Author Archives: shaliniverma

June 17-19 – Educational Webinar Series: Copy Number and Allelic Event Measurements, Aneuploidy, and ASCAT

Webinar Description
This is the third webinar of the educational series where we go from the very basics of copy number analysis to more advanced analysis topics. Fundamental concepts such as copy number measurement methods, quality assessment, and different approaches/algorithms used for detecting copy number changes and allelic events as well as unique complications encountered in different applications will be presented.

Today’s webinar will cover the following three mini-courses:

Copy Number and Allelic Event Measurements from SNP Arrays – Calculation of log ratio, BAF calculation, how the additional genotype information is helpful, how to interpret results from combined copy number and B-Allele frequency examination

Dealing with Aneuploidy - What is it, why does it occur, how to account for it, re-centering data

ASCAT Algorithm – What it does and how it accounts for complications of aneuploidy, tumor heterogeneity, and contamination from normal cells in tumor sample analysis.

Audience
This webinar is for those who want to learn the fundamentals as well as advanced concepts in copy number variation analysis.

Register for a session now by clicking a date below:

Mon, Jun 17, 2013 5:00 PM – 6:00 PM PDT / 1:00 – 2:00 GMT

Tue, Jun 18, 2013 10:00 AM – 11:00 AM PDT / 18:00 – 19:00 GMT

Wed, Jun 19, 2013 7:30 AM – 8:30 AM PDT / 15:30 – 16:30 GMT

Constitutional and Cancer Sample Review for Cytogeneticists: Copy Number and Sequence Variant Analysis Using Nexus Copy Number 7

Webinar Description
In this presentation we will demonstrate CNV, LOH and sequence variant analysis tools for cytogeneticists which will accelerate their sample review workflow and allow for better decisions on the significance of events being detected. Using Nexus Copy Number 7 as a platform independent solution for analysis and visualization of CNV, LOH, and sequence variation, we will review individual case examples for both constitutional and cancer samples. We will demonstrate how data from any platform can be loaded and processed to automatically identify regions of copy number change and LOH. Enhanced filtering options and quick comparison with online public databases (e.g. ISCA, AGRE, TCGA) in Nexus Copy Number 7 allows for quick creation of customized reports with notes and annotations.  Finally, we will co-visualize sequence variation results with copy number calls for samples with data from multiple modalities for integrated genomic evaluation.

Audience
This webinar is geared towards cytogeneticists performing CNV, LOH, and sequence variant analysis from aCGH, SNP array, and NGS data. Existing Nexus users will benefit from learning about the new features in the new version 7 of Nexus Copy Number and Nexus Solo and how to use them effectively.

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BioDiscovery Releases Nexus Copy Number Version 7 for DNA Copy Number and Sequence Variation Analysis and Visualization

Hawthorne, CA, April 16, 2013 – BioDiscovery, Inc. a leader in integrated software solutions for genomics data analysis from high-throughput microarray and Next-Gen sequencing technologies, announced today the release of version 7 of Nexus Copy Number software, the leading platform independent and user friendly application for analysis of structural variation from CGH array, SNP array and NGS platforms. Version 7 offers numerous new capabilities including support for small sequence variations, such as point mutations, InDels, inversions, etc. as well as new computational and visualization tools for identifying and displaying significant co-occurring aberrations, and processing samples using ASCAT2. Nexus Copy Number is platform independent and can load virtually any data using its predefined data types or user-created custom data types.

BioDiscovery Nexus Copy Number has enabled users to efficiently detect, visualize, and interpret copy number and allelic event changes across many application areas for several years. With Nexus Copy Number version 7, sequence variations can now be interpreted alongside copy number changes for an integrated view of genomic aberrations.  This unique feature of integrated analysis allows identification of mutations overlapping copy number aberrations or homozygous regions in addition to identification of novel disease causing mutations. A new concordance tool allows identification of co-occurring aberrations and many new filtering schemas facilitate quickly narrowing down list of genes implicated in specific types of aberrations.

“With sequencing costs decreasing and widespread use of NGS technologies, researchers have much more sequence variation data at hand and need a way to make sense out of them,” said Dr. Soheil Shams, CEO, BioDiscovery, Inc. “Nexus Copy Number offers a unique composition of analysis and visualization of sequence variations, copy number changes, and allelic event changes together, allowing researchers to advance their findings with a broad picture of the genomic landscape.”

