Correction of Recent Note on the "Tissue of Origin" of Malignant Lesions

In a recent note on identifying the "tissue of origin" of malignant lesions based on new technology from Pathwork Diagnostics (see: "Tissue of Origin" Genomic Test Receives FDA Approval), I received the following comment from Glenda G. Anderson:

As founder of Pathwork and its technology, it is very encouraging to hear that you have found the raw agreement indices to be "important descriptive statistics with unique common-sense value". We worked particularly hard on this aspect of the product with a hope to accomplish just that. You likely share my belief that result reporting is an oft overlooked, but critically important element of good clinical diagnostic product design. Wanted to offer one correction. The test uses a high density oligonucleotide microarray (in fact, a GeneChip), not a tissue microarray. A test of this sort requires the high level of platform reproducibility available only from the former.

The press release that my original note was based on referred to the underlying technology of the test as a "microarray" and I jumped to the incorrect conclusion that this meant a "tissue microarray" rather than, as Glenda now indicates, a high density oligonucleotide microarray (i.e., a GeneChip).

Here is a definition for a DNA microarray from the Wikipedia:

A DNA microarray is a high-throughput technology used in molecular biology and in medicine. It consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles of a specific DNA sequence. This can be a short section of a gene or other DNA element that are used as probes to hybridize a cDNA or cRNA sample (called target) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by fluorescence-based detection of fluorophore-labeled targets to determine relative abundance of nucleic acid sequences in the target. In standard microarrays, the probes are attached to a solid surface by a covalent bond to a chemical matrix....The solid surface can be glass or a silicon chip, in which case they are commonly known as gene chip or colloquially Affy chip when an Affymetrix chip is used....DNA microarrays can be used to measure changes in expression levels or to detect single nucleotide polymorphisms (SNPs)....

Here are more details about the test from the company (see: Pathwork Diagnostics’ Core Technology):

The Pathwork Tissue of Origin Test is currently available through Pathwork Diagnostics Laboratory and an FDA-cleared kit version of the test will be available to clinical laboratories. For the test, frozen tissue biopsy specimens are processed on the company’s custom Pathchip microarray. Test processing includes RNA extraction, amplification, hybridization and scanning. The data is analyzed using the Pathwork Tissue of Origin Test’s proprietary analytics, and test results reports are provided to both the oncologist and pathologist. Pathwork Diagnostics’ microarray tests run on the proven, commercially available Affymetrix GeneChip  System. A version of the test for formalin-fixed, paraffin-embedded (FFPE) tumor specimens and needle biopsy specimens, including core and fine needle aspiration (FNA), will be available through Pathwork’s CLIA laboratory later this year.

Note the exciting news that the test will soon be available for formalin-fixed, paraffin-embedded (FFPE) tumors as well as FNA specimens.