Insights from genomic microarrays into structural chromosome rearrangements

Abstract

Array-based comparative genomic hybridization allows high-resolution screening of copy number abnormalities in the genome, and becomes an increasingly important tool to detect deletions and duplications in tumor and post-natal cytogenetics. Here we illustrate that genomic arrays can also provide novel clues regarding the structural basis of chromosome rearrangement, including instability and mechanisms of formation of ring chromosomes. We also showed that array results might impact the recurrence risks for relatives of affected individuals. Our data indicate that chromosome rearrangements frequently involve more breaks than current cytogenetic models assume.

Ring chromosome formation as a novel escape mechanism in patients with inverted duplication and terminal deletion

“…10,13,14 After conventional cytogenetic screening (Figure 1a), the karyotype of the proband was described as 46,XX,r(14)(p12q32). To further map the breakpoint, array-CGH was performed with a resolution of about 1 Mb (Figure 2).…”

“…The clones were grown, amplified and spotted as described previously. 10,11 Genomic DNA of the patient was isolated using standard techniques, and 500 ng was labeled with Cy3-dCTP (GE Healthcare, Diegem, Belgium) using the BioPrime s DNA Labeling System (Invitrogen, Breda, The Netherlands). As a reference DNA, 500 ng female human genomic DNA (Promega, Leiden, The Netherlands) was labeled using Cy5-dCTP.…”

“…Final analysis of the intensity ratios of the hybridized DNA was preformed using Microsoft Excel according to published standards. 10 For further high-resolution analysis of duplications and deletions, oligo array-CGH was performed using the Agilent Human Genome CGH Microarray Kit 244K (Agilent, Amstelveen, The Netherlands) according to the manufacturer's instructions following protocol version 4.0. Data analysis was performed with the CGH Analytics 3.4 software platform (Agilent, Amstelveen, The Netherlands).…”

Frequent deletion of the CDKN2A locus in chordoma: analysis of chromosomal imbalances using array comparative genomic hybridisation

“…This BAC set is distributed to academic institutions by the Welcome Trust Sanger Institute (UK) at no cost, and information regarding the full set is available at the Sanger Center mapping database site, Ensembl (http://www.ensembl.org). The clones were spotted in triplicate, and the slides used in the current study were produced at Leiden University Medical Center, as previously described (Knijnenburg et al, 2005). DNA isolation, labelling, and microarray hybridisation were performed as described previously (Rozeman et al, 2006;Knijnenburg et al, 2007).…”

Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer

“…PCR products were spotted onto CodeLink (GE Healthcare, Munich, Germany) slides using an OmniGrid arrayer (Genomic Solutions, Ann Arbor, MI, USA) at the Leiden Genome Technology Center (www.lgtc.nl) as described. 18 Differential methylation hybridisation DMH was performed according to Yan et al 14 Cy5-labeled amplicons, representing methylated DNA fragments derived from tumours and paired normal mucosa samples, were cohybridized to the CpG island microarrays with a Cy3-labeled common reference amplicon consisting of a pool of DNA from the six colorectal cancer cell lines described above. Detection was done on a G2565BA scanner (Agilent Technologies, Santa Clara, CA, USA) and image analysis using GenePix6.0 (Molecular Devices, Union City, CA, USA).…”