Peter D'Adamo

  • Opus 23 now supports multiple platforms

    The recent change in the reporting done by 23andMe from the V4 to V5 chip has thrown things into a bit of a dither. The earlier V4 SNP array was more robust, at least with SNPs of interest to those who work in nutrigenomics. For example, V4 reported over ten MAO SNPs of nutritional interest, whist V5 reports none. To circumvent the problem, I’ve recoded Opus 23 to allow the clinician to upload, singly or in combination, data files from 23andMe (V3, V4, V5), Ancestry DNA and the ‘Export to Promethease’ file available from Genos. To move Opus in this direction required a lot of recoding and I thank all our users for their support and patience.

    The first time you load an existing client profile into Opus it will take a bit longer to process the file. This is because they are being upgraded to the new data storage system. After that they should load as usual. Manage->Profiles->Append Raw Data to Current Client will take you to the BLENDER app,which allows you to merge raw data files. This will only be important as people begin to use Ancestry DNA, perhaps in combination with 23andMe V5. Since almost everyone currently in Opus is 23andMe V4 you really don’t need to do anything.

    The ‘Upload New Client Raw Data’ script has been extensively re-written. You still upload a ZIP file, but the script will identify the platform (V3/V4, V5, Ancestry DNA) and let you know. It also now features and extra screen so that you can verify/validate your form input before doing the final upload. Hopefully this will cut down on people contacting us having uploaded the same client twice.

    Uploading and merging  V5 and Ancestry DNA client data have about 74% of Opus-curated snps, while the prior V4 has about 79% coverage.

    If you do upload Ancestry DNA data, be advised that Ancestry names its raw data files in a non-unique manner, usually something like ‘dna-data-2017-09-03.zip’. This blunts the ability of the program to warn you that you are using the same data file on two different clients. You should rename the client raw data ZIP file on your hard drive to something unique (we recommend replacing Ancestry DNA filename with the client’s first and last initials and date of birth; in this case ‘dna-data-2017-09-03.zip’ might become ‘MG-11-22-1956.zip.’ But you can use any system you wish as long as each uploaded filename is unique.

    It looks like the best short term solution will be to have the client do BOTH 23andme V5 and Ancestry.  Opus 23  now allows you to sequentially upload the raw data and merge it. We will eventually move towards a dedicated chip. However this change from v4 to v5 caught everyone (not just Opus/Datapunk) flat-footed as to the huge drop in clinically significant SNPs that are reported in v5. Even in the best of circumstances it will be weeks and months until a specialized chip will become available. However, in the meantime, piggybacking 23andMe v5 with Ancestry DNA appears to be not all that bad of a temporary fix. Many of these SNP panels are having significant price drops, so having the client do bot 23andMe V5 and Ancestry DNA should not be prohibitively expensive.

     

    In Other News

    You can now compare V5, V4, Genos Promethease export, and Ancestry data as compared to the core 2600 Opus snps. Just log in, click the ‘Informatics’ pull down, the select ‘Tools/ Extras’ and “Platform Comparisons’. Table is searchable, sortable and filterable.

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  • Basic and advanced in-person training seminar, May 20-21.

    Most patients improve through committing themselves to lifestyle, diet, mindset and environmental changes. When they don’t, additional history and sleuthing is needed. As our patients get more complex, the need for quickly evaluating thousands of genes is needed. Peter’s Opus23 allows one to do exactly this. I highly recommend using Opus23 for those patients who have ‘tried everything’ and are still stuck. It could very well find the answers to your patient’s riddle.” — Dr. Ben Lynch

    There will be an in-person training at the Center of Excellence in Generative Medicine (University of Bridgeport, Connecticut) for the weekend of May 20-21.

    A weekend training hosted by the Center of Excellence in Generative Medicine at the University of Bridgeport, Bridgeport CT, USA. A rare opportunity to receive hands-on training in Opus23 from Peter D’Adamo, Jacqueline Greenfield and Tom Greenfield, the key developers of the platform.

    SEMINAR DESIGN

    The seminar is a mix of some lecture and extensive hands-on learning. During experiential sessions, attendees will break up into 4-5 person workgroups. Each workgroup will have its own teaching assistant (TA) a GM/COE student with extensive experience with Opus. Attendees will work directly in Opus on a series of different clients.

