Optimization of the Affymetrix GeneChip Mapping 10K 2.0 Assay for Routine Clinical Use on Formalin-fixed Paraffin-embedded Tissues

@article{LyonsWeiler2008OptimizationOT,
  title={Optimization of the Affymetrix GeneChip Mapping 10K 2.0 Assay for Routine Clinical Use on Formalin-fixed Paraffin-embedded Tissues},
  author={Maureen A. Lyons-Weiler and Jill Hagenkord and Christin M. Sciulli and Rajiv Dhir and Federico A. Monzon},
  journal={Diagnostic Molecular Pathology},
  year={2008},
  volume={17},
  pages={3-13}
}
The use of chromosomal copy number changes as markers for tumor behavior or as prognostic markers for patient outcome has been suggested. However, current clinically used technologies cannot perform genome-wide assessment of chromosome copy number and analysis of loss of heterozygosity in the same assay for paraffin-embedded tissue. We have optimized the Affymetrix GeneChip Mapping Assay for the 10K 2.0 array for use with formalin-fixed, paraffin-embedded (FFPE) tissues. This technology uses… 
Reproducibility and Performance of Virtual Karyotyping With SNP Microarrays for the Detection of Chromosomal Imbalances in Formalin-fixed Paraffin-embedded Tissues
  • K. AlvarezS. Kash F. Monzon
  • Biology
    Diagnostic molecular pathology : the American journal of surgical pathology, part B
  • 2010
TLDR
SNP arrays are a reliable, reproducible, and robust platform for the virtual karyotyping of FFPE tumor tissues with performance characteristics adequate for clinical application.
A Predictive Factor of the Quality of Microarray Comparative Genomic Hybridization Analysis for Formalin-fixed Paraffin-embedded Archival Tissue
TLDR
The double-stranded DNA ratio of tumor DNA is the most significant predictive factor of DLRSpread, and valuable FFPE archival tissue samples can be utilized for aCGH analysis.
A multicenter, cross-platform clinical validation study of cancer cytogenomic arrays.
High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays
TLDR
High quality CN data with MIP technology was generated in 88% of FFPE samples from seven diverse collections and the performance of F FPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%).
Oligonucleotide Probe Array for p53 Gene Alteration Analysis in DNA from Formalin‐Fixed Paraffin‐Embedded Breast Cancer Tissues
TLDR
Although OPA detected fewer gene alterations than direct sequencing, the difference was not significant and the OPA may be safely used to identify individual genetic variations of human p53 gene in BC specimens.
Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors
TLDR
Results show that SNP arrays can detect characteristic chromosomal aberrations in paraffin-embedded renal tumors, and thus offer a high-resolution, genome-wide method that can be used as an ancillary study for classification and potentially for prognostic stratification of these tumors.
Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors
TLDR
Results show that virtual karyotypes generated by SNP arrays can be used as a practical ancillary study for the classification of renal epithelial tumors with complex or ambiguous morphology.
Virtual-Karyotyping With SNP Microarrays in Morphologically Challenging Renal Cell Neoplasms: A Practical and Useful Diagnostic Modality
TLDR
It is concluded that virtual karyotypes generated by SNP arrays are a valuable tool for increasing diagnostic accuracy in morphologically challenging or unclassified renal neoplasms.
Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection
TLDR
The challenges of solid tumor assay design/analysis are discussed, the need to include complementary technologies (i.e., arrays) and germline analysis in tumor testing to reliably identify copy number alterations and actionable variants are highlighted.
...
...

References

SHOWING 1-10 OF 20 REFERENCES
Whole genome SNP arrays using DNA derived from formalin‐fixed, paraffin‐embedded ovarian tumor tissue
TLDR
It is shown that it is possible to achieve high‐performance outcomes using FFPE‐derived DNA in the Affymetrix 10 K mapping array and this advance will open up vast archival tissue resources to high‐resolution genetic analysis and unlock a wealth of biological information.
Glioma test array for use with formalin-fixed, paraffin-embedded tissue: array comparative genomic hybridization correlates with loss of heterozygosity and fluorescence in situ hybridization.
TLDR
The 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.
Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays.
TLDR
It is shown that the Mapping 500K arrays can be used with FFPE-derived samples to produce genotype, copy number, and LOH predictions, and guidelines and suggestions are provided for application of these samples to this integrated system.
Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of affymetrix single-nucleotide-polymorphism genotyping microarrays.
TLDR
A simple but highly sensitive method for genomewide detection of allelic composition, based on the Affymetrix single-nucleotide-polymorphism genotyping microarray platform, without dependence on the availability of constitutive DNA, is described and should substantially improve the ability to dissect the complexity of cancer genomes.
Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array
TLDR
Data show that it is feasible to utilize high-density SNP arrays to generate concordant LOH and CNA profiles at high resolution, and a proof of principle is performed on a panel of deletion and trisomy cell lines with known chromosomal alterations.
Whole genome DNA copy number changes identified by high density oligonucleotide arrays
TLDR
A novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA), to identify genome-wide chromosomal gains and losses at high resolution and can tolerate samples which contain a mixture of both tumour and normal DNA.
High-resolution analysis of DNA copy number using oligonucleotide microarrays.
TLDR
The studies demonstrate that combining the genotype and copy number analyses gives greater insight into the underlying genetic alterations in cancer cells with identification of complex events including loss and reduplication of loci.
A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays.
TLDR
Improvements in signal-to-noise ratios and the use of an optimized reference make CNAG a useful tool for high-resolution detection of copy number alterations which can help in the understanding of the pathogenesis of cancers and other diseases as well as in exploring the complexities of the human genome.
Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer.
TLDR
The results indicate that array-based CGH is capable of diagnosing the vast majority of renal cell carcinomas based on their genetic profiles, and may help to differentiate relevant subsets of tumors, biologically and clinically.
...
...