Webinar: Cancer Cytogenetics – Affymetrix CytoScan HD Arrays Analyzed with Nexus Copy Number for Affymetrix

Due to disease complexity, interpreting array data for cancer samples remains challenging. Nexus Copy Number software is the leading solution for CNV analysis, and has special tools to aid in the analysis and interpretation of complex cancer samples. The Affymetrix CytoScan HD array platform can be used for many different types of clinical conditions, including hematological cancers, and a recently launched product, Nexus Copy Number for Affymetrix, has been tailored for Affymetrix genomic platforms. Nexus Copy Number for Affymetrix provides rapid identification of copy number changes, identification of LOH events, detection of low-level mosaic events, and assessment of sample heterogeneity. Additional tools for matched paired analysis for matched tumor-normal samples simplify sample review. The software dynamically builds a comprehensive project database of all prior samples, including their raw probe-level data, and ability to query previous cases or public data (at the aberration level) in seconds. The presentation will provide a live analysis of some cancer samples analyzed on CytoScan HD arrays.

Audience
This webinar is geared towards those using or planning on using CytoScan HD arrays in cancer applications.

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Genomic studies of neurodevelopmental disorders: the move from arrays to sequencing

Presenter: Dr. Alistair Pagnamenta, Wellcome Trust Centre for Human Genetics, University of Oxford

Molecular diagnosis of intellectual disability disorders has typically consisted of sequential testing of candidate genes known to be associated with disease phenotypes but cannot always detect the causative mechanism. A better approach involves use of sequencing for greater diagnostic yield. Here we will examine a few different cases of early-onset epilepsy and hyperphosphatasia with intellectual disability (Mabry syndrome), an autosomal recessive form of ID, where different strategies were used to ascertain the molecular basis of the disorders. For hyperphosphatasia with ID, autozygosity mapping and exome sequencing was used for some cases and a targeted sequencing approach in other cases, with both methods leading to convergent findings – mutations in PGAP3. In an Ohtahara Syndrome case, use of WGS revealed paternal isodisomy of Chr9 leading to homozygosity of a missense mutation as the causative agent. We were able to identify novel genes for ID disorders using WGS in concert with traditional arrays and have demonstrated that WGS can provide comprehensive and rapid molecular diagnosis for patients with complex genetic diseases.

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Webinar: TCGA Premier – Curated CNVs for improved, efficient, and more accurate analysis

The TCGA is an amazing resource with copy number and sequence variant information along with annotations for over 10,000 tumor samples across various cancer types. The processed data (referred to as “Level 3”) is freely available via the TCGA data portal and has already been quite useful in large-scale studies, but has a lot more potential. By manually reviewing and curating this data set, we have dramatically improved the quality and usefulness of CNV information.

What you’ll learn

  • How TCGA copy number data can be improved through manually curating samples.
  • Biomarker results on a per-sample and population-wide basis for a selected cancer type.
  • How to access the data, and easily query and analyze data sets.
  • How to make use of this data in the context of other, non-TCGA datasets.

Audience
This webinar is geared towards those working with cancer samples and requiring easily accessible, robust copy number and sequence variant data.

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May 31 – Jun 3
European Society of Human Genetics (ESHG)

Milan, Italy

NxClinical – A Revolutionary New Solution for Clinical Labs! NxC2014Mar

Come get a personal demonstration of a revolutionary platform, built on Nexus, the standard for oncology and constitutional research and case analysis. A dynamic genomic browser, integrated public data and lab cases for confident interpretation, and intelligent decision support tools streamline the entire review process from instrument to final clinical report generation.

