Degenerate Oligonucleotide Primed-Polymerase Chain Reaction-Based Array Comparative Genomic Hybridization for Extensive Amplicon Profiling of Breast Cancers

Daigo, Yataro; Chin, Suet-Feung; Gorringe, Kylie L.; Bobrow, Lynda G.; Ponder, Bruce A.J.; Pharoah, Paul D.P.; Caldas, Carlos

doi:10.1016/s0002-9440(10)64118-1

Cited by 91 publications

(59 citation statements)

References 22 publications

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“…8 The arrays were similar to those used by Hui and colleagues, 19,20 consisting of oncogenes, and therefore not well suited for detection of deletions. We have established that in this tumor cohort direct random-prime labeling of DNA extracted from paraffin-embedded tissue yields quantitative data (ie, good signal to noise) and gives results comparable to established techniques such as CGH.…”

Section: Resultsmentioning

confidence: 99%

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High-Resolution Analysis of Paraffin-Embedded and Formalin-Fixed Prostate Tumors Using Comparative Genomic Hybridization to Genomic Microarrays

Paris¹,

Albertson²,

Alers³

et al. 2003

The American Journal of Pathology

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We have used prostate cancer, the most commonly diagnosed noncutaneous neoplasm among men, to investigate the feasibility of performing genomic array analyses of archival tissue. Prostate-specific antigen and a biopsy Gleason grade have not proven to be accurate in predicting clinical outcome, yet they remain the only accepted biomarkers for prostate cancer. It is likely that distinct spectra of genomic alterations underlie these phenotypic differences, and that once identified, may be used to differentiate between indolent and aggressive tumors. Array comparative genomic hybridization allows quantitative detection and mapping of copy number aberrations in tumors and subsequent associations to be made with clinical outcome. Archived tissues are needed to have patients with sufficient clinical follow-up. In this report, 20 formalin-fixed and paraffin-embedded prostate cancer samples originating from 1986 to 1996 were studied. We present a straightforward protocol and demonstrate the utility of archived tissue for array comparative genomic hybridization with a 2400 element BAC array that provides high-resolution detection of both deletions and amplifications. Array comparative genomic hybridization (aCGH) affords high-resolution quantitative information regarding DNA copy number changes within tumor genomes. Recurrent deletions and amplifications reveal loci encoding tumor suppressor genes and oncogenes, respectively, and their identification is now facilitated by completion of the human genome sequence. Moreover, it is increasingly evident that differing clinical behavior of histologically similar tumors is because of distinct and recurrent patterns of genomic alterations and that these may define distinct subsets of disease and thus be prognostic.

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Section: Resultsmentioning

confidence: 99%

“…Paraffin-embedded tissue has recently been reported to be suitable for aCGH; however the array in their study only consisted of 58 BACS containing known oncogenes. 8 In addition, their technique required degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) amplification of the tumor material.…”

mentioning

confidence: 99%

High-Resolution Analysis of Paraffin-Embedded and Formalin-Fixed Prostate Tumors Using Comparative Genomic Hybridization to Genomic Microarrays

Paris¹,

Albertson²,

Alers³

et al. 2003

The American Journal of Pathology

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“…Array CGH technology permits detection of specific genes with copy number variations, and it has been used to screen human solid cancers for genomic imbalances. [27][28][29][30][31][32][33][34] We also used a genomic DNA microarray to investigate DCNAs for 287 target clones in HCV-HCC; however, the number of DNA clones was very small. Array CGH detected DNA copy number alterations for the HRAS, THRA, TNFRSF6B/DCR3, FGR/SRC2, and GSCL genes, whereas conventional CGH did not always detect such changes.…”

Section: Discussionmentioning

confidence: 99%

Analysis of DNA copy number aberrations in hepatitis C virus-associated hepatocellular carcinomas by conventional CGH and array CGH

