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

  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},
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
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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.


Whole genome SNP arrays using DNA derived from formalin‐fixed, paraffin‐embedded ovarian tumor tissue
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.
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.
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.
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.
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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
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.
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.
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.
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.