Abstract
Starting with the launch of the Human Genome Project three decades ago, and continuing after its completion in 2003, genomics has progressively come to have a central and catalytic role in basic and translational research. In addition, studies increasingly demonstrate how genomic information can be effectively used in clinical care. In the future, the anticipated advances in technology development, biological insights, and clinical applications (among others) will lead to more widespread integration of genomics into almost all areas of biomedical research, the adoption of genomics into mainstream medical and public-health practices, and an increasing relevance of genomics for everyday life. On behalf of the research community, the National Human Genome Research Institute recently completed a multi-year process of strategic engagement to identify future research priorities and opportunities in human genomics, with an emphasis on health applications. Here we describe the highest-priority elements envisioned for the cutting-edge of human genomics going forward—that is, at ‘The Forefront of Genomics’.
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Acknowledgements
The strategic vision described here was formulated on behalf of the NHGRI. We are grateful to the many members of the institute staff for their contributions to the associated planning process (see http://genome.gov/genomics2020 for details) as well as to the numerous external colleagues who provided input to the process and draft versions of this strategic vision. The National Advisory Council for Human Genome Research (current members are J. Botkin, T. Ideker, S. Plon, J. Haines, S. Fodor, R. Irizarry, P. Deverka, W. Chung, M. Craven, H. Dietz, S. Rich, H. Chang, L. Parker, L. Pennacchio, and O. Troyanskaya) ratified the strategic planning process, themes, and priorities associated with this strategic vision.
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Green, E.D., Gunter, C., Biesecker, L.G. et al. Strategic vision for improving human health at The Forefront of Genomics. Nature 586, 683–692 (2020). https://doi.org/10.1038/s41586-020-2817-4
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DOI: https://doi.org/10.1038/s41586-020-2817-4
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Planning science is futile. Michael Lerman, PhD, MD.
majid ali
The GIO-GENO Vision of Living Well With COVID-19
Majid Ali, M.D.
The writer is encouraged to offer this brief communication concerning the possibility of learning how to live well with COVID-19 by the excellent review of these subjects by Green et al. (ref.1).
In 2006, the writer, the solo author of The Principles and Practice of Integrative Medicine (in 12 volumes) published THE Rooster, the FLU, and the Imperial Medicine (ref.2) in which he precisely predicted in great detail tee prevailing COVID-19 pandemics in the preface of the book. The writer invites the readers to read that free-access preface posted on the writer's FACEBOOK page as well as his website. www.majidali.me
In this brief communication, the writer offers some reflections on learning to live well with COVID-19 now and in coming years.
1. COVID-19 is here to stay just as its innumerable cousins, including 1918 Spanish flu (which claimed over seventy million lives worldwide) and seasonal flu viruses (which visited humankind yearly and claimed an average of 81,000 American lives every three years (according to the official records of CDC) in spite of the ready availability of flu vaccine throughout the country.
2. COVID-19 will keep mutating freely and claiming many lives yearly worldwide, more in some years than in others.
3. The loss of life worldwide (which we have witnessed in 2020) will be dramatically reduced by a radically different vision of human health foreseen and designated "GIO-GenoVision" here and considered earnestly and then accepted by well-informed and enlightened societies world.
4. The GIO-GENO Vision outlined below and published in the form of a monograph will be considered by a growing number of caring, compassionate, and knowledgeable women and men worldwide who have the courage to consider the science and philosophy of holism in health and healing to which the writer devoted his 12-volumes The Principles. and Practice of Integrative Medicine.2004, which gave the writer to envision a different future of World Health Organization (WHO) which will turn the GIO-GENO vision into shared and concerted global effort to reach beyond the prevailing structures of N2D2 Medicine -- a medicine that begins with the name of a disease and ends with the name of a drug.
5. The growing global awareness of the plight of our world's children will compel our world's moms and dads to rise in defense of their children and find the strength to defy the champions of N2D2 medicine and turn to authentic medical scientists of our world in all matters of true science of health and healing and will also turn to authentic truth-seekers of our world about all matters of the needed philosophy of health and healing.
