe/125 bp. This high-density custom-made array enabled us to pinpoint the breakpoint on the derivative chromosome 7 to a 3.3 kb region (Chr7: 96463274–96466595) and the breakpoint on the derivative chromosome 13 even to a 130 bp region (Chr13: 98184265–98184394 (Fig. 3).

Bottom Line: The analysis of structural variants associated with specific phenotypic features is promising for the elucidation of the function of involved genes.There is, however, at present no approach allowing the rapid mapping of chromosomal translocation breakpoints to the basepair level from a single chromosome.The amplification products of the der(7) and of the der(13) were hybridized to custom-made arrays, enabling us to define primers at flanking breakpoint regions and thus to fine-map the breakpoints to the basepair level.

View Article: PubMed Central - PubMed

Affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.

ABSTRACT
The analysis of structural variants associated with specific phenotypic features is promising for the elucidation of the function of involved genes. There is, however, at present no approach allowing the rapid mapping of chromosomal translocation breakpoints to the basepair level from a single chromosome. Here we demonstrate that we have advanced both the microdissection and the subsequent unbiased amplification to an extent that breakpoint mapping to the basepair level has become possible. As a case in point we analysed the two breakpoints of a t(7;13) translocation observed in a patient with split hand/foot malformation (SHFM1). The amplification products of the der(7) and of the der(13) were hybridized to custom-made arrays, enabling us to define primers at flanking breakpoint regions and thus to fine-map the breakpoints to the basepair level. Consequently, our results will also contribute to a further delineation of causative mechanisms underlying SHFM1 which are currently unknown.

Show MeSH
Related in: MedlinePlus