Introduction: Gene amplification/deletion is a common tactic employed by tumor cells to proliferate uncontrollably. Multiple methods have been developed to determine gene copy numbers, such as FISH, qPCR, and, more recently, Next Generation Sequencing (NGS). However, these methods have limitations: FISH and NGS are very labor intensive; and FISH and qPCR can detect only a limited number of targets. Therefore, it is imperative to develop methods that are more user-friendly and have increased multiplexing capabilities to detect copy number variations (CNV). Using a novel digital barcode technology, NanoString Technologies (Seattle, WA) has developed the nCounter® technology to meet these needs. This new technology will be especially valuable after the recent FDA approval of the ProsignaTM assay, a breast cancer gene signature assay for subtype classification to help guide treatment decisions. In the BioPharma group at Genoptix, Inc., Carlsbad, CA, we have started to assess the nCounter technology for copy number determinations in a CLIA laboratory setting.

Methods: A cancer gene CNV panel composed of 55 genes was custom designed and evaluated. The CNV results of a subset of genes generated from our gene panel using the nCounter technology were compared with the results generated from qPCR, digital droplet PCR (ddPCR), FISH, publications, and NGS. Furthermore, assay robustness was tested by using different amounts and quality of input FFPE DNA. An initial comparison on the CNVs obtained from genomic DNA digested by Alu1 enzyme or sonicated by Bioruptor® Pico (Diagenode Inc, Denville, NJ). Finally, the effects of different DNA isolation methods on copy number determinations were also evaluated.

Results: Overall, the copy numbers generated using nCounter technology were concordant with results from the abovementioned methods as analyzed by comparing selected genes with known CNVs. A wide range of FFPE DNA input (200ng-4ug) could be tolerated by the assay. Based on a limited number of samples, DNA isolation methods, such as Qiagen, Promega Maxwell® CSC, or Roche Cobas®, have minimal effect on copy numbers.

Conclusions: With the short hands-on time, relative high level of automation, and no amplification requirements, nCounter technology is able to generate CNVs in good agreement with other established CNV methods. This new 55 cancer gene CNV assay may be useful in clinical trials to assist in patient stratification and care.

Citation Format: Tingdong Tang, Wenge Shi, Loretta Hipolito, Julie Mayer, Jelveh Lameh, Shabnam Tangri, Reinhold Pollner. Development of a nanostring copy number assay for a customized 55 gene panel using challenging formalin-fixed paraffin-embedded (ffpe) tumor samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3734. doi:10.1158/1538-7445.AM2014-3734