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

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.

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

Register for a session now by clicking a date below:

Tue, Apr 22, 2014 5:00 PM – 6:00 PM PDT / 00:00 GMT

Wed, Apr 23, 2014 7:30 AM – 8:30 AM PDT / 14:30 GMT

Wed, Apr 23, 2014 10:00 AM – 11:00 AM PDT / 17:00 GMT

Cancer Genetics Expands BioDiscovery’s Nexus Copy Number Platform to Identify Novel Biomarkers Predictive of Cancer Outcomes

Hawthorne, CA and Rutherford, NJ, April 2, 2014

Cancer Genetics, Inc. (Nasdaq: CGIX) and BioDiscovery, Inc. have announced expansion of the Nexus Copy Number Discovery platform in CGI research to uncover novel biomarkers which are predictive of cancer outcomes.

“Cancer Genetics has been able to leverage the Nexus Copy Number platform’s unique ability to quickly digest large data sets to uncover correlations between genomic events and clinical factors in their discovery efforts,” says Louis J. Culot, Vice President of Business Development and Marketing at BioDiscovery. “Cancer Genetics is an emerging leader in DNA cancer diagnostics. We are excited about the opportunity to play a role in the work being done and the impact that work is having on improving patient outcomes.”

“The Nexus Copy Number product is one of the primary analytic and collaboration tools for CGI’s R&D platform” says Jane Houldsworth, PhD, Vice President of Research and Development at CGI, “allowing our scientists to quickly mine complex data sets for underlying diagnostic and prognostic markers.” CGI expects to utilize the many new features in Nexus Copy Number version 7.5, such as the ability to automatically classify samples with particular genomic aberrations, and plans to take advantage of the NGS support in the updated version. According to CGI, the team at BioDiscovery has been highly responsive to scientists’ needs, accelerating research and development.

BioDiscovery Nexus Copy Number software offers simple yet powerful tools for copy number and sequence variation (CNV) analysis and visualization from microarrays and next generation sequencing (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.

About Cancer Genetics:
Cancer Genetics, Inc. is an emerging leader in DNA-based cancer diagnostics, servicing some of the most prestigious medical institutions in the world. Our tests target cancers that are difficult to diagnose and predict treatment outcomes. These cancers include hematological, urogenital and HPV-associated cancers. We also offer a comprehensive range of non-proprietary oncology-focused tests and laboratory services that provide critical genomic information to healthcare professionals, as well as biopharma and biotech companies. Our state-of-the-art reference lab is focused entirely on maintaining clinical excellence and is both CLIA certified and CAP accredited and has licensure from several states including New York State. We have established strong research collaborations with major cancer centers such as Memorial Sloan-Kettering, The Cleveland Clinic, Mayo Clinic and the National Cancer Institute. For further information, please see www.cancergenetics.com.

About BioDiscovery, Inc.
BioDiscovery is a leader in the development of breakthrough software and services for advanced copy number variation and expression analysis, enabling customers in drug discovery, research, and diagnostics by efficiently managing, integrating, and analyzing data generated using high-throughput microarray and next-generation sequencing technologies.

Cancer Genetics contact information:
Investor Relations
Michael Rice
Life Science Advisors LLC

Media Relations
RedChip Companies, Inc.
Paul Kuntz, 800-733-2447800-733-2447, ext. 105

BioDiscovery Inc. contact information:
Louis Culot




N-of-One and BioDiscovery Partner to Deliver Tumor Genomics Analysis and Interpretation Platform

Partnership Equips Laboratories and Oncologists with a Foundation for Genomic Data Analysis through to Therapeutic Options

HAWTHORNE, CA and LEXINGTON, Mass., March 25, 2014

BioDiscovery, Inc., a leader in DNA structural variant analysis laboratory software for copy number (CNV) and sequence variation, and N-of-One, the leading provider of molecular interpretation and therapeutic strategies for precision medicine in oncology, today announced a partnership to jointly provide integrated genomic analysis interpretation solutions. This partnership will bring together integrated, best-in-class components to enable clinicians to use genomic data generated by laboratories more easily and efficiently to identify targeted therapeutic options appropriate for each specific patient as well as better understand the molecular profile of the patient’s tumor. Financial terms of the agreement are not disclosed.

Under the terms of the agreement, N-of-One and BioDiscovery will jointly market and sell N-of-One’s interpretation solutions and content together with BioDiscovery’s genomic analysis software, providing laboratories and oncologists with an integrated platform from genomic data analysis through to therapeutic decision support.