    Choose between the Level I (basic certification) needed for access to Opus23 or Level II (advanced training) for those who have already completed a basic webinar or seminar.  

    Level I covers the  fundamentals of Opus23: The user interface and design philosophy; the key informatic  apps, and curating a client report.

    Level II covers advanced topics in Opus23:  Advanced informatics apps, microbiome integration, and advanced prescriptives and protocol generation.

    Successful completion of the level I training allows you full access to the Opus23 software, with the ability to upload and analyze raw data from 23andMe and uBiome, and produce notes and patient reports. 

    Cost of the seminar is $800 USD. Proceeds go to the Center of Excellence in Generative Medicine (COEGM) which provides advanced clinical and didactic postgraduate training for the College of Naturopathic Medicine (UBCNM). Because of the hands-on nature of this seminar, seating is limited to 18 attendees.

    Please visit this link to register for the conference via our secure PayPal link.

    SEMINAR SCHEDULE

    The seminar will run from 9AM-5PM Saturday May  20 and 9AM-12 NOON May 21. You should arrive at 8:30AM for registration and to meet your TA. Classes will take  place on the University of Bridgeport campus, at the Center of Excellence in Generative Medicine, 115 Broad Street Bridgeport CT 06604. Lunch will be provided on Saturday at the COEGM as well as dinner at a local restaurant.

    HOTEL/LODGING

    Bridgeport Holiday Inn
    1070 Main Street
    Bridgeport CT 06604
    Phone: 203 334-1234
    Fax: 203 696-1985

    http://www.ihg.com/holidayinn/hotels/us/en/bridgeport/bgdct/hoteldetail

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  • Three new interactive networks

    We’ve added new mapping networks to Opus 23 MAPPER app. The MAPPER app allows you to visualize your client’s genomic data directly in a number of hand-curated pathway maps. In addition to allowing for quick pattern recognition, MAPPER uses combinatorics and graph theory to ascertain certain functional characteristics of genes in the network, based on their position in a web of interconnections. All gene nodes in MAPPER trigger extensive information popup windows.

    TSH Signaling Network

    tsh

    Human thyroid stimulating hormone (TSH) is a glycoprotein secreted by the anterior part of the pituitary gland. TSH plays an important physiological role in the regulation of the hypothalamic-pituitary-thyroid axis by modulating the release of the thyroid hormones from the thyroid gland. TSH is mainly expressed in adenohypophysis , thyroid gland, leukocyte, pituitary gland, stratum basale, stratum corneum, stratum granulosum, stratum spinosum and keratinocyte. Impairment of TSH signal transduction pathway leads to thyroid disorders such as goitre, hypothyroidism and hyperthyroidism, with complex clinical manifestations. T

    Endoplasmic Reticulum Stress and Unfolded Protein Response

    upr

    The endoplasmic reticulum (ER) is a dynamic intracellular organelle with multiple functions essential for cellular homeostasis, development, and stress responsiveness. In response to cellular stress, a well-established signaling cascade, the unfolded protein response (UPR), is activated. This intricate mechanism is an important means of reestablishing cellular homeostasis and alleviating the inciting stress. Now, emerging evidence has demonstrated that the UPR influences cellular metabolism through diverse mechanisms, including calcium and lipid transfer, raising the prospect of involvement of these processes in the pathogenesis of disease, including neurodegeneration, cancer, diabetes mellitus and cardiovascular disease. [PMC3039444]

    AR Signaling Network

    ar

    Androgens, mainly testosterone and 5alpha-dihydrotestosterone (DHT) play significant role in the growth and development of the male reproductive organs. AR is found to be expressed in a number of tissues and cells including prostate, testis, seminal vescicle, epididymis, skin, skeletal muscle, cardiac muscle, liver and central nervous system. The androgen receptor is known to bind to many co-regulators at different time points and in different cell types. This DNA protein complex triggers the expression of various target genes that are associated with the male phenotype. Androgen receptors are known to induce apoptosis under certain conditions. Various regulators that regulate androgen induced apoptosis include BRCA1 and Smad3 and Akt. Mutation in AR are also known to be associated in a number of diseases including spinal and bulbar muscular atrophy (SBMA) or Kennedy’s disease and Androgen Insensitivity syndrome (AIS). Abnormal amplification of the androgen gene as well as deregulation of AR gene expression have been shown to be associated with prostate cancer.

    To learn more about Opus23 training webinars, click here.

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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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