BioDiscovery Releases ImaGene 9.0 for Array Image Quantification and Visualization

El Segundo, CA – BioDiscovery Inc., the leading developer of integrated software solutions for high-throughput technologies announced today the release of ImaGene 9.0 for microarray image analysis. The new features include improved memory performance for the latest high density arrays, streamlined processing pipeline focused on image quantification and intensity extraction, and new modular design with options to add modules for analysis of gene/miRNA expression or CGH data.

Continuing in its tradition of providing a versatile and robust image quantification software, ImaGene 9.0 further strengthens its core function of image analysis and replaces its GeneSight-Lite analysis feature with optional external modules for downstream analysis. “We have revamped the design of version 9.0 to bring to the forefront its principal function of spot quantification by removing internal downstream analysis tools.” said Dr. Soheil Shams, President of BioDiscovery. “Instead, a new modular design allows more choices and flexibility in providing an option to add modules for gene regulation analysis as well as CGH analysis. These modules are versions of BioDiscovery’s popular Nexus family of products. The gene regulation analysis module is Nexus Expression-Lite designed for analysis of a small number of samples (24). Nexus Solo, based on Nexus Copy Number, provides an easy to use interface and integration with external databases for single sample analysis of CNVs from CGH arrays. We feel this new design with a strong core for image quantification and additional optional downstream analysis modules provides a complete and highly efficient package for array image and data analysis.”

ImaGene is recognized by industry experts as the most complete with highest quality results and the easiest to use microarray analysis package available.  With single click automation, integrated advanced quality control parameters, numerous patented segmentation and contamination removal algorithms, and hundreds of active customers worldwide, ImaGene remains the leader in microarray image analysis.  ImaGene is available for OS X, Linux and Windows operating systems.

About BioDiscovery
BioDiscovery is a leader in the development of microarray advanced bioinformatics software and services that enable its customers to revolutionize drug discovery and diagnostics by efficiently managing, integrating, and analyzing data generated using high-throughput microarray technology. Contact BioDiscovery: 310-414-8100 or www.biodiscovery.com

BioDiscovery and Exiqon Sign OEM Agreement to Provide Complete microRNA Analysis Solution

EL SEGUNDO, CA, AND COPENHAGEN, DK, May 5, 2010 – BioDiscovery, Inc. a leader in integrated software solutions for microarray-based research, and Exiqon A/S, a leader in microRNA analysis products and services, announced today an OEM Agreement incorporating BioDiscovery’s array analysis and visualization software with Exiqon’s arrays. The agreement allows Exiqon to package BioDiscovery’s array image analysis and data analysis and visualization software with Exiqon’s microRNA arrays for a complete solution offering.

“The partnership between BioDiscovery and Exiqon provides a complete well integrated solution for microRNA array studies, going from array experiment with Exiqon’s miRCURY LNA™ microRNA Arrays to final results with data analysis and visualization from BioDiscovery software.” said Soheil Shams, President of BioDiscovery. “Now, regardless of the scanning equipment the customer is using, our ImaGene software will allow efficient and accurate quantification of the signals and our Nexus Expression for ImaGene software will provide pre-processing and statistical analysis to identify differentially expressed microRNAs and perform clustering analysis.”

“The integration of ImaGene 9 and Nexus Expression 2 with the miRCURY LNATM microRNA Arrays from Exiqon results in the most optimized and simplified workflow available today.” said Henrik M. Pfundheller, VP Sales & Marketing of Exiqon. “We can now provide researchers with the best performing microRNA arrays on the market together with all other needed reagents, kits and software analysis tools enabling researchers to get from RNA extraction, labeling of samples, array hybridization, and further on to data analysis and bioinformatics in an easy, fast and accurate way. As we also offer solutions for downstream validation of array results including our LNA™ Universal RT microRNA PCR product, customers can get a complete package for their microRNA research at Exiqon. ”

BioDiscovery’s software is platform independent and available for Mac OS X, Linux and Windows operating systems. ImaGene is recognized by industry experts as the most complete solution for array image analysis with the highest quality results and the easiest to use microarray analysis user interface. With single click automation, integrated advanced quality control parameters, numerous patented segmentation and contamination removal algorithms, and hundreds of active customers worldwide, ImaGene remains the leader in microarray image analysis. Nexus Expression for ImaGene is a complete analysis package allowing up to 24 samples to be simultaneously analyzed and visualized to identify differentially regulated probes, cluster samples and probes and identify common biological themes through gene set enrichment. With an intuitive interface and rich graphical and numerical outputs that are publication ready, Nexus Expression for ImaGene is an ideal product for those performing gene or microRNA expression analysis.

