The Holistic Genome

The Holistic Genome – blog

Brains, DNA and Direct to Consumer Genetic testing

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In the recent months, I have had the unfortunate (and humbling) experience of being on the receiving end of healthcare.  While laying in the MRI machine today, I have come to an important conclusion regarding direct to consumer genetic testing.  As I left the radiology suite today, I was offered a copy of my scans on a CD-ROM.  I realized that patients, myself included, have come to expect this practice.  (Especially, if the patient pays for most if not all of the scan themselves).  After all, it is my body being scanned and I was paying for (at least in part) the service.

These CD-ROMs which contain the radiology images are not unlike the results from direct to consumer genetic testing companies.  These images are composed of a bunch of ones and zeros, just like out DNA is composed of A,G,T and C s. Many of these radiology CD-ROMs even include software for viewing these images and I, like many other patients, rushed home to look at them.

How should the interpretation of these ones and zeros be regulated?  What if there is a computer algorithm analyzes my brain images and is able to calculate my hat size … my brain volume … my personality score … my risk for brain cancer?  It is a slippery slope, my friend.

My point is our DNA sequence, just like the images from a radiologic scan, is just data.  A bunch of ones and zeros, or A, G, T and C s.  I have trust in the licensed and board certified radiologist who will interpret this data and I have faith in the credentialing process.   ( disclaimer: I am a doctor, remember)

Hands down, I think that patients should have access to their own genetic data.

However, when a person, or company (shielded by a computer algorithm), makes interpretations about this data which has clinical implications, such as being a carrier of a disease or how one metabolizes drugs, then like it or not that is ‘practicing medicine’ and should be regulated accordingly.  Problem is… who?

Listening to the recent open meeting held by the FDA about laboratory developed tests, it is my opinion that analytic validity should be separated from clinical utility when it comes to direct to consumer genetic testing.  The real argument is in the interpretation of the data, either by qualified experts, or increasing, by smart algorithms.  ( disclaimer : I am a biomedical informatician creating these smart algorithms and I am not keen on regulation. )

The real problem is that the FDA does not have the resources to regulate software or computer algorithms, nor is it in their mission to do so.  Well… if not the FDA, then who?

My guess… Certification Commission for Health Information Technology or CCHIT, but they only just formed a few years ago.  And as the saying goes, ” The horse is out of the barn!”


Written by Jonathan Holt, DO

July 21, 2010 at 7:57 pm

Posted in DTC, genetic testing

International classification of health codes – ICH 1

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iStock_000007804869XSmall.jpg Have you ever wondered why we have the International Classification of Disease codes, or ICD for short, but we don’t have an International Classification of Health? This is a major short-coming! Really! How are we to understand the significance genomic contributions towards our health, unless we have a standardized why to describe it? This goes back to my prior discussion, what is Health? It can’t just be the absence of disease!

The ICD codes have been around for a while and we are on the 9th iteration. Mostly they are used for billing purposes for insurance companies to approve or deny coverage. However, during my experiences with billing, I found it frustrating to try to classify a patient as ‘Healthy’. The only way I was able to get reimbursed from the insurance company was if I found something wrong with them. This is a fundamentally conflicting philosophy if my mission was to keep them well!

Ergo, I propose that we concentrate our efforts for a structured vocabulary to take Health into consideration and I therefore declare the start of the ICH codes, International Classification of Health, version 1 – ICH-1. Anyone want to help me?

Written by Jonathan Holt, DO

August 4, 2009 at 9:50 am

Posted in health, holism

The low hanging fruit in the garden of good and evil.

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low hanging fruit

low hanging fruit

I have been told that cancer genetics is the ‘low hanging fruit’ of personalized medicine. 

I have my reservations about this analogy.  As you all know, I am a big proponent of personalized medicine.  And I also remain optimistic that personalized medicine will be a fruitful and rewarding endeavor.  However, part of me is concerned that we are like ants picking away at the fruit of the tree of life.  This sacred tree that hold the source code of life, that which holds our very identity… that which make us unique.  Perhaps we should be more mindful of our actions and how we conduct ourselves during this technological adolescence.  Sometimes, I think that the Genomic era is much like a modern day Gold Rush with everyone climbing over each other in a mad dash to stack their claim to the bounty. 

By seeking the true knowledge of ourselves within our DNA, we seek a deeper understanding of ourselves and our place in the Universe, both from a Darwinian as well as a spiritual viewpoint.  To this end, we should remind ourselves to walk uprightly, square our actions and walk confidently in this garden of good and evil motivated by the search of truth and not by material gain.       

Written by Jonathan Holt, DO

April 20, 2009 at 11:44 am

Mercerism and the pursuit of knowledge

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Much like the plight of Wilbur Mercer or Sisyphus, I have been faced with a challenging uphill-battle in my pursuit of knowledge and enlightenment.  Much like Wilbur Mercer, I feel like I am being pelted with stones as I struggle uphill only to have the struggle recur over and over again.  More recently, I have had to wait out a powerful financial storm that has temporarily halted my accent of the sacred mountain of knowledge.  As such, I have plotted an alternative course to better prepare me for this task.  

