Dataset Information

Detection of tetraploidization in chromophobe renal cell carcinoma: insights and pitfalls [Affymetrix OncoScan_CNV]

ABSTRACT: Chromophobic renal cell carcinomas (chRCC) typically have a hypodiploid genome, including a loss of chromosomes 1, 2, 6, 10, 13, 17 and 21, but few cases in the literature showed a gain of many chromosomes, suggesting a tetraploidy. The detection of this characteristic performed by comparative genomic hybridization (CGH-array), is very helpful for the diagnosis. To better characterize the phenomenon of tetraploidization and to explore the consequence and the difficulties of its detection, we studied a subset of 26 chRCC, including five cases of tetraploid chRCC, for which complementary analyses were performed. Our main objective was to determine whether these four cases displayed chromosomal losses typical of chRCC whitin a near-polyploid genome instead within a near-diploid one. We discuss the hazards and limitations of different molecular methods in the detection of polyploidization and its potential clinical consequences. In our study we show that this phenomenon of tetraploidization affects about 19% of chRCC and that is probably overlooked using standard molecular methods. The potential clinical consequences of this phenomenon are not identified yet.

ORGANISM(S): Homo sapiens

PROVIDER: GSE140390 | GEO | 2019/11/15

REPOSITORIES: GEO

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Project description:Near-haploid chromosome numbers have been found in less than 1% of cytogenetically reported tumors, but seem to be more common in certain neoplasms including the malignant cartilage-producing tumor chondrosarcoma. By a literature survey of published karyotypes from chondrosarcomas we could confirm that loss of chromosomes resulting in hyperhaploid-hypodiploid cells is common and that these cells may polyploidize. Sixteen chondrosarcomas were investigated by single nucleotide polymorphism (SNP) array and the majority displayed SNP patterns indicative of a hyperhaploid-hypodiploid origin, with or without subsequent polyploidization. Except for chromosomes 5, 7, 19, 20 and 21, autosomal loss of heterozygosity was commonly found, resulting from chromosome loss and subsequent duplication of monosomic chromosomes giving rise to uniparental disomy. Additional gains, losses and rearrangements of genetic material, and even repeated rounds of polyploidization, may affect chondrosarcoma cells resulting in highly complex karyotypes. Loss of chromosomes and subsequent polyploidization was not restricted to a particular chondrosarcoma subtype and, although commonly found in chondrosarcoma, binucleated cells did not seem to be involved in these events. Tumor DNA was hybridized onto Illumina Human Omni-Quad v1.0 BeadChip or Human CNV370-Quad v3.0 BeadChip (Illumina, San Diego, CA, USA), following standard protocols supplied by the manufacturer. Data were extracted from the GenomeStudio software (Illumina), and subsequently normalized and segmented using thresholded quantile normalization (tQN) and BAFsegmentation, respectively (Staaf et al. Normalization of array-CGH data: influence of copy number imbalances. BMC Genomics 2007, 8:382; Staaf et al. Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biol 2008, 9:R136). Base pair positions are indicated according to the NCBI build 36 (hg18).

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Detection of tetraploidization in chromophobe renal cell carcinoma: insights and pitfalls [Affymetrix OncoScan_CNV]

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