The document discusses 6 case reports of patients who underwent genetic testing to identify pathogenic variants contributing to their conditions. The cases include patients with mitochondrial disease, gastrointestinal dysmotility, cardiomyopathy, abnormal movements, and Leigh disease. Next-generation sequencing identified likely pathogenic variants in genes involved in mitochondrial function, metabolism, and neurological pathways. Identifying causative genetic variants allowed for improved treatment and management of the patients' conditions.
Ankylosing spondylitis is a type of arthritis which affects the spine. It causes inflammation and fusion in the vertebrae, which are the bones that make the spine. In some people, it can involve other joints as well. This disease develops at a very young age and mostly affects the youngsters in the form of back pain. It commonly occurs in men as compared to women.
The cause of this disease can be either genetic or environmental and can be diagnosed by medical history or physical examination.
Radiological and blood test is also involved. The main gene associated to Ankylosing Spondylitis is called HLA-B27, the presence of which can be detected in the blood of the patient.
The introduction of stem cells has raised the hope for the treatment of Ankylosing Spondylitis which are the basic cells of the body and can differentiate into several other types of cells present inside the body.
Learn more in details in the presentation.
Ankylosing spondylitis is a type of arthritis which affects the spine. It causes inflammation and fusion in the vertebrae, which are the bones that make the spine. In some people, it can involve other joints as well. This disease develops at a very young age and mostly affects the youngsters in the form of back pain. It commonly occurs in men as compared to women.
The cause of this disease can be either genetic or environmental and can be diagnosed by medical history or physical examination.
Radiological and blood test is also involved. The main gene associated to Ankylosing Spondylitis is called HLA-B27, the presence of which can be detected in the blood of the patient.
The introduction of stem cells has raised the hope for the treatment of Ankylosing Spondylitis which are the basic cells of the body and can differentiate into several other types of cells present inside the body.
Learn more in details in the presentation.
Prof. Dr. Vladimir Trajkovski - Epigenetics of ASD-10.05.2019Vladimir Trajkovski
President of MSSA Prof. Dr. Vladimir Trajkovski presented this topic "Epigenetics of Autism Spectrum Disorders" at the mini simposyum in Voerandaal, Holland, organized by ReAttach Academy at May 10th 2019.
BRM is a successful biopharmaceutical company formed in 1996 by Dennis Guberski and Dr. Arthur Like of the University of Massachusetts Medical School (UMass). Over the course of 20 years the founders developed proprietary diabetes research models under the sponsorship of the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK). BRM licensed this intellectual property portfolio from UMass in 1998 and since that time has used these proprietary tools to become one of the leading sources of customized preclinical contract research specializing in type 1 and type 2 diabetes.
Exercise and nutrition in Mitochondrial Diseasemitoaction
Mark Tarnopolsky, MD, PhD, FRCP,
Depts. of Pediatrics (Neuromuscular + Neurometabolic Disease) and Medicine (Cell Biology/Metabolism, Neurology and Rehabilitation), McMaster University, Hamilton, CANADA
Powerpoint presentation on my topic for the term paper. Highlights some basic information as well as various applications and impacts of human genetic manipulation.
Myasthenia gravis (MG) is a long-term neuromuscular disease that leads to varying degrees of skeletal muscle weakness. The most commonly affected muscles are those of the eyes, face, and swallowing.
Diagnostic Testing for Mitochondrial Diseasemitoaction
Review traditional diagnostic pathways
Discuss newer testing that has become available in recent years
Review new approaches to attempt to shorten time to diagnosis and increase precision
Social Security Disability Insurance (SSDI) and Supplemental Security Income ...mitoaction
Please join us on Friday, August 7, 2015 as we welcome two experts in the field of Social Security Disability Insurance (SSDI) and Supplemental Security Income (SSI) provide an overview of these public benefits for Mito patients. Topics to be covered in this conference call include:
Overview of SSI and SSDI programs;
The differences between SSI and SSDI;
Social Security’s definition of disability as it pertains to mitochondrial disease;
How SSDI is designed to work, eligibility criteria, and the full range of SSDI benefitts;
The application and appeals processes for SSI and SSDI;
Resources available to support SSI and SSDI applications and appeals processes;
Information on SSI and SSDI benefits for adult disabled children;
Returning to work after obtaining social security benefits (the "Ticket to Work Program");
Specific challenges for individuals with mitochondrial disease in applying for SSDI and how to address them; and
The benefits of professional representation and how to evaluate representation options.