Exiqon’s miRCURY LNA™ microRNA Array system is a complete system for global microRNA expression profiling. Featuring validated and Tm-normalized LNA™-based capture probes, the miRCURY LNA™ microRNA arrays offer microRNA expression profiling with unmatched specificity and sensitivity. With the recent launch of our 5th generation array Exiqon now offers the most updated content on the market with the array containing probes targeting more than 2520 human, mouse and rat microRNAs as well as viral microRNAs and 385 new proprietary human miRPlus™ sequences. Exiqon also offers products for downstream validation of arrays results including the miRCURY LNA™ Universal RT microRNA PCR for validation by qPCR and miRCURY LNA™ microRNA Detection probes for validation by in-situhybridization.

About BioDiscovery, Inc.

BioDiscovery is a leader in the development of advanced microarray bioinformatics software and services that enable its customers to revolutionize drug discovery and diagnostics by efficiently managing, integrating, and analyzing data generated using high-throughput microarray technology. Contact BioDiscovery: 310-414-8100 or www.biodiscovery.com.

About Exiqon A/S

Exiqon’s products are based on the proprietary LNA™ technology. This technology offers unique advantages for detection of miRNA biomarkers for life science researchers, drug developers and cancer treating physicians working towards personalizing medicine. Exiqon operates in two business areas: Exiqon Life Sciences is one of the market’s leading providers of miRNA research products for miRNA analysis in cells. Exiqon Life Sciences is also collaborating with pharmaceutical companies in their effort to develop new medicines based on miRNA as biological markers (Exiqon Pharma Services). Exiqon Diagnostics is developing a series of new molecular diagnostic products based on miRNA. Exiqon’s goal is to gain a market-leading position for miRNA-based diagnostics. Exiqon is listed on the NASDAQ OMX in Copenhagen. For more information, please visit www.exiqon.com.

Affymetrix selects BioDiscovery as OncoScan™ FFPE Express preferred software provider

Custom Nexus Copy Number™ solution and consulting streamlines difficult cancer sample analysis.

EL SEGUNDO, Calif., and SANTA CLARA, Calif., May 27, 2011 – Affymetrix, Inc. (NASDAQ: AFFX) today announced a co-marketing agreement naming BioDiscovery, Inc. its preferred software provider for Affymetrix OncoScan™ FFPE Express Service data analysis. BioDiscovery, a leader in integrated software for high-throughput microarrays and other technologies, customized its Nexus Copy Number™ solution for Affymetrix to make the most user-friendly, flexible, and compatible tool available for OncoScan FFPE Express microarray data analysis. Cancer researchers using the OncoScan Service and Nexus software can now obtain critical cancer genome measurements from archived formalin-fixed, paraffin-embedded (FFPE) tumor samples and obtain an end-to-end solution for faster data visualization and analysis.

“By simplifying data interpretation with the Nexus Copy Number software, we’re providing a complete solution to our customers,‖ said Nargol Faravashi, Affymetrix Global Strategic Marketing Manager, DNA Cancer Applications. ―Our array technology accommodates challenging FFPE tumor samples as old as 28 years. Now that it’s coupled with a best-in-class software solution for visualizing the cancer genome at fine resolution, researchers have a very powerful method to streamline their data analysis processes and accelerate scientific discoveries”

Under the co-marketing agreement, customers accessing the OncoScan FFPE Express Service through the Affymetrix® Research Services Laboratory (ARSL) will receive a preliminary Nexus Copy Number data analysis. Additionally, BioDiscovery will provide a one-on-one consultation session to assist each researcher with the downstream analysis of their data to elucidate pathways and identify copy number variations (CNV) and copy-neutral loss of heterozygosity (LOH) events, which are important for understanding characterizations of mutations.

“Pairing Nexus Copy Number software with Affymetrix’ unique service is an ideal solution for a comprehensive workflow—from FFPE samples to final analysis and visualization of CNV and LOH results,‖ said BioDiscovery CEO Dr. Soheil Shams. ―The latest 6.0 version of our Nexus Copy Number solution is well-designed to analyze data generated from the OncoScan FFPE Express Service, especially with the addition of custom tools for cancer sample analysis.”

The OncoScan™ FFPE Express Service, based on Affymetrix’ unique molecular inversion probe (MIP) array technology, was designed in collaboration with leading cancer scientists. It overcomes the challenge of analyzing DNA from FFPE tissues to extract important retrospective clinical data from archived samples and goes beyond the limitations of standard array comparative genomic hybridization (CGH) methods to yield copy number, allelic ratio, and somatic mutation data from minimal amounts of input DNA.

“Many leading cancer researchers are avid users of Nexus Copy Number for its ease of use, robustness, and flexibility to suit each individual’s needs,‖ added BioDiscovery CEO Dr. Shams. ―Now, customers of the OncoScan FFPE Express Service will receive not only high-quality raw data from Affymetrix, but also reliable analysis of experimental results that further streamline and speed their research.”

