Overexpression of LRP12, a gene contained within an 8q22 amplicon identified by high-resolution array CGH analysis of oral squamous cell carcinomas

Garnis, Cathie; Coe, Bradley P.; Zhang, Lewei; Rosin, Miriam P.; Lam, Wan L.

doi:10.1038/sj.onc.1207367

Cited by 60 publications

(41 citation statements)

References 13 publications

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“…Extraction of this quantity of DNA from paraffin sections is frequently not feasible, especially when microdissection is needed for preinvasive malignant lesions. Some investigators have recently reported results from as little as 100 ng of FFPE DNA, 22,23 and Daigo and colleagues 5 used DOP PCR amplification of very limited amounts of tumor DNA, but these results were from smaller arrays, including a commercial array consisting of 57 oncogenes. The limited number of targets used in these studies makes interpretation of the hybridization quality difficult; it appears that their amplification made interpretation of deletions difficult, and oncogene amplification levels may not have been linear.…”

Section: Discussionmentioning

confidence: 99%

Array-Based Comparative Genomic Hybridization from Formalin-Fixed, Paraffin-Embedded Breast Tumors

DeVries

Nyante

Korkola

et al. 2005

The Journal of Molecular Diagnostics

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Identification of prognostic and predictive genomic markers requires long-term clinical follow-up of patients. Extraction of high-quality DNA from archived formalin-fixed, paraffin-embedded material is essential for such studies. Of particular importance is a robust reproducible method of whole genome amplification for small tissue samples. This is especially true for high-resolution analytical approaches because different genomic regions and sequences may amplify differentially. We have tested a number of protocols for DNA amplification for array-based comparative genomic hybridization (CGH), in which relative copy number of the entire genome is measured at 1 to 2 mb resolution. Both random-primed amplification and degenerate oligonucleotide-primed amplification approaches were tested using varying amounts of fresh and paraffin-extracted normal and breast tumor input DNAs. We found that randomprimed amplification was clearly superior to degenerate oligonucleotide-primed amplification for arraybased CGH. The best quality and reproducibility strongly depended on accurate determination of the amount of input DNA using a quantitative polymerase chain reaction-based method. Reproducible and highquality results were attained using 50 ng of input DNA, and some samples yielded quality results with as little as 5 ng input DNA. We conclude that randomprimed amplification of DNA isolated from paraffin sections is a robust and reproducible approach for array-based CGH analysis of archival tumor samples. (J Mol Diagn 2005, 7:65-71)Genomic analysis of tumor DNA allows identification of alterations in sequence and copy number for individualized diagnostic, prognostic, and therapeutic decision making. This is especially relevant as personalized treatments for cancer patients based on specific genomic alterations become clinically available. Although DNA extracted from freshly acquired samples is optimum for these analyses, it is not always feasible to freeze away such samples given the constraints of clinical practice. Thus, having optimized protocols for extraction of DNA from formalin blocks is a necessary adjunct to recently developed clinical testing for tumor DNA alterations.One of the most useful approaches for analysis of DNA copy number alterations over the entire genome uses an array-based comparative genomic hybridization (CGH) analysis of DNA clones at 1-mb resolution.1-3 Current protocols for array CGH commonly require g quantities of high-quality DNA.4 Such material is generally not available from paraffin sections of formalin-fixed material, especially when tumors are small or require microdissection to remove contaminating normal or necrotic elements.A number of protocols have been reported for extraction and genomic amplification of archival material for application to standard (chromosome-based) or even array-based CGH, with varying quality of the resultant analyses. Degenerate oligonucleotide-primed (DOP) polymerase chain reaction (PCR) 5,6 and genomic representation amplification 7,8 have been tested using s...

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Section: Discussionmentioning

confidence: 99%

Array-Based Comparative Genomic Hybridization from Formalin-Fixed, Paraffin-Embedded Breast Tumors

DeVries

Nyante

Korkola

et al. 2005

The Journal of Molecular Diagnostics

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“…Generally, investigations have focused on identification of single driver genes within a region of aberration. For example, CCNL1 and LRP2 were identified in this way as genes overexpressed in oral SCC (Redon et al, 2002;Garnis et al, 2004).…”

Section: Introductionmentioning

confidence: 95%

Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma

et al. 2005

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“…With the release of the Human Genome Sequence and its subsequent refined versions very accurately annotated clone and gene assemblies for this region are available. In addition, the development of array comparative genomic hybridization (array-CGH) allows reliable assessment of DNA copy-number changes in a high-throughput manner and has proved to be very useful in the characterization of well-known amplicons (Pinkel et al, 1998;Albertson et al, 2000;Garnis et al, 2004). In a recent study, 1 Mb coverage array-CGH in combination with Southern blot analysis was used to characterize the 8p11-12 amplicon in three breast cell lines (Ray et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

A 1 Mb minimal amplicon at 8p11–12 in breast cancer identifies new candidate oncogenes

et al. 2005

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Amplification of 8p11-12 is a well-known alteration in human breast cancers but the driving oncogene has not been identified. We have developed a high-resolution comparative genomic hybridization array covering 8p11-12 and analysed 33 primary breast tumors, 20 primary ovarian tumors and 27 breast cancer cell lines. Expression analysis of the genes in the region was carried out by using real-time quantitative PCR and/or oligo-microarray profiling. In all, 24% (8/33) of the breast tumors, 5% (1/20) of the ovary tumors and 15% (4/27) of the cell lines showed 8p11-12 amplification. We identified a 1 Mb segment of common amplification that excludes previously proposed candidate genes. Some of the amplified genes did not show overexpression, whereas for others, overexpression was not specifically attributable to amplification. The genes FLJ14299, C8orf2, BRF2 and RAB11FIP, map within the 8p11-12 minimal amplicon, two have a putative function consistent with an oncogenic role, these four genes showed a strong correlation between amplification and overexpression and are therefore the best candidate driver oncogenes at 8p12.

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Overexpression of LRP12, a gene contained within an 8q22 amplicon identified by high-resolution array CGH analysis of oral squamous cell carcinomas

Cited by 60 publications

References 13 publications

Array-Based Comparative Genomic Hybridization from Formalin-Fixed, Paraffin-Embedded Breast Tumors

Array-Based Comparative Genomic Hybridization from Formalin-Fixed, Paraffin-Embedded Breast Tumors

Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma

A 1 Mb minimal amplicon at 8p11–12 in breast cancer identifies new candidate oncogenes

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