Recent Bog Posts
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    A review of “Emerging landscape of oncogenic signatures across human cancer”

    One of the main goals of large-scale in-depth analyses of cancer samples is to uncover the common alterations that define a tumor, in hopes of targeting these changes with directed drug therapies.  Historically, we have found that genomic alterations in …

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    Estimating copy number from log ratios

    We often get questions such as these from customers: “How can I calculate the actual copy number of my samples in Nexus?” “Is the probe median value the log ratio of the actual copy number?” “Can I estimate the actual …

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    Going to ASHG? Check out this presentation on whole-exome sequencing as a first tier diagnostic test

    ASHG 2013 in Boston starts next week. If you are attending, please stop by the BioDiscovery booth (#1011) and see what’s new in copy number variation analysis, particularly CNVs from NGS, and check out our poster (see below for details). …

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    Changing Analysis Settings in Nexus

    Many users of Nexus Copy Number simply use the default settings to analyze their data.  This is fine.  For some samples, however, it may be necessary to adjust the analysis settings to optimize the results.  But often users are either …

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    Recent webinar: Frequency Significance Testing (STAC & GISTIC) and Enrichment Analysis

    We recently held a webinar addressing identification of common aberrations using STAC and GISTIC and when to use one or the other. The webinar also covered downstream enrichment analysis. The webinar recording was split into the different topics and is …

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    Copy Number Variation Cancer Applications Seminar and Workshop – Boston, Oct. 22, 2013

    Want to see what’s new in copy number variation in cancer genomics? Join us at our Copy Number Variation Cancer Applications Seminar and Workshop in Boston on October 22, just before the ASHG meeting. The event will be held in …

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    Gene Ontology Enrichment: Which Pathways or Processes are enriched in my data set?

    During the course of your analysis with Nexus Copy Number, you may want to know about the specific pathways and processes that may be targeted by copy number alteration.  We can think about this enrichment in two different respects: Whole …

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    Where did my probes go?

    A Nexus Copy Number error seen when first loading and processing results: And your first thought is often “Hey – Where did my probes go?” When doing your copy number analysis, we always recommend applying systematic correction.  However, it is …

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    Identifying Statistically Significant Frequent Copy Number Alterations: STAC and GISTIC

    When evaluating recurring copy number alterations in a larger data set, two questions come to mind: (1) What are the most frequent alterations and (2) are they statistically significant? The discovery edition of Nexus copy number software has two different …

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    Using CoNIFER to Detect Copy Number Variations from Exome Sequencing Data

    I’ve had the pleasure of having a bioinformatics student from UCI, Ryan Bertwell, working with me this summer. He, along with my colleague Alessio, recently reviewed the paper on the CoNIFER algorithm. I thought it would be good to share …

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    New ISCA Consortium Data in Nexus DB

    The ISCA Consortium (International Standards for Cytogenomic Arrays), now known as ICCG (International Collaboration for Clinical Genomics), is a group of clinical cytogenetics and molecular genetics laboratories sharing its data generated in clinical testing laboratories. The consortium submits curated clinical …

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    Concordance: Identifying Significant Co-occurring Alterations

    In cancer research, the widely accepted multiple-hit hypothesis states that cancer is the result of accumulated mutations, and is dependent on both the activation of proto-oncogenes and deactivation of tumor suppressor genes.  Thus, after identifying a change of interest in …

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    Utility of visualizing and analyzing sequence variants alongside copy number changes

    There has been a significant increase in use of next-gen sequencing technologies for genomic data analysis. NGS is a rich source for data that can be used in several different types of analyses and is a great way to accomplish …

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    Check out the new Nexus 7 at ESHG in Paris!

    If you are going to the European Human Genetics Conference (ESHG) in Paris (June 7 – 11), don’t miss the BioDiscovery Satellite event, New! Nexus 7 – A Single Platform for Copy Number and Sequence Variation Analysis with Built-in Reference …

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    Diploid Recentering: When, Why and How

    It is well established that cancer frequently undergoes copy number changes, which is why copy number is frequently evaluated in cancer samples for diagnostic and research purposes.  However, when beginning copy number analysis of a sample using a SNP array, …

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    How to Identify Chromothripsis in Tumor Samples

    Chromothripsis, or chromosomal shattering, occurs at a frequency of 1%-5% in most cancer types, though has been described as being upwards of 25% in bone cancer (Cell. 2011 Jan 7;144(1):9-10). It has been associated with poor prognosis (Cancer Res. 2012 …

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    Evaluating sequencing methods against microarrays for copy number analysis

    Sequencing is increasing in popularity as a platform for copy number analysis. But how does it stack up to traditional methods (typically microarrays) ? To answer this, or at least begin to, the question has to be reframed around “which” …

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    Genome annotations – now on the Downloads page!