BioDiscovery’s software is platform-independent and available for Mac OS X, Linux, and Windows operating systems. In a single project, Nexus Copy Number can integrate and process the data from nearly all commercial array platforms, as well as custom arrays. With free access to a web-based repository for querying and storing genomic data from any location across the globe, Nexus Copy Number is a powerful solution for large study groups and consortia. The software is applicable to many types of studies, from focused cytogenetic projects studying chromosome defects to large-scale cancer or genome-wide association studies (GWAS).

About Affymetrix
Affymetrix technology is used by the world’s top pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government and nonprofit research institutes. More than 2,000 systems have been shipped around the world and more than 23,000 peer-reviewed papers have been published using the technology. Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Santa Clara, Cleveland, Ohio, and Singapore. The company has about 900 employees worldwide and maintains sales and distribution operations across Europe, Asia, and Latin America. For more information about Affymetrix, please visit http://www.affymetrix.com.

About BioDiscovery
BioDiscovery is a leader in the development of advanced microarray bioinformatics software and services that enable its customers to revolutionize drug discovery and diagnostics by efficiently managing, integrating, and analyzing data generated using high-throughput microarray technology. Contact BioDiscovery at (310) 414-8100 or www.biodiscovery.com.

NOTE: Affymetrix, the Affymetrix logo, and OncoScan are trademarks or registered trademarks of Affymetrix, Inc.; Nexus Copy Number is a trademark or registered trademark of BioDiscovery, Inc.

SOURCE: Affymetrix, Inc.


November 12 – 15
AMP Annual Meeting

National Harbor, MD

Association for Molecular Pathology Annual Meeting

Visit us at Booth #723

Get a firsthand look at the NEW BioDiscovery NxClinical!

A revolutionary new solution for Clinical Labs

Key features in NxClinical that improve lab efficiency and reduce turn-around time:

  • Automated decision support for pre-classification of events
  • Visualization of segments and associated probes together in a single interface
  • Ability to define workflows to enforce established lab SOPs
  • Admin-controlled permissions for defined access levels for each user account
  • Secure, scalable, and without need for IT involvement

Learn about our curated cancer data collection – TCGA Premier!

The Cancer Genome Atlas is an amazing resource and by re-processing and improving the data we’ve made it more useful for many types of studies.

  • Improved copy number profiles (re-processed level 1 data and manually reviewed by a team of scientists)
  • Integrated sequence variants provides a more comprehensive genomic picture
  • Nexus Copy Number interface to TCGA data (query and download data for further analysis)

Schedule a one-on-one meeting to learn more about our solutions.

October 18 – 22
ASHG Annual Meeting

San Diego, CA

American Society of Human Genetics Annual Meeting

Visit us at Booth #836

Get a firsthand look at the NEW BioDiscovery NxClinical!

A revolutionary new solution for Clinical Labs

Key features in NxClinical that improve lab efficiency and reduce turn-around time:

  • Automated decision support for pre-classification of events
  • Visualization of segments and associated probes together in a single interface
  • Ability to define workflows to enforce established lab SOPs
  • Admin-controlled permissions for defined access levels for each user account
  • Secure, scalable, and without need for IT involvement

Secure a slot now for a personalized demo of NxClinical at ASHG or attend one of our in-booth scheduled demos:

  • Sunday, Oct. 19 – 3:45pm & 6:00pm
  • Monday, Oct. 20 – 10:00am & 3:00pm
  • Tuesday, Oct. 21 – 10:15am & 2:15pm

And just for attending a one-on-one demo or an in-booth presentation you’ll get a BioDiscovery NxClinical T-shirt!*

 

 

*Supplies are limited.

Utilizing the AGRE Consortium Data via BioDiscovery Nexus Software to Accelerate Research on Autism Spectrum Disorders

Description

Genetic studies of various diseases and disorders requires researchers to sift through vast amounts of accumulated data from diverse sources in order to identify key factors that play a role in these disorders. Having the right tools makes all the difference in processing the data efficiently to accelerate discovery. The Autism Genetic Resource Exchange, a program of Autism Speaks, has a large collection of genotype and phenotype data for individuals with ASD and their family members. This data has been available to AGRE members but now AGRE is providing the copy number and allelic event array data via BioDiscovery Nexus DB so that researchers can quickly and efficiently analyze the data enabling faster discoveries. In this presentation we will show how to access and efficiently explore the AGRE data using BioDiscovery Nexus Copy Number and Nexus DB. The system integrates the information from the AGRE consortium with other databases, such as DGV, UCSC, etc. into a single user interface and allows querying of the AGRE data against a specific case or a population of samples to aid the researcher in making the best interpretation of the observed data. An example workflow using different array platforms will be presented.

Audience

This webinar is geared towards researchers performing copy number and allelic event analysis of the Autism Spectrum Disorders. It is also applicable to anyone interested in a more efficient system to extract meaningful results from genomic aberration data.

