Posts Tagged ‘genomics screen’

1:00PM 11/13/2014 – 10th Annual Personalized Medicine Conference at the Harvard Medical School, Boston

REAL TIME Coverage of this Conference by Dr. Aviva Lev-Ari, PhD, RN – Director and Founder of LEADERS in PHARMACEUTICAL BUSINESS INTELLIGENCE, Boston

1:00 p.m. Panel Discussion Genomics in Prenatal and Childhood Disorders

Genomics in Prenatal and Childhood Disorders


David Sweetser, M.D., Ph.D.
Unit Chief, Division of Medical Genetics; Attending Physician in Pediatric Hematology/Oncology,
Massachusetts General Hospital for Children

Genomics revolutionized medicine and genetic variation in a larger scale

Cases one on Causing Autism – mutations in a gene of synapse formation, clinical trials

Treatment: IGF1

Genetics: embryo – implant only the healthy embryo – newborn comprehensive genetics testing in the medical record integrated – Standard language of GENE-DRUG interaction not only drug-drug interaction

Potential Harms: May or may not happen disease – stigma issues

Explaining to parents the conditions is very difficult for MDs


3. Diana Bianchi, M.D.
Executive Director, Mother Infant Research Institute;
Vice Chair for Research and Academic Affairs,
Department of Pediatrics; Attending Geneticists and Neonatologist;
Natalie V. Zucker Professor, Tufts University School of Medicine

Medical Geneticist – Pediatrics

  • Prenatal screening and diagnosis – chromosomal abnormality – Down Syndrome, testing is more precise 70% fewer procedures to correct defects due to screening prenatally.
  • Prenatal diagnostics — patient is not in front of us, ultrasound examination, options to terminate pregnancies, genetic counseling — changed due to Genomics
  • Prenatal treatment to down syndrome before the birth – Transcriptomic approach, treat the fetus prebirth
  • Standard of care – all pregnant women – must receive from MD the option for screening for down syndrome, it is a test positive or negative
  • NOW – DNA allows to test for  fetal sex, chromosome in maternal circulation fetal and maternal genetics — Mother may have chromosomal variation
  • high false positive – DNA for Down Syndrome, 97% effective Micro duplication only 5%
  • genetics information protection act – sue prospective employer using Genome, life insurance issues
  • most data available is on Down Syndrome, of all parents informed of a fetus with Down Syndrome – 40% continues the pregnancy
  • accuracy in testing, offering choice and treatment are LEADING principles NOT elimination of a disease (i.e. down syndromes)

for reference see Prenatal Treatment of Down’s Syndrome: a Reality?

and ref list by Dr. Bianchi

2. Holmes Morton, M.D. @ClinicSpecChild
Medical Director, Clinic for Special Children

Small population in Lancaster, PA – risk for untreatable disease 52,000 screens 4.2 millions in US are screened Target mutation analysis, diagnosis very effectively. Harrisburg, PA – small scale natural history studies

Carrier testing offered in 70s. Discourages  from marriage, culture reaction is different. Working in the community, clinical practice using exon sequencing, combine population genetics and molecular biology.Translate Genomics to Clinical, small number of risk factors

History of genetics in population important to establish treatment

Upon birth, affected newborns get matching bone marrow transplant, thus, bypass stem cells – Gene therapy is another thing

1. Benjamin Solomon, Ph.D., M.D.
Chief, Division of Medical Genomics,
Inova Translational Medicine Institute

Longer term, statistical model in asthma research,  rigorous process on patient consent, life insurance, mutation that parents also have. Consequences: actionable findings are communicated
135 Genes – sequencing for some conditions

Questions from the Podium

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 What is the key method to harness Inflammation to close the doors for many complex diseases?


Author and Curator: Larry H Bernstein, MD, FCAP


The main goal is to  have a quality of a healthy life.

When we look at the picture 90% of main fluid of life, blood, carried by cardiovascular system with two main pumping mechanisms, lung with gas exchange and systemic with complex scavenger actions, collection of waste, distribution of nutrition and clean gases etc.  Yet without lymphatic system body can’t make up the 100% fluid.  Therefore, 10% balance is completed by lymphatic system as a counter clockwise direction so that not only the fluid balance but also mass balance is  maintained. Finally, the immune system patches the  remaining mechanism by providing cellular support to protect the body because it contains 99% of white cells to fight against any kinds of invasion, attack, trauma.

These three musketeers, ccardiovascular, lyphatic and immune systems, create the core mechanism of survival during human life.

However, there is a cellular balance between immune and cardiovascular system since blood that made up off 99% red cells and 1% white blood cells that are used to scavenger hunt circulating foreign materials.   These three systems are acting with a harmony not only defend the body but provide basic needs of life.  Thus, controlling angiogenesis and working mechanisms in blood not only helps to develop new diagnostic tools but more importantly establishes long lasting treatments that can harness Immunomodulation.

The word inflammation comes from the Latin “inflammo”, meaning “I set alight, I ignite”.

Medical Dictionary description is:

“A fundamental pathologic process consisting of a dynamic complex of histologically apparent cytologic changes, cellular infiltration, and mediator release that occurs in the affected blood vessels and adjacent tissues in response to an injury or abnormal stimulation caused by a physical, chemical, or biologic agent, including the local reactions and resulting morphologic changes; the destruction or removal of the injurious material; and the responses that lead to repair and healing.”

The five elements makes up the signature of  inflammation:  rubor, redness; calor, heat (or warmth); tumor swelling; and dolor, pain; a fifth sign, functio laesa, inhibited or lost function.   However, these indications may not be present at once.

Please click on to the following link for genetic association of autoimmune diseases (Cho Et al selected major association signals in autoimmune diseases) from Cho JH, Gregersen PK. N Engl J Med 2011;365:1612-1623.