As to the three letters of GIO in the GIO-GENO VISION in the title, they stand for the following:
1. G for Gut bioenergetics (ref.3)
2. I for Insulin bioenergetics (4,5)
3. O: for Oxygen bioenergetics (ref.6,7)
As to the four letters of GENO, they make up an abbreviation of genomics which would come under the auspices of WHO and our truly authentic scientist community.
One more thing, in the writer's GIO-GENO Vision, GIO is an individual's own responsibility since no drugs or vaccines exist for chronic bioenergetic problems related to gut, insulin, and oxygen.
Geno simply is an abbreviation of genomics. Our world is amply blessed with enough truly authentic scientists who are willing and able to accept the challenge of viral genomics as well as of developing vaccines for COVID-19 and its cousin corona viruses in coming years.
COVID-19 Morbidity Problems and GIO Solutions
The next time the readers hear a doctor or public health official speak about COVID-19 morbidities on radio or TV, they are likely to hear the names of following three morbidities at the top of the list:
1. Diabetes (ref.4,5)
2. Asthma and Respiratory disorders (ref,6,8)
3. Immune-inflammatory diseases, such as Crohn’s disease, ulcerative colitis, lupus, rheumatoid arthritis, sarcoidosis, and scleroderma.
On a deeper study of the above subjects, readers will learn that:
1. Diabetes is a disease which results from long-neglected hyperinsulinism (insulin toxicity, by a clearer name) since the prevailing medical standards do not require that a diligent assessment of insulin homeostasis with measurements of serum insulin concentrations in timed post-glucose-challenge blood samples be undertaken for all patients with compromised glucose tolerance and /or the metabolic syndrome (see reference # 1 for details of a 2017 study of insulin homeostasis in 486 patients in the general population of New York metropolitan studies (ref. 1)
2. Asthma is disease largely triggered by allergy to molds and other environmental triggers.
3. Crohn’s disease, ulcerative colitis, lupus, rheumatoid arthritis, and other chronic immune-inflammatory diseases are rooted in altered states of gut ecology and gut microbiome with yeast overgrowth.
4. In the writer’s clinical experience, the above chronic diseasesare best treated by the patients themselves who are willing and able to learn well how to become their own primary physicians – by diligent personal studies and experience with natural remedies and spiritual healing.
5. Crohn’s disease, ulcerative colitis, rheumatoid arthritis, and other chronic immune-inflammatory lupus, c
COVID-19 pandemic have taught many of us crucial lessons. The two most important lessons it taught this writer are:
1. COVID-19 relishes human tissues and organs that are low on oxygen and high on acids. Here are two is important questions: (1) What is common among the COVID-19 comorbidities listed above which are held responsible for COVID fatalities: You got it right: Body organs in all of them are low in oxygen and high on acids; and (2) Are their simple, low-cost foods, spices, herbs, home-remedies, and self-regulatory healing practices that can increase oxygen in low-oxygen body organs, and decrease acids in high-acid tissues and organs. Again, you right, if your answer is yes.
Below are some general comments about the areas I which genomics play crucial roles. Here again, the honest answers based on authentic knowledge encourage those of us willing and able to recognize their God-given love for knowledge. The writer suggests that readers consider the excellent review of these subjects by Green et al (ref.1)
COVID-19 is an ultrascopic tiny string of a natural compounds called nucleic acids which exist in the cells in all of us. Yet, when we allow our tissues and body organs to become low in oxygen and high in acids can wreak global havoc on humankind. In this monograph, the writer reveals what thousands of his teachers taught him about oxygen and acids, and health and healing.
Yes, the writer did say ‘thousands of his teachers.’ For five decades, he considered his patients his best teachers, not professors, not medical experts, not even the books they wrote. The single most important lesson my patients taught me is this: The truest teachers any physician can have are her /his patients. That, for this writer, is the truest of all truths in healing arts and sciences.
