Monthly Archives: November 2016

  • Utopia: Advice, Intelligent interface with Opus23

    Advice: Intelligent Interface with OPUS23

    ADVICE is an app in Utopia that gives algorithmic considerations of multiple bacterial strains in conjunction with the client’s own genome to provide true/false clinical outcomes. ADVICE automatically pulls the client’s Opus23 genetic data where relevant, and incorporates it into algorithmic calculations. (comparable to LUMEN in Opus23).

    Getting around ADVICE

    From the Utopia drop down menu, hover over ‘Algorithms’ until a second list appears, then select ‘Advice’. You are presented with a list of algorithms, those that are true are at the top and display the word ‘TRUE’ in a green box, followed by those that are false, which display the word ‘FALSE’ in an orange box. Each algorithm will display the repute (risk, benefit or neutral), and the magnitude. If an algorithm suggests prescriptive metabolites which enhance or reduce specific bacteria, they will be listed under Encourage or Discourage.

    The client’s relevant genes will be displayed beneath the listed ‘microbiota’ information in the same format found in the Opus23 LUMEN app. Clicking on the colored semicircle will open a pop-up window with a description of the gene and giving details of the client’s SNPs for the gene from their Opus23 data.

    Utopia Advice algorithm

    An ADVICE algorithm for gluten-induced immunopathology

    All metabolites and taxa are clickable. Clicking a metabolite opens a pop-up window with a list of bacteria affected by it. Clicking a bacterium opens a pop-up window as described in previous apps. To add an algorithm to the client report, click on the ‘Add/ Uncurated’ button.

    Individual genera may also be curated and added to the client report for the current dataset by selecting the taxon to open its pop-up information and then clicking the ‘Add/Uncurated’ button.

    Screen shot of Metabolomics pop-up window

    Pop-up window in ADVICE showing metabolomics information

    Using the Algorithm Aggregate Analysis

    At the bottom of the page is the Algorithm Aggregate Analysis. This is a summary of all advice for the client listed under either an ‘increase’ and ‘decrease’ section heading. Each section provides both the microbiota and beneficial/ harmful metabolites that are suggested to be increased or decreased by your client. The ‘result’ information can be a useful tool for streamlining complex treatment strategies. Each metabolite listed in the Algorithm Aggregate Analysis details whether or not the metabolite has mixed results (included as both encourage and discourage in ADVICE algorithms), and whether it is specific to an algorithm.

    Algorithm Aggregate Analysis screenshot

    Algorithm Aggregate Analysis for the ADVICE app

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  • Upcoming Opus 23 In-Person Seminar

    Because of media obligations associated with the re-release of Dr. D’Adamo’s first book, there is a schedule conflict with the January 7-8 seminar date. The seminar will be rescheduled for a later date.  Please check back for further news and details.


    If you are even thinking about doing this sign up.Opus 23 has been a game changer for my patients who have had ‘mysterious’ problems that, after seeing many integrative practitioners, still were not better until Opus 23 ‘sang’ the perfect healing words. –Robert Lang, MD

    Dr. D’Adamo periodically does these for those practitioners who prefer a more hands-on approach to learning Opus 23 (vs. the wonderful 5 hour webinars done by Drs. Greenfield).

    Dr. D’Adamo writes:

    ‘Attendees work in 2-3 person pods under the direct supervision of one of my COE wunderkids. You also get a healthy dose of me lecturing on stuff: In this case a heavy focus on the new ‘Utopia’ module that allows you to mash up client genomic and microbiome data. Attendance is purposely kept to 10-12, to insure an intimate learning environment. You get lunch and I typically spring for dinner at a nice restaurant.’

    If you are interested in this type of hands-on training, contact Carol Agostino at carol@dadamo.com (203 761-0042) for full details.

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  • Utopia: Pansophia, sequential outcome analysis

    PANSOPHIA – sequential outcome analysis

    The genomic DNA analysis software Opus 23 includes the Utopia suite of apps for analyzing sequential uBiome data, comparing sequencing-based clinical microbiome data with the client’s own genomic DNA.

    Utopia logo

    PANSOPHIA is an Utopia app that gives you the power to sort your client’s data based upon associations with health and disease as well as several other useful categories including keystone, probiotic, core species and butyrate production.  For those clients who have more than one data sample, PANSOPHIA allows you to visualize treatment progress in a graphical format that can be easily added to your client’s report.

