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Bio-Rad Diabetes Division

Two New NGS Panels to Improve Inherited Disease and Cancer Diagnostics

By Labmedica International staff writers
Posted on 15 Jul 2014
Image: The design of xGen Lockdown Panels is typically based on 1X tiling of xGen Lockdown Probes. Probes are tiled end-to-end and each base in the region of interest will be covered at least once (Photo courtesy of Integrated DNA Technologies).
Image: The design of xGen Lockdown Panels is typically based on 1X tiling of xGen Lockdown Probes. Probes are tiled end-to-end and each base in the region of interest will be covered at least once (Photo courtesy of Integrated DNA Technologies).
Specially developed next generation sequencing (NGS) panels for inherited diseases and cancer have been designed to enhance convenience, efficiency, and effectiveness in diagnosis and screening.

Integrated DNA Technologies (IDT; Coralville, IA, USA) is extending its portfolio of NGS panels with the addition of the xGen Inherited Diseases Panel and the Pan-Cancer Panel. Joining the xGen Acute Myeloid Leukemia (AML) Cancer Panel, IDT now offers multiple panels for deep sequencing.

The xGen Inherited Diseases panel, designed in collaboration with Emory Genetics Laboratory, was created to combine the ease of whole exome sequencing with the low cost of panels. Emory leveraged IDT “Lockdown Probes” to create a library targeting all exons in HGMD (human gene mutation database) listed genes. The creation of this library simplifies workflow and lowers costs, while facilitating rapid sequencing and providing the high coverage levels needed for clinical diagnostic NGS application - one library, many tests.

The xGen Pan-Cancer Panel has been developed based on the findings of TCGA (The Cancer Genome Atlas) network. NGS has enabled the discovery and characterization of gene-specific mutations that have the potential to be tumorogenic, but it also implicates irrelevant genes. A shortlist of significant genes that have been deemed relevant across numerous cancer types, which can be expanded through the inclusion of additional tumor-specific genes, would be extremely valuable to both clinical and research applications. TGCA network has identified 127 significantly mutated genes across 12 tumor types. The Pan-Cancer Panel has been designed to target coding regions in all 127 genes.

Target enrichment enables users to focus their sequencing efforts on specific regions of the genome, providing a cost-effective and reliable alternative to whole genome sequencing, making NGS more accessible. Ibrahim Jivanjee, product manager for NGS at IDT, said, “Having launched our xGen AML Panel last October, we have invested a significant amount of time and resource into the further development of our NGS capabilities. As a rapidly advancing area, next gen sequencing is key to the development of personalized medicine, and these two new panels will aid us in supporting the developing advancements in human health and clinical research.”

All three IDT NGS Panels use xGen Lockdown Probes—120mer oligonucleotides with a 5’ biotin modification. Synthesized individually using the IDT Ultramer synthesis platform, Lockdown Probes incorporate the highest coupling rate currently available, 99.6%, to provide high quality, long oligos. The quality of each capture probe is assessed using electrospray ionization mass spectrometry and even probes with a high GC content can be synthesized.

Related Links:

Integrated DNA Technologies 
xGen Panels




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