Complex chromosome 22 rearrangements in astrocytic tumors identified using microsatellite and chromosome 22 tile path array analysis

Abstract

Many studies have reported chromosome 22 as being abnormal in astrocytic tumors. In an attempt to map precisely the abnormal region or regions that potentially harbor tumor-suppressor genes or oncogenes, we constructed a chromosome 22 tile path array covering 82% of 22q with the use of 441 chromosome 22 clones. A 10-Mb whole-genome array consisting of 270 clones from all autosomes was included in the array. A total of 126 astrocytic tumors-5 diffuse astrocytomas (A), 29 anaplastic astrocytomas (AA), and 92 glioblastomas (GB)-were examined for chromosome 22 alterations both by microsatellite analysis (using 28 markers to identify allelic imbalance) and with the tile path array. The results showed that chromosome 22 alterations in astrocytic tumors could be complex. A number of tumors had a combination of deletions with and without reduplication of the retained chromosome, as well as copy number gains and amplifications. In two glioblastomas, overlapping homozygous deletions were identified that involved three genes (DEPDC5/KIAA0645, YWHAH, C22ORF24/HSN44A4A). The terminal region telomeric to the clone RP3-398C22 appeared to be the most frequently deleted region. The estimated incidence of any chromosome 22 alteration was 5% in A, 33% in AA, and 38% in GB. This study demonstrated the advantages of combining array comparative genomic hybridization and microsatellite analysis in elucidating complex genomic rearrangements in primary human tumor tissue. Supplementary material for this article can be found on the Genes, Chromosomes and Cancer website at http://www.interscience.wiley.com/jpages/1045-2257/suppmat/index.html.

Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells

“…3,15 Briefly, 400 ng of test (tumour) and reference DNA were labelled using a Bioprime Labelling Kit (Invitrogen, Carlsbad, CA, USA) with a modified dNTP reaction mixture. Test DNA was hybridised with sex-mismatched reference DNA from samples of pooled blood from 20 normal males or 20 normal females.…”

“…The precipitated DNA was dissolved in hybridisation buffer and hybridised to an array that had been prehybridised with 80 mg Cot-1 DNA and 400 mg herring sperm DNA for 2 h. Arrays were allowed to hybridise overnight at 371C then washed as described. 3 aCGH Data Analysis aCGH slides were scanned using an Axon 4100A scanner (Axon Instruments, Burlingame, CA, USA). Scanned images were quantified using GenePix Pro 5.1 software (Axon Instruments) and primary data analysis and normalisation carried out using Microsoft Excel.…”

“…Scanned images were quantified using GenePix Pro 5.1 software (Axon Instruments) and primary data analysis and normalisation carried out using Microsoft Excel. 3 An average between the duplicate spotted BACs was calculated and results were analysed using plots of log 2 -transformed normalised Cy5:Cy3 intensity ratios against clone position.…”

“…Genomewide BAC arrays at megabase (1 Mb) or submegabase (100 kb) size are now available for screening of genomic gains/losses. 1,2 Genomic copy number changes can be further characterised by use of chromosome-specific or customised tiled arrays, 3,4 which can be tailor made at any desired resolution. In addition, chromosome-specific tiled arrays can be used for characterisation of chromosomal translocation breakpoints when the derivative chromosome is isolated and used as the source of DNA.…”

Recent advances in array comparative genomic hybridization technologies and their applications in human genetics

“…28,30 -32 Furthermore, arm-specific arrays have been used to profile astrocytic tumors and other various cancers. 33,34 In terms of genome-wide approaches, cDNA microarrays and interval LIC arrays have yielded much information on the genomic landscape of a variety of cancers and the discovery of recurrent genetic alterations. 5,35 -38 In addition, genome-wide profiles are used to deduce features for disease classification including drug response.…”