SCIENTIST STUDYING BLOOD SAMPLE
Integrative Personal ‘Omics’ Profile: Medicine’s Future?
Jacquelyn K. Beals, PhD
April 2, 2012
See Dr. Pinna’s comments below…
NOTE: FOR THE READER’S UNDERSTANDING OF THIS ARTICLE I HAVE TAKEN FROM WIDIPEDIA A LIST OF ALL THE “OMICS”.
THIS IS A NEW AREA IN MEDICINE!
- Cognitive genomics: Examines the changes in cognitive processes associated with genetic profiles. Cognitive processes are very important for human behavior. It is about knowledge and the way people use their knowledge.
- Comparative genomics: Study of the relationship of genome structure and function across different biological species or strains
- Epigenomics: Study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. ChIP-Chip and ChIP-Seq technologies used.
- Functional genomics: Gene and protein functions and interactions (uses microarray kind of techniques)
- Genomics: Study of the genomes of organisms.
- Immunoproteomics: study of large sets of proteins (proteomics) involved in the immune response
- Metabolomics: Scientific study of chemical processes involving metabolites. It is a “systematic study of the unique chemical fingerprints that specific cellular processes leave behind”, the study of their small-molecule metabolite profiles
- Metabonomics: The quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification
- Metagenomics: Study of metagenomes, genetic material recovered directly from environmental samples.
- Nutrigenetics: studies the effect of genetic variations on the interaction between diet and health with implications to susceptible subgroups
- Nutrigenomics: Study of the effects of foods and food constituents on gene expression. Studies the effect of nutrients on the genome, proteome, and metabolome
HERE IS THE ORIGINAL ARTICLE FROM MEDSCAPE:
Researchers from Stanford University in California have compiled a detailed molecular profile of an individual, with the goal of learning how to construct an integrative personal “omics” profile (iPOP), how the profile changes in health and disease, and how to use this information to gauge risk and better understand disease states.
The researchers’ report, published in the March 16 issue of Cell, analyzed the molecular changes observed in health and disease, including the unexpected development of type 2 diabetes during the study.
Group leader Michael Snyder, PhD, chair of the Department of Genetics, Stanford University School of Medicine, provided about 20 blood samples during the 14-month study for iPOP analyses, using peripheral blood mononuclear cells, plasma, and sera.
Although the 14-month study has now been published, the sampling and analysis continue. “Realistically, other things may happen to me over the rest of my life, and we hope to capture those as well,” Dr. Snyder told Medscape Medical News via Skype.
Initial whole-genome sequencing (WGS) of Dr. Snyder’s DNA was performed using several technologies, as was exome sequencing (the part of the genome coding for proteins and other gene products). Overall, his blood samples were analyzed for nearly 40,000 variables, including profiles of 19,000 or more transcripts that carry the information from about 12,000 genes, levels of 4000 proteins, and 5000 metabolite peaks (only 1000 are known).
WGS revealed disease variants associated with emphysema, aplastic anemia, type 2 diabetes, and hypertriglyceridemia, among other diseases. The RiskOGram algorithm, which “integrates information from multiple alleles associated with disease risk,” indicated an elevated risk for coronary artery disease, basal cell carcinoma, hypertriglyceridemia, and type 2 diabetes.
“Right now we’re trying to collect as much information as we can, and we’d like to do this, obviously, with multiple individuals. It may be, at the end of the day, you don’t need to make 40,000 measurements like we did on me,” said Dr. Snyder. However, “for the average person, I still think it’s going to be more than 20 like we do now…. We should be profiling hundreds, if not thousands, kind of routinely as part of an exam.” More information is available that way, he said.
Asked which analyses were most informative clinically, Dr. Snyder laughed. “I know this will sound like a cop-out, but for me, it was best to analyze everything.” The transcriptome found the most information, but if they had only looked at the transcriptome, they would have missed other equally relevant things, he said.
“Some signatures showed up with just the proteomics, and some only showed up with all 3 profiles [transcriptome, proteome, metabolome]…. There’s really more information in all 3 than in any 1 of these alone,” Dr. Snyder added. “We didn’t know that for sure going in, but it was refreshing and somewhat reassuring to see this. It makes sense that you’ll get a more complete picture when you follow everything.”