The writer offers information about how to increase oxygen in oxygen-depleted in our body tissues and organs. Understanding the mechanisms involved in the transmission of the virus, viral invasion and clearance, as well as the highly variable and at times disastrous physiological responses to infection, are fertile grounds for genomics research. Genomics rapidly assumed crucial roles in COVID-19 research and clinical care in areas such as (1) the deployment of DNA- and RNA-sequencing technologies for diagnostics, tracking of viral isolates, and environmental monitoring; (2) the use of synthetic nucleic acid technologies for studying SARS-CoV-2 virulence and facilitating vaccine development; (3) the examination of how human genomic variation influences infectivity, disease severity, vaccine efficacy, and treatment response; (4) the adherence to principles and values related to open science, data sharing, and consortia-based collaborations; and (5) the provision of genomic data science tools to study COVID-19 pathophysiology. The growing adoption of genomic approaches and technologies into myriad aspects of the global response to the COVID-19 pandemic serves as another important and highly visible example of the integral and vital nature of genomics in modern research and medicine.
Reaching agreement on the appropriate terminology for long COVID is key, says Felicity Callard, a human geographer at the University of Glasgow,UK, who also has long COVID. Callard and Alwan are among a group of researchers who have experienced long COVID — and who last week wrote a blog post for the British Medical Journal (go.nature.com/2sv47wr), urging the research and medical communities to start using the term long COVID, instead of some of the alternatives. Words such as ‘post’, ‘syndrome’ and ‘chronic’ risk delegitimizing suffering, the authors argue, and that will make it harder for people to access care.
Such terms also carry assumptions about the condition’s underlying physiology that have not yet been properly investigated. Long COVID, by contrast, states clearly that people’s experience of illness after infection is long, but it doesn’t presume to know anything else, Callard says.
It seems the WHO is listening. In August, director-general Tedros Adhanom Ghebreyesus told a meeting of COVID patient groups: “We have received your SOS. We have heard loud and clear that long COVID needs recognition, guidelines, research and ongoing patient input and narratives, to shape the WHO response from here on.”
Public-health authorities, too, are taking note — and some have started to use the term long COVID. Researchers, clinicians and funders must also consider how they will refer to the illness, and how to more accurately define recovery from COVID-19.
And they must always give proper consideration to the voices of people with COVID-19 and their representatives, who have done so much to put long COVID on the health-research and policy agenda.
In 1980, the author coined the term bowel ecology in a monograph entitled Altered States of Bowel Ecology17 to underscore the need for ecologic thinking in clinical medicine. That book was devoted to ecologic considerations and concepts in the investigation of the pathogenetic mechanisms underlying common metabolic, infectious, allergic, autoimmune, inflammatory, neurodevelopmental and degenerative disorders.
In 1998, the author reported mitochondrial dysfunction and mycotoxicosis in a four-year-old-boy with autism.18 In 2000, he published Oxygen and Aging,3 a volume devoted to molecular biology of oxygen, focusing on dysfunctional oxygen signaling in diverse clinicopathologic entities. The book opened with the following words: ”Oxygen is the organizing principle of human biology and governs the aging process.” The body of work covered in this volume delineated some previously unappreciated dimensions of oxygen bioenergetics.
In 2004, in his first column on molecular biology of oxygen in Townsend Letter, he presented evidence for respiratory-to-fermentative shift in ATP generation in diverse chronic immune-inflammatory disorders accompanied by persistent fatigue (ref. 2)
To facilitate communication, the author borrowed the word GIO (made up of the first three letters of (gut, insulin, and oxygen) from Punjabi, his mother’s tongue to collectively refer to the three classes of adverse bioenergetic factors that were found to be associated, singly or in concert, with autism in nearly all study subjects, namely those that disrupt gut bioenergetics, insulin bioenergetics, and gut bioenergetics. In Punjabi, it may be added here that GIO is a commonly used prayer word for long purposeful life.