“The number of genomic variants identified as prognostic indicators, or available as possible therapeutic targets, continues to increase at a very fast rate. BioDiscovery’s solutions excel at helping cytogenetic and molecular laboratories quickly identify likely actionable variants from the thousands present in typical cancer cases, with a particular emphasis on copy number variants (CNVs) that drive a large number of tumor types but remain difficult to interpret”, said Dr. Soheil Shams, CEO, BioDiscovery, Inc. “N-of-One completes the solution by taking this narrowed list and elucidating the possible therapeutic options based on an understanding of these variants in the context of the disease biology.”

“We are committed to our mission of enabling precision medicine for clinicians and researchers by providing outstanding molecular interpretation,” said Chris Cournoyer, CEO, at N-of-One. “Working with BioDiscovery, developer of genomics visualization and analysis software that is already in use at many cancer centers, hospitals, and independent laboratories, we are able to strengthen the point-of-care by adding a wealth of disease-specific knowledge from the latest research findings and drug trials. This gives oncologists and treating clinicians additional
insights into possible therapeutic strategies that are informed by the patient’s disease, genomic profile, available therapies and trials, and current research.”

About BioDiscovery
A leading provider of genomics software for translational research and clinical settings, BioDiscovery makes the Nexus Copy Number and NxClinical software solutions for confident analysis, visualization, and interpretation of copy number and sequence variation from virtually all genomic microarray and NGS platforms. For more information visit www.biodiscovery.com or call 310-414-8100310-414-8100.

About N-of-One
N-of-One, a leader in precision medicine for oncology, leverages its world-class team of experts to translate molecular data specific to each patient into state-of-the-art, clinical insights and therapeutic options focused on the point of care. N-of-One’s team of experts has interpreted more than 6,000 tumors for oncologists and patients worldwide, through partnerships to provide clinical interpretation for leading diagnostic companies (such as Foundation Medicine and Clarient), through agreements with provider networks (such as Fox Chase Cancer Center in Philadelphia), directly to oncologists and through employee access benefit programs (such as Life Technologies). N-of-One does not provide medical advice or promote any product or service. For more information, please visit www.n-of-one.com or call 617-202-9808617-202-9808.

Media Contacts
Louis Culot

Kathryn Morris
The Yates Network

March 25-29
ACMG Annual Clinical Genetics Meeting

NxC2014MarNashville, TN

Come to the unveiling of our new platform for clinical labs!

Join us for a preview 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.

Friday, March 28, 2014, 12:30 pm – 1:00 pm
Exhibit Theater 2
NxClinical – Speeding End-to-End Cytogenetics Case Review and Reporting
>> Register Now

A special early access program will be made available at ACMG to select laboratories interested in exploring this new technology. Visit us at Booth #813 or attend our exhibit theater presentation to learn more.

Also, check out our poster (#376), “Identification of a multi-exon hemizygous NRXN1 deletion in a complex phenotype”

Schedule an appointment to speak with a BioDiscovery representative at the meeting.
ACMG 2014 Meeting website

Poster #376, Friday, March 28, 2014, 10:30 am – 12:00 am

Identification of a multi-exon hemizygous NRXN1 deletion in a complex phenotype
Andrea O’Hara, Louis Culot, Raja Keshavan, Soheil Shams

In a clinical cytogenetics lab, constitutional samples vary widely in phenotypic presentation. However, the end goal remains the same: to identify potential pathogenic copy number variants in an individual sample with speed and accuracy. In addition to public reference databases, the historical laboratory sample base can be used as an important new reference point for later individual profiles. Here we will present a streamlined analysis of an array copy number profile for individual case review using a user-defined workflow in BioDiscovery’s NxClinical software system. A proband presenting with a complex phenotype, including mild dysmorphia, severe language disorder, mild intellectual disability, attention deficit hyperactivity disorder (ADHD), and a mood disorder was evaluated for potential pathogenic copy number alterations. The sample was processed on the Affymetrix SNP 6.0 array platform, followed by segmentation and event calling using the SNP-FASST2 algorithm. Using the intelligent decision support tool, we were able to automatically filter out known areas of normal copy number variation and identify potential pathogenic regions of interest. This process reduced the number of events for manual review from over 80 to less than 35. Using the enterprise database for quick reference to historical sample sets, we narrowed down the unique copy number alterations to a potential pathogenic hemizygous deletion of NRXN1. Quick reference of public databases (ISCA and ClinVar) within the workflow confirmed this as a pathogenic change which can be ultimately reported in the final report for the clinician.

ACMG 2014 Exhibit Theater Presentation Registration

  • This field is for validation purposes and should be left unchanged.