Goal to Compare Profiles in Health vs Illness
One goal of the study was to compare molecular analyses in health and disease. Dr. Snyder developed 2 viral infections during the study: a rhinovirus infection on day 0, and a respiratory syncytial virus (RSV) infection starting on day 289. Twelve days later (day 301), his glucose levels became elevated. The elevation lasted several months until, based on glucose levels and HbA1c, his physician diagnosed type 2 diabetes on day 369.
“People have associated diabetes with stress responses before, but to the best of my knowledge, not with viral infections. So this was a new angle,” Dr. Snyder noted. “It could be that the virus acted like a stress inducer. Our interpretation of this is that my genome has me predisposed and that, in combination with the viral infection, maybe the stress-response part of the viral infection induced the disease.”
Asked why this infection induced diabetes when previous infections had not, Dr. Snyder said: “This RSV is a pretty nasty one. Another factor may be the case as well: I’m in my 50s and, to be honest, that’s when things break down. It’s quite likely that the combination of being in my 50s, with this viral stress and, again, my genome combination is what triggered it.”
Diabetes should be regarded as “hundreds of diseases,” noted Dr. Snyder. “Some people are insulin-resistant, some aren’t; some respond to metformin, some don’t; some seem to be associated with inflammation, some aren’t.
So I think diabetes probably is many diseases, all lumped together, because the 1 common characteristic is high glucose. I’m hopeful that by doing more of these sorts of studies, we can look at the molecular breakdown of how many types there are, and then be able to better stratify it and better treat it,” Dr. Snyder said.
His vision for these studies was reflected in emails to Medscape Medical News from several experts in the field.
“I foresee that a longitudinal ‘Omics’ study as described in Snyder’s landmark paper will indeed become common in the next 10 to 20 years,” said Jan Korbel, PhD, group leader at the European Molecular Biology Laboratory, Heidelberg, Germany. “A first promising application would be in families with particular hereditary risk factors, where whole-omics profiling could be used to monitor disease onset closely.”
George M. Church, PhD, professor of genetics at Harvard Medical School, Boston, Massachusetts, anticipates that work-ups of this type might become common for individuals in “maybe 4 years.”
Eric J. Topol, MD, professor of translational genomics at the Scripps Research Institute, La Jolla, California, expects that such work-ups could “be common now for select individuals with a rare, disabling, even life-threatening condition. Unlike the Snyder study of 20 serial blood draws…a single assessment is eminently doable and could shed considerable light on root cause and potential targeted therapy.”
“I think it’s going to be the future of medicine,” concluded Dr. Snyder. “I’d love to see medicine in the future be a case where you get a little prick in your finger, just like a diabetes test, and you measure 5000 things instead of 1 thing (just glucose) right now. I’d love to see it be a home test, where you can monitor your own health routinely,” he said. “That’s my vision for medicine in the future.”
Dr. Pinna says…
This article correctly exposes the personal problem of
We are NOT simply human beings. Our cellular make up
combined with an environment of micro-organisms that
live in us and around us is a universe that is distinct from
every other human on the planet.
Every type of micro-organism that exists on this planet
resides in and on our body.
We have viruses and fungi and bacteria on our skin
and inside our vital organs.
When our defenses weaken they attack!
Our own complex universe of cells tries to resist
these attacks. If we have the proper genes and the cells
that derive from those genes, we will be able to defend
The idea that “diabetes” and other diseases are
complicated disorders with a host of causes is unique
As doctors, our treatments are standardized, and
conform to group beliefs.
We wouldn’t dare treat diabetes with anything
but the standard protocol which has been authorized
by the medical community.
BUT THIS IS WRONG!
We should consider the genetic background of
the patient, his or her tendencies, both physical and
mental, and sculpture a treatment that addresses
I know diabetics that love carbs. They have been
raised on rice or potatoes or bread or pasta.
Changing this behavior is almost impossible.
However, modifications can be made.
The best way of modifying risky behavior is
The desire to stay alive and healthy is supreme.
If we can demonstrate, through testing and trials,
what is beneficial and what is detrimental, we can
usually lead the patient or ourselves to the best
potential state of good health.