BioDiscovery Nexus Copy Number can integrate and process together, in a single project, data from commercial array platforms such as Agilent, Affymetrix, Illumina, Roche NimbleGen, Next-Gen read depth and small sequence variations, as well as custom arrays. With its free access to a web-based repository for querying and storing genomic data from any location across the globe, BioDiscovery Nexus Copy Number is a powerful solution for large groups such as special consortia. The software is applicable to many types of studies from focused projects of a cytogeneticist to large scale cancer or GWAS studies. BioDiscovery is attuned to such different needs and offers the product in a flexible and modular system allowing users to create configurations that are suited to their needs.

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.

BioDiscovery Nexus Copy Number software offers simple yet powerful tools for copy number and sequence variation analysis and visualization from CGH arrays, SNP arrays, as well as next-generation sequencing, for analysis of complex data such as solid tumor samples. The elegant user-interface and powerful statistical tools designed specifically for the end-user allow detection of chromosomal aberrations and identification of affected pathways with just a few mouse clicks.

Contact BioDiscovery: 310-414-8100 or http://www.biodiscovery.com

Integrated analysis of sequence variations and copy number in TCGA data with the new Nexus Copy Number 7

Description
In this webinar, we will present an integrated analysis of copy number and sequence variation using data from The Cancer Genome Atlas (TCGA).  TCGA data is publicly available via the TCGA portal and includes copy number data and whole exome sequencing data. Nexus Copy Number 7 has a number of new features including support for sequence variations (in various formats including VCF, MAF, and Affymetrix OncoScan somatic mutation files). Other new features particularly applicable to cancer studies are identification of co-occurrent regions and ASCAT2. Using the Discovery Edition of Nexus Copy Number 7.0, we will present findings which include: identification of areas of copy number enrichment using GISTIC analysis, identification of frequently mutated genes, comparison of copy number profiles between groups of tumors within the sample set, determination of co-occurrence between specific sequence variation and copy number alterations, and survival analysis.

Audience
This webinar is geared towards researchers interested how CNV, allelic events, and seq. variations can aid in the discovery process in cancer studies.

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Affymetrix and BioDiscovery announce software for analysis of whole genome copy number data generated from FFPE solid tumor samples for accelerating cancer translational research

Santa Clara, CA, April 10, 2013 – Affymetrix, Inc. (NASDAQ: AFFX) and BioDiscovery announce the availability of the Nexus for OncoScan® Software for analysis of whole genome copy number data generated from formalin-fixed, paraffin-embedded (FFPE) solid tumor samples using the OncoScan® FFPE Express 2.0 Service. Through a joint arrangement, this software, based on BioDiscovery’s flagship Nexus Copy Number™, is available to customers who are analyzing data generated using this service.

Obtaining high-quality copy number data using limited amounts of DNA from degraded FFPE samples is extremely challenging for cancer researchers. Utilizing Affymetrix’ unique Molecular Inversion Probe (MIP) technology, the OncoScan FFPE assay is capable of analyzing highly degraded DNA in FFPE tumor samples, even from less than 100 ng of starting DNA material, and is currently available as a service through Affymetrix Research Service Laboratory (ARSL) based in Santa Clara, California.

OncoScan FFPE Express 2.0 Service has been successfully used by more than 30 leading cancer research institutes, including M. D. Anderson Cancer Center, University of California San Francisco, and the Huntsman Cancer Institute at the University of Utah.

“Cancer translational researchers have been able to quickly and easily analyze hundreds of degraded FFPE samples to correlate copy number aberrations with outcomes data,” said Andy Last, Executive Vice President of the Genetic Analysis and Clinical Applications Business Unit at Affymetrix. “Nexus for OncoScan Software is especially optimized for solid tumor copy number analysis and can generate whole genome copy number calls from raw data in minutes. We are very excited to continue to partner with BioDiscovery to bring this powerful and easy-to-use software to the cancer research community.”