The pursuit is a noble one and its rewards are open to all those who seek it. This journey has truly been character building. However, I have come to realize that it is not without its sacrifices and difficulties. It is true that Personalized Medicine is gaining popularity. Even President Obama administration has a plan that hopes to modernize our use of electronic medical records and personalize medical therapies.

Personalized Medicine really does have a chance of revolutionizing the way that we practice medicine. I honored to be accompanied by others who seek the knowledge and experience to usher in this new paradigm of personalized medicine.

I am hoping that once I climb this sacred mountain that I will find the old wise man who will be able to impart wisdom and knowledge onto me.  Perhaps, I will find myself alone at the top, only to realize that the wise man that I sought is really myself.

Written by Jonathan Holt, DO

March 15, 2009 at 9:21 pm

Nature verses nurture

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Life is about balancePut simply….  life is about balance!

We see it in our everyday life.  Work and play, day and night, life and death, mind and body…. etc.

We are born from an already vast collection of information that has taken billions of years to evolve. 

Our genes are a blue print that start us off and our environment nurtures us and allows us to thrive to reach our fullest potential.  Thus life could be considered the complex interactions between genes and the environment. 

I see it everyday in the delicate art of practicing medicine.  I advise all of my patient to find balance in their lives.  My mantra has always been …  Work less, eat healthy, relax more, exercise more, find balance. 

I also see it when I prescribe medications, too much medication they have an adverse reaction, not enough and they are under-treated.  Find balance. 

Thus I have come to the conclusion that life is about balance.  It was once said that, “Life is the blended harmony of the yin and yang”

The yin-yang is an appropriate symbol for the struggle to find this balance.  It represents the two sides of the equation, yet both in balance.  And at the center of the other you find its opposite.  Yin and yang are complementary opposites within a greater whole.

Written by Jonathan Holt, DO

December 23, 2008 at 8:19 am

Posted in health, holism, spirit

Reductionism is dead! Long live Reductionism!

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istock_000006766876xsmall1The western philosophy of science has long been depended upon reductionism. To put it simply; in order to understand a complex system some reduce it to more manageable parts.

Reductionist thinking is the basis of many areas of modern science.  Biology and chemistry being a subset of physics, for instance.  Or trying to identify the smallest subatomic particle, such as what we are trying to do with the Hadron collider.  

Western medicine has, over the millennia, attempted to adapt to a more rigorous scientific primer,  and as a consequence, adopted reductionism as it’s foundational philosophical approach.  However, we, in medicine, know that there are so many things that we do that is such an art and not a science … from the empathy and compassion that we show, to holding someone’s hand when they need it or just listening to a patient without interrupting. 

Moreover, medicine is more than the sum knowledge of applied biology and chemistry.  It is social, psychological, spiritual and at times, existential.  A patient is more than the sum of their parts. Why should their genes be any different? 

Reductionism does do it’s job for us in science.  We are, after all, human, and we can’t simultaneously comprehend the larger whole and how everything interconnects.  However, we must know it’s limitations. 

We should be mindful about the bigger picture.  We must realize, we are not just the sum of our parts!  We are more that it!  We have a mind, a body and a spirit. 

Genomics should be no different.  We should approach the integration of genomic information into the clinical practice of medicine as yet another modality that facilitates expression of this magnificent art of medicine and not use it to divide us, or place us into bins! 

“Wherever the art of medicine is loved, there is also a love of humanity!” 

                                                                               Hippocrates, c. 400BC

Written by Jonathan Holt, DO

December 2, 2008 at 10:26 pm

Posted in holism, spirit

Family History

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Family Medical History

As you gather with your family to give thanks, perhaps it is a good time to talk about the family tree and discuss your family’s medical history.

Some direct-to-consumer genetic testing companies try to argue that their services are a replacement for a family history.   I strongly disagree. 

However, I am always amazed at the lack of knowledge my patients have regarding their family’s medical history. I have rarely seen a compete and thorough family history documented in a primary care chart. 

Why is this?

Partly, busy primary care physician do not have the time it take to take a thorough family history. It takes on average 9 minutes, but average new appointment time is only 15-20 minutes.  

There is also the concern regarding the security of family member records being stored in a patient’s medical record. 

I have also noticed that this is because it just not discussed or family members are ashamed to discuss it, or the details get lost in translation.  A family history of ‘stomach cancer’ which was only revealed to be ‘ovarian cancer’ suddenly changes my approach in the setting of associated cancers such as Breast Cancer. The specifics on the type of cancer can very helpful.  I have at time resorted to getting death certificate documentation for the actual cause of death, when this is necessary.  A great service is call Vitalchek where your can order these documents electronically. 

There is also a great tool offered by the United State’s Surgeon General’s website that helps families input their family’s medical history and makes it downloadable and accessible.  

So, at this time of reflection, take a moment to share this with your family and have a discussion around the dinner table.  

Happy Thanksgiving!

Written by Jonathan Holt, DO

November 27, 2008 at 12:54 pm