Booth #346

Schedule an appointment to get a personal demo of this system at ESHG.
ESHG 2014 Meeting website

Webinar: BioDiscovery’s Nexus Copy Number software for CNV analysis from Affymetrix Axiom arrays

Description
Affymetrix Axiom arrays are typically used for large-scale genotyping studies but the same arrays can yield even further information. The SNP probes on the arrays can be used to calculate log2 ratios and BAF frequencies allowing researchers to uncover copy number variants from the same data. Many studies benefit from investigating both copy number and SNPs and the ability to garner both types of information from the same platform is extremely efficient and cost effective. Recently Affymetrix has designed tools to harness copy number data from Axiom arrays which can subsequently be loaded into BioDiscovery’s Nexus Copy Number software. Nexus Copy Number is a leading CNV analysis and visualization software used at hundreds of institutions worldwide. Its intuitive user interface with an interactive genome browser allows facility in visualization of CNV data and numerous statistical analysis tools allow for advanced research analysis. The presentation will give an overview of the Axiom and Nexus Copy Number platforms with a live demo of CNV analysis from the Axiom array data.

Audience
This webinar is geared towards researchers using or planning on using Affymetrix Axiom arrays and are interested in obtaining copy number data.

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BioDiscovery awarded National Institutes of Health SBIR Grant to Improve TCGA Copy Number Profiles

Hawthorne, CA July 8, 2014

BioDiscovery, Inc., maker of Nexus Copy Number software, announced today the award of a Small Business Innovation Research (SBIR) Phase I grant from the National Institute of Health to improve the copy number variation (CNV) data from The Cancer Genome Atlas (TCGA), and has selected Huntsman Cancer Institute (HCI) at the University of Utah to assist in developing and validating the new product. The commercial release of the improved TCGA copy number and sequence variant data will let researchers make further discoveries into tumorigenesis and disease progression and provide a meaningful validation set for internal studies.

“Our techniques for analyzing CNVs from raw data is unique and has proven highly effective, being used and cited in hundreds of publications.” says Soheil Shams, Ph.D., BioDiscovery’s Chief Scientific Officer. “We are applying methods, algorithms, and best practices learned from our experiences in clinical pathology settings to TCGA data. It’s a painstaking process, but the result will be the highest-fidelity CNV data from TCGA, and will integrate with our analysis platform to let researches quickly access and interrogate this database.”

“Copy number aberrations have been established as important drivers of many types of cancer, and as distinct from tumor classes driven primarily by somatic mutations,” says Louis Culot, Vice President of Marketing and Business Development at BioDiscovery. “The NIH has recognized this, along with BioDiscovery’s unique expertise in CNV data analysis in the issue of this award. We are pleased to begin this work and expect it to have significant impact on further understanding of cancer genetics.”

Joshua Schiffman, M.D., medical director of the High Risk Pediatric Cancer Clinic at Huntsman Cancer Institute (HCI) and associate professor of pediatrics at the University of Utah will be the lead investigator on the HCI arm of the project.

“The TCGA project, funded by NIH, has amazing potential but has proven challenging to unlock due to the processing of CNV information and difficulty in data access and analysis,” says Schiffman. “At HCI, we will work with the BioDiscovery team to help test and validate their approach to improved interaction with TCGA data sets.  Results from these efforts will further our understanding of many types of cancer and hopefully lead to improved clinical care for patients.”  As part of the SBIR grant, Schiffman will work with BioDiscovery to demonstrate the clinical utility and translational impact of the TCGA data.

About BioDiscovery

BioDiscovery produces software and databases for genomic analysis, including its flagship Nexus Copy Number software. The Company offers simple yet powerful tools for CNV and sequence variation analysis and visualization from microarrays and next generation sequencing platforms (NGS), for analysis of complex data such as solid tumor samples and complex constitutional disease.  The scientist-driven software embeds powerful statistical tools designed specifically for the end-user, allowing rapid detection of chromosomal aberrations and identification of affected pathways. For more information about BioDiscovery, please visit www.biodiscovery.com.

Media Contact: Louis J. Culot
Vice President, Business Development and Marketing
+1 617-233-4921
lculot[at]biodiscovery[dot]com