“The OncoScan FFPE assay is an amazing technology for cancer researchers allowing them to unlock DNA information from masses of archived FFPE samples to obtain high quality data,” said Soheil Shams, President of BioDiscovery. “Combining
the powerful OncoScan FFPE technology with the proven power of Nexus Copy Number gives scientists a unique solution that is sure to accelerate cancer research, impact diagnosis, and ultimately lead to better patient care and treatment. We are very pleased to partner with Affymetrix in offering this powerful solution”

A next generation OncoScan FFPE product will be available in late 2013 enabling researchers to perform the assay and analysis in their own lab. Delivering results in about 48 hours, this new product will provide whole genome copy number coverage with high resolution in known cancer genes, loss of heterozygozity (LOH) as well as clinically relevant somatic mutation data – all from a single assay. An updated version of Nexus for OncoScan Software will be released in conjunction with the launch.

PLEASE NOTE: Affymetrix®, the Affymetrix logo, and OncoScan® trademarks are the property of Affymetrix, Inc. All other trademarks are the property of their respective owners.
Products mentioned in this release are for research use only. Not for diagnostic procedures.

SOURCE: Affymetrix, Inc.

Forward-looking statements
All statements in this press release that are not historical are “forward-looking statements” within the meaning of Section 21E of the Securities Exchange Act as amended, including statements regarding Affymetrix’ “expectations,” “beliefs,” “hopes,” “intentions,” “strategies,” or the like. Such statements are subject to risks and uncertainties that could cause actual results to differ materially for Affymetrix from those projected. These and other risk factors are discussed in Affymetrix’ Form 10-K for the year ended December 31, 2012, and other SEC reports for subsequent quarterly periods.

About Affymetrix
Affymetrix technologies enable multiplex and simultaneous analysis of biological systems at the cell, protein, and gene level, facilitating the rapid translation of bench-top research into clinical and routine use for human health and wellness.

We strive to provide leadership and support, partnering with our customers in pharmaceutical, diagnostic, and biotechnology companies, as well as leading
academic, government, and non-profit research institutes in their quest for answers toward using biology for a better world.

More than 2,300 microarray systems have been shipped around the world and more than 48,000 peer-reviewed papers have been published citing our technologies. Affymetrix is headquartered in Santa Clara, California, and has manufacturing facilities in Cleveland, Ohio, San Diego, Vienna and Singapore. The Company has about 1,100 employees worldwide and maintains sales and distribution operations across Europe, Asia, and Latin America. For more information about Affymetrix, please visit www.affymetrix.com.

About BioDiscovery, Inc.
BioDiscovery (www.biodiscovery.com) 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.

BioDiscovery Nexus Copy Number software offers simple yet powerful tools for copy number and sequence variation analysis and visualization from CGH arrays, SNP arrays, as well as next-generation sequencing, for analysis of complex data such as solid tumor samples. The elegant user-interface and powerful statistical tools designed specifically for the end-user allow detection of chromosomal aberrations and identification of affected pathways with just a few mouse clicks.

Affymetrix, Inc.
Media Contact:
Mindy Lee-Olsen
Vice President, Marketing Services
408-731-5523
mindy_lee-olsen@affymetrix.com
OR
Investor Contact:
Doug Farrell
Vice President, Investor Relations
408-731-5285
doug_farrell@affymetrix.com
BioDiscovery, Inc.
Media Contact:
Louis Culot
Vice President, Business Development and Marketing
310 414 8100
lculot@biodiscovery.com

May 9-10
International Collaboration for Clinical Genomics (ICCG) Meeting

Bethesda Marriott (Pooks Hill)
Bethesda, MD
Meeting website

Visit us at the 2013 ICCG meeting.  Click here to schedule a meeting with a representative.

Check out our poster on integrated analysis of sequence variants and copy number changes using Nexus Copy Number 7:

A software solution for reviewing, visualizing, and annotating sequence variants alongside copy number changes
Soheil Shams,  Zhiwei Che, Louis Culot, Shalini Verma, Andrea O’Hara , Raja Keshavan
BioDiscovery, Inc. 5155 Rosecrans Ave, Hawthorne, CA 90250
Sequence variants (specifically point mutations, insertions, deletions, and inversions) can be penetrant for constitutional diseases as well as cancer, and should be considered alongside larger copy number variation. In Smith-Magenis syndrome, for example, the majority of cases are due to deletions of 17p11.2; but some cases have a mutation in RAI1 without a deletion. Since genome-wide copy number is typically arrived at through aCGH or SNP array analysis, and sequence variation through other methods, such as Next Generation Sequencing (NGS), an integration of the two data sources provides a more comprehensive picture of the genome than would otherwise be possible. We present here a software system for interpretation of these events simultaneously, presentation of integrated results for cytogenetics reporting (including the ability to create visualizations focused on suspected pathogenic events), case query of these events against history of previously analyzed samples, along with several actual cases.

