PAXgene Protocol: “Letting the genomics out of the bottle”

In 2011, I began seeking collaboration with docs around the country to expand the genomic data base for chronic illnesses like CFS, fibromyalgia, Lyme and mold, among others. This effort ran into all kinds of seemingly trivial regulatory roadblocks that it has taken a year to get to the point where I can now say, “Let’s get started.”

The idea is simple enough. For patients with a chronic, multi-symptom, multisystem illness, let’s look at a one tube of blood that can show us a collation of 1700 genes (out of over 22,000) and let that look tell us what is really going on metabolically.  As you will see, the tools that we now use-symptoms, labs, response to selected treatment-are just a small fraction of what we can see with differential gene activation and/or suppression.

The beauty of the genomics approach to CFS and its related illnesses is that by combining history, physical, differential diagnosis, lab assessment (proteomics) and gene assessment together we can now get all the best of what the diagnostic and therapeutic worlds have to offer.

It has taken over five years of clinical work to get to this point.  Excited in Pocomoke? You bet! If you are willing to share the excitement of the journey of discovery, the patient improvements are sure to follow.

We invite you to join us!

For the first time we are reaching out to physicians who might be interested in participating in our genomics testing program.  By using mRNA (and micro RNA) isolated from special blood tubes called PAXgene tubes we can look at precise gene activation (and suppression) found in given illnesses. We know that such differential gene activation provides a unique fingerprint for a variety of biotoxin illness including those associated with mold, ciguatera and Lyme.  We are working on developing a registry of genomic results seen in patients exposed to mycotoxins or harboring biofilm-formers like the MRCoNS.  We are seeking to show that control patients in Pocomoke, Md and Charleston, SC, for example, are no different from those in Piscataway, NJ or Encinitas, CA. If you are interested in working with us on this program, send us a fax (410) 957-3930 on your letterhead and we will be happy to contact you by phone to discuss your participation.

For physicians participating in genomics testing with this office, we will send PAXgene tubes in sets of four.  Physicians can then choose two cases and two controls for their first four samples to send back to us for genomic testing (at no charge).  When you send us filled PAXgene tubes (please use FedEx, placing the samples on enough dry ice to keep them frozen) on two cases and two controls, together with a copy of their biotoxin labs (HLA DR by PCR; C4a run by Quest, never by LabCorp; TGF beta-1; and a nasal culture done by Diagnostic Lab Medicine) and a brief clinical summary. Upon receipt, we will forward the tubes to the lab that will do the genomics assays.  Then, we will send you four more PAXgene tubes if you want to continue with this venture.  You can send as many filled PAXgene tubes to us as you choose as long as there are at least two controls in every four samples.

The control assays will be run first to assess adequacy of mRNA and quality control.  We don’t expect any problems if the three-step protocol (“invert, develop, freeze”) outlined below is used, as using the PAXgene tubes essentially is foolproof, but we have to verify acceptability of the specimens. We expect to be able to send participating physicians individual reports in six weeks, but this new venture will likely have a “learning process,” so the time to send reports isn’t guaranteed. The cases will be analyzed several different ways so it may take 6-8 weeks before those results are available. Rest assured that you will get them as soon as practical.

We expect to provide quicker turnaround time as this program unfolds. The results of our first efforts are likely to determine what we do with our following efforts.  We have nearly 2000 PAXgene tubes in our freezers now, so when I say there is a lot to learn, I really mean it!

We hope that by providing you with results of the genomics test that there will be questions and stimulus for more questions and research.  Yes, we are dedicated to helping patients, but I feel that a big part of that effort is to first work with physicians to improve  our knowledge base of this fascinating subject of genomics!!

Frequently Asked Questions:

1. Who pays for the dry ice and FedEx shipping costs?

We will reimburse you.  Please send us receipts with the samples. We can’t fund the sots up front.

2. How long do I have to send controls before I send more than two case samples?

Pair each two cases with two controls and send in one batch for the first three batches.  After that we think that we can open up the program to accept more cases than controls.

3. How do I know if a person is a control?

They should be healthy without prior biotoxin illness.  They should not have any illnesses that are not out of control.  So a diabetic sample is OK provided that A1C hemoglobin is less than 6.5, for example.  For controls, we need a symptom roster, HLA DR, C4a and TGF beta-1.

4. What if I have started to treat a patient, can I still send a PAXgene tube?

Yes, just tell us where the patient is in the therapeutic protocol. We will need baseline labs (before treatment) and also current labs if treatment is underway.

5. What if my person has an inflammatory illness, not a biotoxin illness?  Can you use samples from people with RA or ulcerative colitis for example?

Sure, but those assays won’t be run as quickly as the biotoxin cases. We still need the same labs, however.

6. Where can I read about the genomics testing you are doing?

We can send you a bibliography by email but the actual protocol we use isn’t published yet.

7. Will I be recognized in your genomics paper as a contributor?

Yes, if you agree to list your name, you and your practice will be recognized.

8. What kind of preparation do we have to do with the PAXgene tubes?

The tubes stay at room temperature until they are drawn.  Fill with venous blood and invert 10 times (turn upside down and right side up a total of 10 times each) immediately after the draw.  The PAXgene tube should be the last one drawn in a given blood draw so the mixing can be done without delay.  Store the tube at room temperature upright for 4 hours.  This “development” step should not be postponed so that if you draw a tube on Friday afternoon, someone needs to finish processing on Friday night.   After development, write the number of hours on the tube and store the tube in a freezer (please don’t use frost-free freezers!). The tube can be saved almost indefinitely.

9. What do I do if I have more questions?

Call us at 410-957-1550.  Barbara Gray is the lab coordinator but any of us will be happy to help you if Barbara isn’t in the office.

10. What is the purpose of these genomics tests?

We feel that genomics is part of the “final diagnostic frontier” and hope that new answers to questions old (and new!) will follow. The idea is that genomics cure is the ultimate treatment cure. Our initial results are exciting, yet we must verify that our controls are consistent.

11. What happens when the funding for testing these samples dries up?

The program may end or a fee might be charged for the testing.  Don’t delay!

The funding for this program is in place until Christmas 2012.  We would like to tell you that the money will be there next year, but as yet the donor hasn’t told us that she will continue.  The cost for these genomic tests is over $800 each, so please send your samples in quickly!