    Navigating PANSOPHIA

    pansophia

    From the Utopia drop down menu, hover over ‘analytics’ until a second list appears, then select PANSOPHIA. You will then be presented with the default table which shows ‘everything’ and is sorted by ‘rank’ or ‘percent’.

    At the bottom of the window is a jump screen that allows you to move from one screen to the next. You can control how many rows to display be selecting an option from the ‘Show’ pull down menu. The default is 15.

    Pansophia initial screen

    Filtering and sorting results

    PANSOPHIA allows you to parse the taxon data based upon desired treatment goals. Taxa are sortable by benefit as well as pathogenic potential.  There are two ways to filter the data.

    Using category tabs:

    You can use the category tabs at the top of app’s main screen to select taxa grouped by their associations with health and disease. Once a category is selected, the information will be displayed in graph form.

    Pansophia screenshot

    The PANSOPHIA graph uses the following symbols:

    • An orange dot  denotes average %, the bar graphic represents the client data- specific %
    • For those with multiple data sets, a blue diamond denotes % change

    Click on any desired taxon to open up its information pop—up window for detailed information including taxonomy, an overview of known disease or health benefit associations, interactions and metabolomics. Click ‘add/ curate’ to include it in your clients report. Additionally, the graph itself can be printed or added to your client’s report.

    Using individual taxon selections:

    From the main screen, you can sort the taxa by ‘name’ or ‘client %’ then select desired taxa individually using the display box selections on the left hand side of the screen.  Once you have made your selections, click the orange ‘display selections’ button at the top of the screen. The individual taxon information will be displayed in graph form. Click ‘add/curate’ to include the graph in your client’s report.

       

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  • Utopia Demonstration Video

    Dr. Peter D’Adamo and Dr. Tara Nayak present an introduction to Utopia, the free microbiome analysis add-on module to Opus 23 for uBiome test results.

     

    To use Utopia, you will need to  have your client’s 23andMe data already uploaded to Opus 23. You can then upload as many raw data files from uBiome tests as you have for that client. Utopia will work with individual uBiome tests, referencing the client’s 23andMe results where appropriate, and also give sequential analysis for multiple uBiome tests.

    The unique combination of Opus 23 and Utopia make this an opportunity for practitioners to get deep insight into their clients on both a genomic and a microbiological level, all sourced from published medical literature. The interaction between the two genomic analyses provides unparalleled informatics tools, and gives the practitioner an edge over any other genomic analysis tool available today.

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  • Utopia: Spectrum, visual community organization

    SPECTRUM: Visual community organization

    Utopia logo

    SPECTRUM provides a visual representation of the taxonomic data at both the genus and phylum levels. The app demonstrates the weight, influence and diversity of your client’s microbiome in two helpful display formats, each of which are clickable for a deeper look and easy report curation.

    Navigating  SPECTRUM

    Spectrum logo

    From the Utopia drop down menu, hover over ‘analytics’ until a second list appears, then select SPECTRUM.  Phyla and genus are displayed in pie chart format, which is accompanied by the spectrum profiler found below.

    The pie charts follow the color-coding conventions found in OPUS23 indicating beneficial, neutral as well as pathogenic organisms. Click on any desired section to open up its information pop—up window for detailed information including taxonomy, an overview of known disease or health benefit associations, descendants and metabolomics. Click ‘add/ curate’ to include it in your client’s report.

    Spectrum pie charts

    The spectrum profiler demonstrates the trends in your client’s biome diversity in a graphical format. Clicking on any of the category headings will open a pop-up window listing the organisms found in your client’s sample. Each genus listed is also clickable, opening a pop-up window for detailed information, including taxonomy, an overview of known disease or health benefit associations, descendants and metabolomics. Click ‘add/ curate’ to include it in your client’s report.

    Screenshot of Spectrum Profiler

    Metabolomics is a powerful addition to the spectrum profiler that provides a comprehensive list of metabolites associated with GI biome species. A list of all metabolites active in your client is included. Click on an individual metabolite for detailed information, including genera that are enhanced, inhibited, and those which generate the metabolite as an end product. Click on the Metabolomics link to open a pop-up with all active and inactive genera.

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