Educational Webinar Series – Copy Number Analysis and Its Application to Genomic Research: Data QC, GC Wave Correction and Mosaicism

This is the second webinar of a new educational series where we go from the very basics of copy number analysis to more advanced analysis topics. Fundamental concepts such as copy number measurement methods, quality assessment, and different approaches/algorithms used for detecting copy number changes and allelic events as well as unique complications encountered in different applications will be presented.

Today’s webinar will cover the following three mini-courses:

  1. Data QC – learn about the different quality measures, how the quality score is calculated, and how to determine what is a good quality score.
  2. Systematic bias correction (GC wave correction) – identifying systematic biases in your data, different correction approaches, and when and how to apply such correction methods.
  3. Mosaicism and its effect on aCGH measurements – what is mosaicism, how to identify it, and how it affects the calling algorithms

Audience
This webinar is geared towards those who want to learn the fundamentals of copy number variation analysis.

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Sneak Peek at version 7 of Nexus Copy Number

We will be holding different webinars for Discovery Edition and Standard Edition. See below for details, dates, and times for each.

Sneak Peek at version 7 of Nexus Copy Number Standard Edition

Get an overview of the new features and enhancements in Nexus Copy Number Standard Edition. This webinar will focus on features and workflow typically used by cytogeneticists/clinical labs. Using Nexus Copy Number Standard Edition, we will highlight the new and enhanced features for reviewing single cases. This version offers a higher level of user control over how and what to filter out. Many new filtering options have been added allowing you to fully customize case review. See how you can easily filter out a list of variants from your project. See how to save filters and apply across all projects or to a single project or even just to review an individual case. Enhancements to reporting features allow more control as well as the ability to export additional details such as genome build, settings used, and sample factors. Also, the new version supports visualization and reporting of additional structural variant data alongside CNVs and LOH.

Audience
This webinar is geared towards those who use Nexus Copy Number in a cytogenetics setting (e.g. case review).

Register for a session now by clicking a date below:
Thu, Feb 28, 2013 7:30 AM – 8:15 AM PST
Fri, Mar 1, 2013 10:00 AM – 10:45 AM PST

 

Sneak Peek at version 7 of Nexus Copy Number Discovery Edition

This webinar will focus on features and workflow typically used by scientists working in a research setting. Using Nexus Copy Number Discovery Edition, we will highlight the new and enhanced features applicable to research-based analysis. The new version offers support for visualization and analysis of additional structural variant data (e.g. point mutations, deletions, insertion, etc.) obtained from any platform (including NGS). Data can be imported using different data types, including support for VCF files, Affymetrix OncoScan Mutation data, and custom mutation data. A new concordance function identifies co-occurrent regions and displays these as a circos plots. There are many additional enhancements including improvements to several tools and the comparisons module. A number of features have also been added to the base software to expand options on filtering, track selection, etc.

Audience
This webinar is geared towards research users of Nexus Copy Number (those who typically  use of the full spectrum of tools and functions in Discovery Edition).

Register for a session now by clicking a date below:
Wed, Feb 27, 2013 4:30 PM – 5:15 PM PST
Thu, Feb 28, 2013 10:00 AM – 10:45 AM PST
Fri, Mar 1, 2013 7:30 AM – 8:15 AM PST

Educational Series – Copy Number Analysis and Its Application to Genomic Research_ aCGH Principles and Calling Algorithms

In this new series of webinars, held over the next few months, we will sequentially transition from the very basics of copy number analysis to more advanced analysis topics. Fundamental concepts such as copy number measurement methods, quality assessment, and different approaches/algorithms used for detecting copy number changes and allelic events as well as unique complications encountered in different applications will be presented.

Today’s webinar will cover the basic principles of array CGH and various CNV calling algorithms. We will present the common approaches – Hidden Markov Model (HMM), Circular Binary Segmentation (CBS) – as well as other approaches based on these models (Rank Segmentation and FASST2 Segmentation). Goals, mechanisms, and pros and cons of these algorithms will be discussed.

Audience
This webinar is geared towards those who want to learn the fundamentals of copy number variation analysis.

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