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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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: 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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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: 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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Webinar: Give your data a boost with Nexus Express for OncoScan

Description
Nexus Express for OncoScan is a powerful tool for analysis of OncoScan data and is provided by Affymetrix with each FFPE Assay Kit. See how you can take advantage of Nexus Express for OncoScan, to which you have free access, and learn how to analyze your data from start to finish. We will show how to load, process, and analyze your OncoScan data with ease. Topics to be covered include

  • Loading and processing data
  • Adjusting call settings
  • Re-centering to adjust baseline ploidy
  • Identifying mosaicism
  • Reviewing results
  • Querying Nexus DB

We will also briefly cover how you can get more out of your data by integrating TCGA Premier (re-analyzed and manually curated TCGA data) and using additional features available in Nexus Copy Number for Affymetrix (e.g. incorporating data from other  Affymetrix platforms such as CytoScan, , adding mutation data from NGS platforms, and using the GISTIC and ASCAT algorithms).

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

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BioDiscovery Launches NxClinical™ for Complete Case Review and Reporting for Genetics Labs

Hawthorne, CA October 20, 2014

BioDiscovery, Inc., a leader in integrated software solutions for genomics data analysis for life sciences, announced today the launch of its new NxClinical software for clinical case review. Based on the company’s extensive experience in the market with its long-standing and highly regarded Nexus Copy Number software, NxClinical was created specifically for the needs of the clinical users. NxClinical is a groundbreaking and unique solution for case review and reporting handling every aspect of the process, from raw data to reports in a single enterprise-wide database system. The system was designed with a focus on improving efficiency and quality of the case review process through incorporation of multi-user collaborative communication, extensive audit-trail features, and automation of standard processes.

“We have been working closely with our Nexus Copy Number software customers for many years as they used the software as part of their workflow. We designed NxClinical based on their experience with the software and with the goal of improving the speed and quality of the results,” said Dr. Soheil Shams, CEO, BioDiscovery Inc. “Based on the results of our early access program over the summer, we have achieved our goal with many success stories and lots of excitement about this new product. We believe that the software will have a high impact on the ability of all of our customers to become even more productive.”

“Our high throughput microarray laboratory has been looking for a solution that would allow us to efficiently process and interpret microarray results with confidence, thereby reducing turnaround time and enhancing service delivery,” said Dr. Elena Kolomietz, Co-Head, Division of Diagnostic Medical Genetics, Mount Sinai Hospital. “After evaluation during the Early Access Program, we found that NxClinical meets these requirements. The multi-user aspect and full customization of the system allows us to easily implement and enforce our SOPs.”

At the center of a speedier review process is a decision support system utilizing customer specified rules for pre-classification of events, based on any number of combination of sample and event attributes. The rules engine automatically applies the given logic after raw data has been processed to detect copy number and allelic events. The user is then presented with all events already pre-classified waiting for review. Additional features that increase efficiency include centralized storage for easy access by multiple reviewers from any location and the ability to query all cases which are stored automatically, creating a historical sample database rich in information. The system allows enforcement of lab SOPs with assigned user roles and privileges for appropriate user access, extensive audit trail capabilities for potential regulatory demand, and serves all sizes and types of labs with local or cloud-based deployment.

About BioDiscovery, Inc.

BioDiscovery, Inc. is dedicated to the development of state-of-the-art software products for life science research as well as clinical applications. The company’s mission is to enable scientists to eliminate disease and suffering through novel application of computational technologies and translating these findings directly and rapidly to clinical use.

From its inception in 1997, BioDiscovery has been an innovative leader in the genomics field having introduced the first dedicated commercial software tool for analyzing microarray images. Since then, innovation has continued to be a top priority. BioDiscovery’s passion to make a difference has further extended the company’s reach into creating the most comprehensive enterprise-wide system for clinical applications enabling research findings to make direct impact on patient care. For more information, visit http://www.biodiscovery.com.

Media Contact:
Shalini Verma
MarCom Manager
+1 310-414-8100
MarCom[at]biodiscovery[dot]com

Webinar: NxClinical – A complete solution for efficient case review and reporting

Description
NxClinical was conceived with the primary goal of enabling clinical labs to efficiently go from raw data to high-quality reports with high confidence. The system was designed based on many years of experience with our leading Nexus Copy Number software product used across the globe by clinical labs. Our goal was to eliminate unnecessary and error prone manual operations (such as cutting and pasting of regions from one software package to another) to create one completely integrated solution allowing efficient processing from raw data to interpretation of results.

NxClinical improves turnaround time and efficiency in the case review process with ease of sharing among multiple users across many locations, automation of standard processes, and full customization allowing each lab to implement their own unique workflows and SOPs. An intricate decision support system allows pre-classification of copy number or allelic events based on customer designed rules and speeds up the review process. Automatic storing of prior cases provides a rich resource for querying new cases against historical cases and integrated external knowledge bases allow for immediate comparisons for further validation. With audit trail capabilities for potential regulatory demand, on-site deployment meeting institutional policies on secure storage or cloud-based deployment, and user privileges with varying roles, NxClinical is a comprehensive solution for genetics labs of all sizes.

Audience
This webinar is geared towards those performing clinical case review.

Webinar dates/times

Tue, Oct 28, 5:00 PM – 6:00 PM PDT
Wed, Oct 29, 7:30 AM – 8:30 AM PDT
Thu, Oct 30, 10:00 AM – 11:00 AM PDT

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