Inflammatory diseases grouped under two classification: the immune system related due to  inflammatory disorders, such as both allergic reactions  and some myopathies, with many immune system disorders.  The examples of inflammatory disorders  include Acne vulgaris, asthma, autoimmune disorders, celiac disease, chronic prostatitis, glomerulonepritis, hypersensitivities, inflammatory bowel diseases, pelvic inflammatory diseases, reperfusion diseases, rheumatoid arthritis, sarcoidosis, transplant rejection, vasculitis, interstitial cyctitis, The second kind of inflammation are related to  non-immune diseases such as cancer, atherosclerosis, and ischaemic heart disease.

This seems simple yet at molecular physiology and gene activation levels this is a complex response as an innate immune response from body.  There can be acute lasting few days after exposure to bacterial pathogens, injured tissues or chronic inflammation continuing few months to years after unresolved acute responses such as non-degradable pathogens, viral infection, antigens or any  foreignmaterials, or autoimmune responses.

As the system responses arise from plasma fluid, blood vessels, blood plasma through vasciular changes, differentiation in plasma cascade systems like coagulation system, fibrinolysis, complement system and kinin system.  Some of the various mediators include bradykinin produced by kinin system, C3, C5, membrane attack system (endothelial cell activation or endothelial coagulation activation mechanism) created by the complement system; factor XII that can activate kinin, fibrinolysys and coagulation systems at the same time produced in liver; plasmin from fibrinolysis system to inactivate factor Xii and C3 formation, and thrombin of coagulation system with a reaction through protein activated receptor 1 (PAR1), which is a seven spanning membrane protein-GPCR.   This system is quite fragile and well regulated.  For example activation of inactive Factor XII by collagen, platelets, trauma such as cut, wound, surgery that results in basement membrane changes since it usually circulate in inactive form in plasma automatically initiates and alerts kinin, fibrinolysis and coagulation systems.

Furthermore, the changes reflected through receptors and create gene activation by cellular mediators to establish system wide unified mechanisms. These factors (such as IFN-gamma, IL-1, IL-8, prostaglandins, leukotrene B4,  nitric oxide, histamines,TNFa) target immune cells and redesign their responses, mast cells, macrophages, granulocytes, leukocytes, B cells, T cells) platelets, some neuron cells and endothelial cells.  Therefore, immune system can react with non-specific or specific mechanisms either for a short or a long term.

As a result, controlling of mechanisms in blood and prevention of angiogenesis answer to cure/treat many diseases  Description of angiogenesis is simply formation of new blood vessels without using or changing pre-existing capillaries.  This involves serial numbers of events play a central role during physiologic and pathologic processes such as normal tissue growth, such as in embryonic development, wound healing, and the menstrual cycle.  However this system requires three main elements:  oxygen, nutrients and getting rid of waste or end products.

Genome Wide Gene Association Studies, Genomics and Metabolomics, on the other hand, development of new technologies for diagnostics and non-invasive technologies provided better targeting systems.

In this token recent genomewide association studies showed a clear view on a disease mechanism, or that suggest a new diagnostic or therapeutic approach particularly these disorders are related to  genes within the major histocompatibility complex (MHC) that predisposes the most significant genetic effect.  Presumably, these genes are reflecting the immunoregulatory effects of the HLA molecules themselves. As a result, the working mechanism of pathological conditions are revisited or created new assumptions to develop new targets for diagnosis and treatments.

Even though B and T cells are reactive to initiate responses there are several level of mechanisms control the cell differentiation for designing rules during health or diseases. These regulators are in check for both T and B cells.  For example, during Type 1 diabetes there are presence of more limited defects in selection against reactivity with self-antigens like insulin, thus, T cell differentiation is in jeopardy.  In addition, B cells have many active checkpoints to modulate the immune responses like  pre-B cells in the bone marrow are highly autoreactive yet they prefer to stay  in naïve-B cell forms in the periphery through tyrosine phosphatase nonreceptor type 22 (PTPN22) along with many genes play a role in autoimmunity.  In a nut shell this is just peeling the first layer of the onion at the level of Mendelian Genetics.

There is a great work to be done but if one can harness the blood and immune responses many complex diseases patients may have a big relief and have a quality of life.  When we look at the picture 90% of main fluid of life, blood, carried by cardiovascular system with two main pumping mechanisms, lung with gas exchange and systemic with complex scavenger actions, collection of waste, distribution of nutrition and clean gases.  Yet, without lymphatic system body can’t make up the 100% fluid.  Therefore, 10% balance is completed by lymphatic system as a counter clockwise direction so that not only the fluid balance but also mass balance is  maintained. Finally, the immune system patches the  remaining mechanism by providing cellular support to protect the body because it contains 99% of white cells to fight against any kinds of invasion, attack, trauma.


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Inflammation Genomics

Kocarnik JM, Pendergrass SA, Carty CL, Pankow JS, Schumacher FR, Cheng I, Durda P, Ambite JL, Deelman E, Cook NR, Liu S, Wactawski-Wende J, Hutter C, Brown-Gentry K, Wilson S, Best LG, Pankratz N, Hong CP, Cole SA, Voruganti VS, Bůžkova P, Jorgensen NW, Jenny NS, Wilkens LR, Haiman CA, Kolonel LN, Lacroix A, North K, Jackson R, Le Marchand L, Hindorff LA, Crawford DC, Gross M, Peters U. Multi-Ancestral Analysis of Inflammation-Related Genetic Variants and C-Reactive Protein in the Population Architecture using Genomics and Epidemiology (PAGE) Study. Circ Cardiovasc Genet. 2014 Mar 12

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