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December 8 – 10
ASH Annual Meeting

December 8 – 10 in Atlanta

American Society of Hematology (ASH) Annual Meeting

Visit BioDiscovery at Booth #3624

BioDiscovery representatives will be happy to discuss solutions for your data analysis needs on a one-to-one basis at the booth. Just fill out this form indicating times you are available to meet and we will get back to you with a confirmation. Or if you are already a BioDiscovery software user and need help with analysis or just want to chat with us, fill out the form with available times, and we’ll schedule to meet with you at the conference.

ASH 2012 Meeting Website

Be sure to check out the following talks and posters where BioDiscovery Nexus Copy Number was used for analysis:

Saturday, December 8

5:30 – 7:30 PM Hall B1-B2, Level 1, Building B, #1394
Acute Erythroid Leukemia (AEL) Can Be Separated Into Distinct Prognostic Subsets Based On Cytogenetic and Molecular Genetic Characteristics

Sunday, December 9

6:00 – 8:00 PM Hall B1-B2, Level 1, Building B, #2539
Genome-Wide Copy Number Analyses Correlated with Outcomes in Untreated Multiple Myeloma Patients

Monday, December 10

7:00 AM, ORAL B206, Level 2, Building B, #289
IKZF1 and 22q11.22 Deletions and PDGFRA Gains Are Associated with Poor Outcome in Down Syndrome Acute Lymphoblastic Leukemia

2:45 PM, ORAL B207-B208, Level 2, Building B, #517
Sequential Evolution Versus a Single Catastrophic Event (Chromothripsis) in the Pathogenesis of AML with Complex Aberrant Karyotype

6:00 – 8:00 PM Hall B1-B2, Level 1, Building B, #3991
Comprehensive Cytogenetic and Molecular Genetic Characterization of T-PLL Identifies for the First Time BCOR Mutations in a Lymphatic Disease


Seminar and Training on Integrated Genomic Data Analysis

Wed. Dec. 12

Munzer Auditorium, Beckman Center
Stanford University
Palo Alto, CA

Map and directions

Joins us for a seminar on integrated analysis of TCGA lung squamous cell carcinoma followed by a training on how to perform copy number and gene expression analysis using BioDiscovery’s Nexus Copy Number and Nexus Expression software.

9:30 AM – 10:30 AM
Seminar: Integrated Genomic View of TCGA Lung Squamous Cell Carcinoma

Presenter: Dr. Soheil Shams, BioDiscovery, Inc.

Abstract
In this presentation, we will use the data generated by The Cancer Genome Atlas (TCGA) project on approximately 300 lung squamous cell carcinoma samples to demonstrate how copy number, allelic changes, and gene expression data can interactively be explored using the Nexus Copy Number and Nexus Expression systems to gain knowledge about the underlying biology. In particular, we will show how SNP data from Affymetrix SNP 6 arrays have been processed to obtain copy number and LOH differences between samples and their matched normal. We will show how various population analyses can be performed quickly to identify regions that are different between subpopulations or to identify significant common aberrations in the sample. We will then show analysis of the associated expression data and identify differentially regulated genes and pathways. Finally, we will integrate the results between these analyses to identify possible driver events.

10:30 AM – 12:00 PM
Training: Nexus Copy Number and Nexus Expression

Learn how to quickly and easily analyze data to identify common aberrations,
differences between sub-populations, biomarkers, differentially expressed genes,
and more using Nexus Copy Number and Nexus Expression software.

Both events are free. Please RSVP here.

Webinar: Feb. 13 – 14
Cytogenetics Best Practices: Maximizing sensitivity and specificity of CNV detection from microarray and NGS platforms

Presenter
Benjamin W. Darbro, M.D., Ph.D. Assistant Professor of Pediatrics Director, Shivanand R. Patil Cytogenetics and Molecular Laboratory University of Iowa

Description
Copy number variation has increasingly been recognized as an important cause of human disease phenotypes.  Detection of copy number variants (CNVs) has become a routine clinical practice for patients exhibiting developmental delay and other neurocognitive phenotypes.  However, before cause and effect connections can be made, and clinical management altered, copy number variants (CNVs) must be accurately detected and thoroughly annotated by the laboratory performing the testing.  This process is essential and required before any CNV can be appropriately interpreted in the setting of a specific disease or phenotype.  Here we will present methods that allow clinical and research laboratories to 1) calibrate specific chromosomal microarray data metrics to maximize sensitivity and specificity of CNV detection on a genome-wide scale, 2) leverage local and external databases to create custom annotation tracks and filtering algorithms, and 3) integrated methods (including exome sequencing) for interpretation of CNVs in the setting of specific disease phenotypes.

Audience
This webinar is geared towards those working in cytogenetics looking for a workflow and best practices for detection and interpretation of copy number variation from microarray and NGS data.

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