Hashimoto

Mori²,

Tamesa³

et al. 2004

Modern Pathology

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To clarify the genetic aberrations involved in the development and progression of hepatitis C virus-associated hepatocellular carcinoma (HCV-HCC), we investigated DNA copy number aberrations (DCNAs) in 19 surgically resected HCCs by conventional CGH and array CGH. Conventional CGH revealed that increases of DNA copy number were frequent at 1q (79% of the cases), 8q (37%), 6p (32%), and 10p (32%) and that decreases were frequent at 17p (79%), 16q (58%), 4q (53%), 13q (42%), 10q (37%), 1p (32%), and 8p (32%). In general, genes that showed DCNAs by array CGH were usually located in chromosomal regions with DCNAs detected by conventional CGH analysis. Increases in copy numbers of the LAMC2, TGFB2, and AKT3 genes (located on 1q) and decreases in copy numbers of FGR/SRC2 and CYLD (located on 1p and 16q, respectively) were observed in more than 30% of tumors, including small, well-differentiated carcinomas. These findings suggest that these genes are associated with the development of HCV-HCC. Increases of MOS, MYC, EXT1, and PTK2 (located on 8q) were detected exclusively in moderately and poorly differentiated tumors, suggesting that these alterations contribute to tumor progression. In conclusion, chromosomal and array CGH technologies allow identification of genes involved in the development and progression of HCV-HCC.

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“…21,22 However, most studies that have shown that aCGH can be used to quantitate chromosomal copy number in human and mouse tumors have used fresh, frozen tissue.…”

Section: Discussionmentioning

confidence: 99%

“…16,22,23 Daigo and colleagues 22 used FFPE DNA amplified by degenerate oligonucleotide-primed (DOP) PCR and an array consisting of oncogenes. Unfortunately, this array is not as relevant for detecting DNA copy number loss (given the emphasis on oncogene loci), which is of importance for glioma molecular diagnostics.…”

Section: Discussionmentioning

confidence: 99%

Glioma Test Array for Use with Formalin-Fixed, Paraffin-Embedded Tissue

Mohapatra

Betensky

Miller

et al. 2006

The Journal of Molecular Diagnostics

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Array-based comparative genomic hybridization (aCGH) is a powerful, high-throughput tool for whole genome analysis. Until recently, aCGH could only be reproducibly performed on frozen tissue samples and with significant tissue amounts. For brain tumors however, paraffin-embedded tissue blocks from small stereotactic biopsies may be the only tissue routinely available. The development of methods to analyze formalinfixed, paraffin-embedded (FFPE) material therefore has the potential to impact molecular diagnosis in a significant way. To this end, we constructed a BAC array representing chromosomes 1, 7, 19, and X because 1p/19q deletion and EGFR gene amplification provide clinically relevant information for glioma diagnosis. We also optimized a two-step labeling procedure using an amine-modified nucleotide for generating aCGH probes. Using this approach, we analyzed a series of 28 FFPE oligodendroglial tumors for alterations of chromosomes 1, 7, and 19. We also independently assayed these tumors for 1p/19q deletion by fluorescence in situ hybridization and by loss of heterozygosity analyses. The concordance between aCGH, standard loss of heterozygosity and fluorescence in situ hybridization was nearly 100% for the chromosomes analyzed. These results suggest that aCGH could offer an improved molecular diagnostic approach for gliomas because of its ability to detect clinically relevant molecular alterations in small FFPE specimens.

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Degenerate Oligonucleotide Primed-Polymerase Chain Reaction-Based Array Comparative Genomic Hybridization for Extensive Amplicon Profiling of Breast Cancers

Cited by 91 publications

References 22 publications

High-Resolution Analysis of Paraffin-Embedded and Formalin-Fixed Prostate Tumors Using Comparative Genomic Hybridization to Genomic Microarrays

High-Resolution Analysis of Paraffin-Embedded and Formalin-Fixed Prostate Tumors Using Comparative Genomic Hybridization to Genomic Microarrays

Analysis of DNA copy number aberrations in hepatitis C virus-associated hepatocellular carcinomas by conventional CGH and array CGH

Glioma Test Array for Use with Formalin-Fixed, Paraffin-Embedded Tissue

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