    Did you know that you can use data from virtually any genome to identify copy number variations (CNV) and LOH using Nexus Copy Number and Nexus Solo? When you first launch the software and create a new project, you will …

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    Estimation of Aberrant Cell Percentage in Tumor Normal Cell Mixture

    Cancer samples, especially solid tumors, usually contain a mixture of tumor and normal cells.  Using both the SNP and copy number information provided by SNP arrays (Affymetrix or Illumina), the % aberrant cells can be estimated.  Here we are going …

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    Paired Analysis

    Copy number variants (CNVs) are recognised to be part of the natural genetic variation in humans. Although there is still work to do to fully understand biology involved, it is likely that CNVs are responsible for a considerable proportion of …

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    How to analyze NGS data in Nexus

    This post deals with loading NGS data into Nexus for copy number variation and structural variants. BAM files produced from NGS have to be processed before loading into Nexus. Variant calls in VCF format can be loaded into the next …

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    PAG XXI starts in a few days!

    The annual Plant and Animal Genome Sciences (PAG XXI) meeting is starting this weekend in San Diego, CA. This is the largest genomics conference focusing on non-human species and attendance is expected at over 2800. BioDiscovery will be exhibiting at …

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    From Raw Data to Copy Number Calls – Data processing workflow in Nexus Copy Number

    The so-called “Raw Data” for the data analysis in Nexus Copy Number can be intensity values for array probes (Affymetrix CEL files), logRatios after normalization (Agilent Feature Extraction results files and Illumina final report files), or even copy number state …

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    Need software but don’t have the funds?

    ‘Tis the season of giving and BioDiscovery shares that sentiment! We have recently launched a software donation program to benefit pediatric research. It is heartbreaking to see young ones struggle with illness and not be able to share in the …

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    Review of “Statistical Challenges associated with detecting copy number variations with next-generation sequencing”

    With the deluge of data streaming from Next Generation Sequencing (NGS) technologies, scientists are scrambling to find the best methods for Copy Number Variation (CNV) analysis. Of the two main types of NGS data used for CNV analysis – Whole …

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    ASH is here!

    The American Society for Hematology (ASH) Meeting officially starts tomorrow. Approximately 20,000 people will be attending this meeting at the Georgia World Congress Center in Atlanta, GA. With over 4300 oral and poster presentations, it is a daunting task to …

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    How to transition your project from one NCBI build to another?

    It has been over 3 years since NCBI Build 37(hg19) has been released and your lab may want to move your data to this build. Perhaps you are getting new microarray or NGS data that is on the newest build …

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    BioDiscovery is a proud sponsor of the Rare Disease Challenge

    The designation “rare disease” in the US is typically defined as having a prevalence of fewer than 200,000 affected individuals [1]. Considering that there are over 7000 diseases having this designation collectively affecting about 25 million Americans [1], it doesn’t …

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    2012 ASHG Lunch CNV Workshop – What’s on the agenda?

    We hope you will join us at our CNV workshop at the 2012 ASHG Annual Meeting in San Francisco (details below). If you cannot make it to the workshop, please do visit us at Booth #813 for some Nexus fun …

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    TCGA Level 3 Data is Now Available in Nexus DB

    The Cancer Genome Atlas (TCGA) has a multitude of publicly available genomic data that researchers can use in their own projects. Level 3 (segmented/interpreted) copy number data from TCGA is now available in Nexus DB. You can query this data …

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    GC Wave Correction – when to use it, how and why

    Several customers have asked about when and whether to use GC wave correction. What causes waviness? Should a correction be applied even if there is no observable data waviness? Should I use a linear, quadratic, or lowess correction? GC waviness …

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    Autism data from Autism Genetic Resource Exchange is now available via NexusDB.

    The Autism Genetic Resource Exchange (AGRE) consortium has been collecting samples and clinical data from subjects with autism spectrum disorder and their family members for over 15 years. The information available here has been invaluable to numerous researchers but retrieving …

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    How to obtain the number of tests performed for multiple testing when using the Comparisons tool in Nexus Copy Number

    The Comparisons feature in Nexus Copy Number uses a two-tailed Fisher’s Exact test. Instead of using the p-value, one can use the Q-bound value which corrects for multiple testing using the Benjamini-Hochberg FDR correction (Benjamini & Hochberg). If you want …

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    Traditional methodologies are not optimal with genomic data analysis

    Often in scientific discovery, the “division of labor” model allowing compartmentalization of different parts of a broader project is not the optimal solution. Some people don’t realize this until too much effort has already been put into a project or …

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    ISCA database CNV tracks are available in Nexus Copy Number and Nexus Solo

    The ISCA database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. CNV calls and their clinical interpretations are available to the public and this great resource can be viewed easily in the Nexus genome browser. Continue reading →

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    BioDiscovery at the ISCO 2012 Congress,
    March 4-8 Mallorca, Spain

    ISCO 2012 Congress is a joint meeting with the European Workshop on Cytogenetics and Molecular Genetics of Solid Tumors in Mallorca, Spain from March 4-8. BioDiscovery will be presenting a talk on Tuesday, March 6, 13:10 – 13:50 in the Greco room at the meeting venue, Gran Meliá Victoria Convention Center. Continue reading →