March 13-14
Translational Genomics in BioMedicine

Barcelona, Spain

Schedule an appointment to speak with a BioDiscovery representative at the meeting.
Meeting website

Stop by and view this poster at the meeting:

Maximizing the value of detected somatic changes across 12,000 TCGA tumor samples
Soheil Shams

The Cancer Genome Atlas (TCGA) is an amazing resource, with almost 12,000 tumors across more than thirty different cancer types. The TCGA project has already proven useful in large-scale studies1, 2, 3, 4 for which the primary goal for copy number analysis was to identify statistically significant recurrent copy number alternation events. In these cases the GISTIC5 algorithm was used to generate the results which is appropriate for population studies, but is not sensitive to the accuracy of calls made on each individual sample. Therefore, the publically available data, when viewed on a per sample bases, is highly over-segmented and has not been baseline corrected for the tumor ploidy. We believe this reduces the utility of this resource and have undertaken an effort to use a combination of analytical tools as well as human curation to generate a high quality database of TCGA copy number data that can be used for various types of down-stream analyses.

Using the raw (level 1) data, and using the matched “normal” samples to minimize the number of CNPs, we applied the SNP-FASST2 calling algorithm (a multi-state HMM algorithm designed to handle mosaic events), with systematic correction to correct for GC and fragment length biases. The settings were optimized per cancer type to generate accurate calls for events from samples with as low as 20% tumor burden. We applied automated ploidy and %tumor calling methods, such as ASCAT6, but found that in many cases the algorithm did not generate a solution or reported inaccurate solutions. Therefore, we opted to perform manual baseline adjustment for majority-aneuploid samples and found the resultant data were more consistent with the control sets in terms of median number of copy number events, median CNV length, and sample ploidy. The median number and variance of CNVs was substantially reduced to be in line with the control data sets. The number of samples with incorrect initial ploidy assignments ranged from 15% to more than 50%, depending on the tumor type. The resultant CNV database, along with associated clinical annotations and SNVs from exome sequencing, is now available through the Nexus DB repository to the general scientific community and should provide greater utility for further research.


  1. Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008)
  2. Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011)
  3. Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519-525 (2012)
  4. Genome Atlas Research Network. Comprehensive molecular portraits of human breast tumors. Nature 490, 61-70 (2012)
  5. Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl Acad. Sci. USA 104, 20007–20012 (2007)
  6. Van Loo, P. et. al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910-16915 (2010)


Webinar: Feb. 25 – 26
Exploring gene regulation analysis with Nexus Expression (RNA-Seq and Microarray)

Nexus Expression allows researchers to quickly analyze and explore data with confidence and to easily identify differentially expressed genes, affected pathways, and common phenotypes between gene expression profiles, whether the source data is microarray or RNA-Seq data. Ease of statistical comparisons between subgroups, clustering, gene enrichment analysis and integration with copy number changes will be some of the features covered in this presentation. Cancer-specific tools in Nexus Expression include Cox-regression analysis to identify genes predictive of survival and generation of K-M plots. This presentation will take you through the process from data loading and processing to identification of affected pathways using a solid tumor data set.

Please provide us with your information to continue to webinar video.
  • After submission, please wait for the webinar video to load. Because of the length of some webinars it may take several seconds until the video is visible.
  • This field is for validation purposes and should be left unchanged.

Nexus Copy Number 7.5 New Features webinar

This webinar highlights key features and enhancements of soon-to-be released BioDiscovery Nexus version 7.5. Expanded support for sequence variant data, including functional annotations, filtering, and visualization, coming from NGS or other platforms is a major new feature in version 7.5.  Additionally support for loading and processing of BAM files to extracts copy number results from sequencing data has been added. In particular, ngCGH algorithm has been added to support exome sequencing data. And there are more options for seq. variant display (gene/region-based frequency plots and user-defined symbol and color representation of seq. variant events).

Several enhancements have been done to further simplify the case review process. These include additional controls in the sample review window as well as multi-track visualization of events in previous cases overlapping a region of interest in the case under review. The visualization shows events, previous classification (e.g. benign, pathogenic, etc.), notes, as well as details about previous case and the probe distribution visualization. Event filtering has been expanded to include those for removing parental calls from trio cases to display only de novo calls in proband and those for display of events falling in specified regions (complementary to existing filters masking regions).

In addition to BAM files, support for new data types includes that for Affymetrix OSCHP data (from the new OncoScan V3 platform) with a choice of using the Affymetrix TuScan algorithm or BioDiscovery’s SNP-FASST algorithm for segmentation and option to display SNP probes plot as allele peaks or BAF.

View Webinar Video

Please provide us with your information to continue to webinar video.
  • After submission, please wait for the webinar video to load. Because of the length of some webinars it may take several seconds until the video is visible.
  • This field is for validation purposes and should be left unchanged.