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CancerSeq™ Paraffin Tissue Section and Block
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CancerSeq™ Paraffin Tissue Section and Block

Introduction to CancerSeq™ Paraffin Tissue Section and Block

BioChain’s CancerSeq formalin fixed paraffin embedded (FFPE) tissues are tumor tissues that have been prescreened extensively for single nucleotide polymorphisms (SNPs), insertions & deletions (indels), and copy number variations (CNVs).  Targeted Next Generation Sequencing (NGS), using cancer gene panels, was performed to identify mutations and mutational hotspots.  These tissues are ideal for verification, genotyping, or identification of new mutational hotspots.

The advantage of using real tumor tissues versus genetically engineered tumor cell lines, is that the tissues are far more representative of real clinical disease.   Cancer cell lines or genetically altered cell lines have been used widely for in vitro tumor models, but these possess only a small proportion of the genetic variances seen in tumor tissues.  Actual tumors generally carry multiple mutations instead of just one or two.  Numerous studies have  pointed out the striking genetic differences between cell lines and tumor samples by comparing microarrays, copy number changes, mutations, and mRNA expression profiles 1-5.

Briefly, genomic DNA was extracted from the FFPE tissues and validated by targeted NGS with either Illumina’s TruSeq Amplicon - Cancer Panel (TSACP) or ArcherDX’s VariantPlex Solid Tumor Panel which include 48 or 67 cancer-related genes. Our prescreened tissues come with detailed information regarding donor and cancer type, as well as NGS information such as chromosomal position, variant type (SNP or indel), alternate allele variations, quality score, depth of coverage, allele type, transcript ID and more.  We offer the prescreened tissue as mounted sections or curls.  Please inquire for other options such, as whole block or extracted nucleic acids.

CancerSeq™ : Screened by NGS for SNPs, indels with 48 Cancer Gene Panel

CancerSeq™ Plus: Screened by NGS for CNVs, SNPs, indels with 67 Cancer Gene Panel 

Features

  • Deep sequencing by NGS with high coverage
  • FFPE curls or slides available (inquire for blocks)
  • Documentation of the tissue donor's clinical histories is available
  • Information regarding tumor type is available
  • Complete NGS sequencing data available

Applications

  • Validation of cancer marker mutation related drug candidates
  • Controls or verification for genotyping
  • Companion diagnostic assay development
  • Suitable for both IHC and in-situ hybridization assays
  • Cellular localization of tissue specific mRNA and protein expression
  • Isolation of DNA and RNA with specific mutation profiles

Reference

1.  Ertel, A., Verghese, A., Byers, S. W., Ochs, M. & Tozeren, A. Pathway-specific differences between tumor cell lines and normal and tumor tissue cells. Mol. Cancer 5, 55 (2006).

2.  Stein, W. D., Litman, T., Fojo, T. & Bates, S. E. A Serial Analysis of Gene Expression (SAGE) database analysis of chemosensitivity: comparing solid tumors with cell lines and comparing solid tumors from different tissue origins. Cancer Res. 64, 2805–2816 (2004).

3.  Gillet, J. P. et al. Redefining the relevance of established cancer cell lines to the study of mechanisms of clinical anti-cancer drug resistance. Proc. Natl Acad. Sci. USA 108,18708–18713 (2011).

4.  Sandberg, R. & Ernberg, I. Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI). Proc. Natl Acad. Sci. USA 102, 2052–2057 (2005).

5.  Domcke, Silvia, et al. "Evaluating cell lines as tumour models by comparison of genomic profiles." Nature communications 4 (2013).