In 2015, in a seminal paper, the journal Nature24 fully validated the author’s mitochondrial findings previously reported in his initial Townsend column on oxygen homeostasis.4 Spurred by the findings of the Nature paper, the author reviewed mitochondrial data for an additional 315 patients with diverse immune-inflammatory disorders accompanied by persistent fatigue, and concurrently published data of 2004 and 2015 reports in one of his subsequent Townsend columns.25 High level of concordance of Krebs cycle data obtained in two studies done eleven years apart (Table 1) is noteworthy. It strengthens the inferences drawn from the data concerning the clinical value of mitochondrial approach to functional assessment of molecular biology of oxygen in individual patients. Note that increased retention of specific Krebs cycle metabolites, as quantified by their 24-hour urinary excretion, in general follows the order of their generation in the Krebs cycle, suggesting a global pattern of mitochondrial functional impairment resulting from by cumulative disrupting effects of diverse factors rather than regional mitochondrial deficits pointing to specific individual disrupting agents, such as discrete chemical toxins or microbiologic agents. This pattern adverse general pattern supports the author’s increasing appreciation of the clinical value of 24-hour urinary excretion of Krebs cycle metabolites as markers of global mitochondrial dysfunction, status of oxygen homeostasis and oxygen-driven body bioenergetics.
Bold predictions for human genomics (excerpted from an excellent review of the subjects by Green et al. (ref.1)
Some of the most impressive genomics achievements, when viewed in retrospect, could hardly have been imagined ten years earlier. Here are ten bold predictions for human genomics that might come true by 2030. Although most are unlikely to be fully attained, achieving one or more of these would require individuals to strive for something that currently seems out of reach. These predictions were crafted to be both inspirational and aspirational in nature, provoking discussions about what might be possible at The Forefront of Genomics in the coming decade.
1. Generating and analysing a complete human genome sequence will be routine for any research laboratory, becoming as straightforward as carrying out a DNA purification.
2. The biological function(s) of every human gene will be known; for non-coding elements in the human genome, such knowledge will be the rule rather than the exception.
3. The general features of the epigenetic landscape and transcriptional output will be routinely incorporated into predictive models of the effect of genotype on phenotype.
4. Research in human genomics will have moved beyond population descriptors based on historic social constructs such as race.
5. Studies that involve analyses of genome sequences and associated phenotypic information for millions of human participants will be regularly featured at school science fairs.
6. The regular use of genomic information will have transitioned from boutique to mainstream in all clinical settings, making genomic testing as routine as complete blood counts.
7. The clinical relevance of all encountered genomic variants will be readily predictable, rendering the diagnostic designation ‘variant of uncertain significance (VUS)’ obsolete.
8. An individual’s complete genome sequence along with informative annotations will, if desired, be securely and readily accessible on their smartphone.
9. Individuals from ancestrally diverse backgrounds will benefit equitably from advances in human genomics.
10. Breakthrough discoveries will lead to curative therapies involving genomic modifications for dozens of genetic diseases.
References
1. Green ED, Gunter C, Biesecker LG, et al.Nature. 2020;586:683-692.
2. Ali M. The Rooster, the FLU, and the Imperial Medicine of the New Empire. 2000. Life Span Press. Denville, New Jersey.
3. Ali M. Altered States of Bowel Ecology (monograph) 1980). Holy Name Hospital, Teaneck, New Jersey.
4. Ali M. Fayemi AO, Shifting focus from glycemic status to insulin homeostasis for stemming global tides of hyperinsulinism and type 2 diabetes. Townsend Letter for Alternative Therapies. 2017;1:91-96.
5. M. Dysox model of diabetes and de-diabetization potential. Townsend Letter for Alternative Therapies. 2007;286:137-145
6. Ali M. Oxygen and Aging. life Span Press. 2000. Denville, New Jersey.
7. Ali M. Darwin, Dysox, and Disease. 2002. Life Span Press, Denville, New Jersey.
8. Ali M. Respiratory-to-fermentative shift in ATP generation in Chronic Immune-inflammatory Diseases with persistent fatigue. Townsend Letter for Alternative Therapies. 2004;253: 64-65.