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Dx Focus Jan 20, 2011: Clinical and Regulatory PCR and Nucleic Acid Testing News


ARUP Laboratories this week announced the availability of a laboratory-developed test designed to classify breast cancer into clinically significant molecular subtypes that are important for managing the disease.

The new test, called the PAM50 Breast Cancer Intrinsic Classifier, is an RT-qPCR assay that measures the expression of 50 classifier genes and five control genes to identify the intrinsic subtypes known as luminal A, luminal B, HER2-enriched, and basal-like. The test also provides quantitative values for proliferation, luminal gene expression, ESR1, PGR, and ERBB2.

The test is performed by first extracting RNA from formalin-fixed, paraffin-embedded tissue and converting it to cDNA using both random and gene-specific primers. RT-qPCR is then performed on the 55 genes simultaneously in a plate pre-manufactured at ARUP to determine RNA expression levels. Subtype predictions are done using a previously reported centroid-based algorithm, ARUP said.

The development of the PAM50 signature was the result of a decade of work from investigators at the University of Utah, University of North Carolina at Chapel Hill, University of British Columbia, and Washington University School of Medicine.

Virtual company Bioclassifier owns the commercial rights to the PAM50 signature, and in December, it said that ARUP would be launching a laboratory-developed test on the signature this month; and that Seattle's Nanostring had licensed the signature to commercialize a test on its nCounter multiplex gene expression platform (PCR Insider, 12/9/2010).

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.