Enabling Deep Sequencing
Blog Apr 28, 2014
Integrated DNA Technologies (IDT) recently extended its portfolio of NGS panels with the addition of the xGen® Inherited Disease Panel and the xGen Pan-Cancer Panel. These new products join the xGen AML Panel which was launched at the end of last year.
To understand more about the latest additions to the IDT product line we spoke to Ibrahim Jivanjee, NGS Product Manager at IDT.
AB: Can you tell me a little more about the xGen Inherited Disease Panel and the xGen Pan-Cancer Panel?
Ibrahim Jivanjee (IJ): The xGen® Inherited Diseases and Pan-Cancer Panels are pools of biotin-modified oligos that are used for targeted next generation sequencing. These oligos, which are sold as xGen Lockdown Probes, are typically 120 nucleotides long, and they are designed to bind to the DNA fragments which make up the genes that are of interest to researchers. The Inherited Diseases Panel comprises more than 100,000 xGen Lockdown Probes that target 4503 genes and 180 SNPs associated with inherited diseases. The Pan-Cancer Panel targets 127 genes implicated in 12 tumor types. These panels enable deeper coverage during sequencing, providing greater sensitivity for clinical applications.
AB: How do they complement the current IDT product line?
IJ: The two new panels solve unique problems. In CLIA labs, exome sequencing is used to obtain a broad snapshot of disease causing mutations. However, the drawback of this method is that most of the genes in the exome are not relevant for diagnosis or treatment of disease, which results in wasted data (increased cost, but decreased effectiveness). The Inherited Diseases Panel balances the benefits of exome sequencing with the cost effectiveness of custom panel sequencing. The Pan-Cancer Panel serves a slightly different purpose. At IDT, every probe is individually synthesized and assessed for QC, making it really easy for researchers to add more probes to an existing panel. We see the current Pan-Cancer Panel as a starting point for developing a comprehensive, tumor specific panel because researchers can customize it by adding probes to target genes of relevance to the specific cancer under investigation.
AB: The xGen Inherited Disease Panel was designed in collaboration with Emory Genetics, how did this partnership enable development?
IJ: IDT scientists designed the probes and protocols for this panel. However, we relied on the Emory Genetics Lab’s expertise in clinical sequencing to provide us with a curated list of genes. Emory Genetics’ scientists also provided IDT with feedback on functional performance.
AB. The development of the xGen Pan-Cancer Panel was based on the findings of The Cancer Genome Atlas (TCGA) network, what role did TCGA play in this development?
IJ: The genes were identified from publications by the TCGA. We also work with key members from the TCGA network to validate our panels. For example, our first TCGA-based panel targeting acute myeloid leukemia has been used extensively by the Genome Institute at Washington University, which is a member of the TCGA network.
AB: IDT launched its first NGS Panel, the xGen AML Panel, in October 2013. How has this been received, did this reception act as a driver for adding further products to the range?
IJ: We have received excellent feedback from researchers in industry and academia. We are excited about Washington University’s adoption of the panel for AML characterization and monitoring of disease progression in patients. The Washington University scientists presented this data in a poster at the 15th Annual AGBT (Advances in Genome Biology and Technology) Meeting in February 2014.