Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling

Foster, Joseph; Oumie, Assa; Togneri, Fiona S.; Vasques, Fabiana Ramos; Hau, Debra; Taylor, Morag; Tinkler-Hundal, Emma; Southward, Katie; Medlow, Paul; McGreeghan-Crosby, Keith; Halfpenny, Iris; McMullan, Dominic; Quirke, Philip; Keating, Katherine E.; Griffiths, Mike; Spink, Karen G.; Brew, Fiona

doi:10.1186/s12920-015-0079-z

Cited by 81 publications

(72 citation statements)

References 30 publications

(29 reference statements)

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“…The performance of our ASCN analysis method FACETS was validated with 2 independent methods on selected samples. First we analyzed genome-wide DNA copy number alterations and allelic imbalances by SNP array using the Affymetrix OncoScan FFPE Assay in 17 samples (34). This is a molecular inversion probe technology for the identification of copy number alterations and LOH.…”

Section: Methodsmentioning

confidence: 99%

“…To evaluate chromosomal events, we employed fraction and allele-specific copy number (ASCN) estimates from tumor sequencing (FACETS) (33), a novel statistical and computational pipeline for analyzing ASCNs from NGS data of tumor-normal sample pairs. To validate chromosome-level events beyond NGS platforms (WGS, WES, and MSK-IMPACT), an orthogonal approach on assessing genome-wide DNA copy number alterations and allelic imbalances was performed using the OncoScan FFPE Array (Affymetrix) in samples with (34). Furthermore, fluorescence in situ hybridization (FISH) assays utilizing chromosome-specific probes were conducted in select samples with sufficient numbers of available unstained slides to visualize chromosome gains or losses.…”

Section: Wgs On 5 M-hrcc Cases Identifies Recurrent Genomic Aberrationsmentioning

confidence: 99%

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Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma

Casuscelli¹,

Weinhold²,

Gundem³

et al. 2017

JCI Insight

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Section: Methodsmentioning

confidence: 99%

Section: Wgs On 5 M-hrcc Cases Identifies Recurrent Genomic Aberrationsmentioning

confidence: 99%

Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma

Casuscelli¹,

Weinhold²,

Gundem³

et al. 2017

JCI Insight

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“…If a sample consists of pure cancer or normal cells, TuScan™ returns an output of "homogeneous" and it can be interpreted as either 100% cancer or 100% normal cells based on the CNV results [11]. If cancer cells constitute the majority of the sample compared to normal cells, e.g., if cancer cells are nearly homogeneous, the TuScan™ algorithm subtracts the normal cell data from the CNV estimation and calculates CNV only in the tumor component as an integer number (e.g., CN = 2) with a burden of cancer as the percentage of aberration (%AC) [11,18]. Because the integer number is only from cancer cells, CNVs between samples can be compared regardless of different amounts of normal cells.…”

Section: Discussionmentioning

confidence: 99%

“…Scanning takes approximately 7 min per microarray or 14 min per sample. The entire testing process is completed within 48 h. Scanning generates DAT files, and the Affymetrix GeneChip Command Console software converts them to CEL files [11]. The DAT files are scanned array probe imaging files, and the CEL files are array fluorescence intensity files.…”

Section: Molecular Inversion Probe Technologymentioning

confidence: 99%

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Utilization of the oncoscan microarray assay in cancer diagnostics

2017

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Current strategies for cancer patient management include the use of genomic and proteomic test results to help guide therapeutic selection. The need for multi-target variant analysis is highlighted by the growing number of novel therapies to treat tumors with specific profiles and the increasing recognition that cancer is an extremely heterogeneous syndrome. Microarray analysis is a powerful genomic tool that provides genome-wide genetic information that is critical for guiding cancer treatments. Unlike constitutional applications of microarray analysis which are performed on whole blood samples, microarray analysis of solid tumors is challenging because tumor tissues are typically formalin fixed and paraffin embedded (FFPE). Genomic DNA extracted from FFPE tissues can also be fragmented into small pieces and yield much lower concentrations of DNA. We validated and implemented the Affymetrix OncoScan® FFPE assay to enable genome-wide analysis from these types of samples. The Affymetrix OncoScan® assay utilizes molecular inversion probes that generate multiplexed array hybridization targets from as short as 40 base-pairs of sequence and as low as approximately 80 ng of genomic DNA. OncoScan microarray analysis provides genomic information that includes structural variations, copy number variations and SNPs in a timely and a cost-effective manner from FFPE tumor tissues.

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Genomic profiling identifies GPC5 amplification in association with sarcomatous transformation in a subset of uterine carcinosarcomas

Chui

Have

Hoang

et al. 2018

The Journal of Pathology CR

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Uterine carcinosarcoma, also known as Malignant Mixed Müllerian Tumour, is a high‐grade biphasic neoplasm composed of sarcomatous elements thought to originate via transdifferentiation from high‐grade endometrial carcinoma. To identify molecular factors contributing to the histogenesis of this tumour, we analyzed DNA extracted from matched carcinoma and sarcoma components from 12 cases of carcinosarcoma by a molecular inversion probe microarray to assess genomic copy number alterations (CNAs) and allelic imbalances. Widespread CNAs were identified in tumours with serous histology in the carcinoma component (9/12), while the remaining three cases with endometrioid carcinoma were near‐diploid. Quantification of the extent of genomic aberrations revealed a significant increase in sarcoma relative to carcinoma in tumours with well‐delineated histologic components. Focal amplification of 13q31.3 was identified in 6/12 profiled tumours, of which four harboured the aberration exclusively in the sarcoma component. This result was verified by fluorescence in situ hybridization against GPC5, the only gene situated within the minimal region of amplification. In a validation cohort composed of 97 carcinosarcomas and other uterine sarcomas, amplification of GPC5 (GPC5/CEP13 ratio ≥ 2.2) was identified in 11/97 (11.3%) cases (9/64 carcinosarcoma, 1/3 rhabdomyosarcoma, 1/21 leiomyosarcoma, 0/8 adenosarcoma, 0/1 undifferentiated endometrial sarcoma) and an additional 4 (2.8%) cases had low level gains (GPC5/CEP13 ratio ≥1.5 but <2.2). The functional relevance of Glypican‐5, the gene product of GPC5, in regulating differentiation and lineage commitment was demonstrated in an endometrial carcinoma cell line in vitro. In conclusion, we identified GPC5 amplification as a molecular event mediating epithelial‐mesenchymal transdifferentiation in a subset of uterine carcinosarcomas.

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Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling

Cited by 81 publications

References 30 publications

Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma

Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma

Utilization of the oncoscan microarray assay in cancer diagnostics

Genomic profiling identifies GPC5 amplification in association with sarcomatous transformation in a subset of uterine carcinosarcomas

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