Prof. Dr. Vladimir Trajkovski - Epigenetics of ASD-10.05.2019Vladimir Trajkovski
President of MSSA Prof. Dr. Vladimir Trajkovski presented this topic "Epigenetics of Autism Spectrum Disorders" at the mini simposyum in Voerandaal, Holland, organized by ReAttach Academy at May 10th 2019.
BRM is a successful biopharmaceutical company formed in 1996 by Dennis Guberski and Dr. Arthur Like of the University of Massachusetts Medical School (UMass). Over the course of 20 years the founders developed proprietary diabetes research models under the sponsorship of the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK). BRM licensed this intellectual property portfolio from UMass in 1998 and since that time has used these proprietary tools to become one of the leading sources of customized preclinical contract research specializing in type 1 and type 2 diabetes.
Exercise and nutrition in Mitochondrial Diseasemitoaction
Mark Tarnopolsky, MD, PhD, FRCP,
Depts. of Pediatrics (Neuromuscular + Neurometabolic Disease) and Medicine (Cell Biology/Metabolism, Neurology and Rehabilitation), McMaster University, Hamilton, CANADA
Powerpoint presentation on my topic for the term paper. Highlights some basic information as well as various applications and impacts of human genetic manipulation.
Myasthenia gravis (MG) is a long-term neuromuscular disease that leads to varying degrees of skeletal muscle weakness. The most commonly affected muscles are those of the eyes, face, and swallowing.
Diagnostic Testing for Mitochondrial Diseasemitoaction
Review traditional diagnostic pathways
Discuss newer testing that has become available in recent years
Review new approaches to attempt to shorten time to diagnosis and increase precision
Social Security Disability Insurance (SSDI) and Supplemental Security Income ...mitoaction
Please join us on Friday, August 7, 2015 as we welcome two experts in the field of Social Security Disability Insurance (SSDI) and Supplemental Security Income (SSI) provide an overview of these public benefits for Mito patients. Topics to be covered in this conference call include:
Overview of SSI and SSDI programs;
The differences between SSI and SSDI;
Social Security’s definition of disability as it pertains to mitochondrial disease;
How SSDI is designed to work, eligibility criteria, and the full range of SSDI benefitts;
The application and appeals processes for SSI and SSDI;
Resources available to support SSI and SSDI applications and appeals processes;
Information on SSI and SSDI benefits for adult disabled children;
Returning to work after obtaining social security benefits (the "Ticket to Work Program");
Specific challenges for individuals with mitochondrial disease in applying for SSDI and how to address them; and
The benefits of professional representation and how to evaluate representation options.
DNA Roulette: Understanding genetics and genetic testing through gamingcarrie.heeter
DNA Roulette was developed by Michigan State University professor Carrie Heeter and Stanford geneticist Barry Starr to help players understand what Direct to Consumer (DTC) testing does and does not tell you about your health. This presentation at Games for Health 2012 in Boston introduces the game.
This is Part 1 of a presentation on Genetic Toxicology that was given by Dr. David Kirkland to scientific staff at Health Canada in Sept. 2010. Part 2 is availabile in ppt
An overview of the current regulatory environment. *This is not legal advice and is written by a non-attorney. This is general information from a student in law school (MSJ program).
Regulatory oversight of genetic testing in Canada: Health Canada perspectiveMaRS Discovery District
Speaker: Patrice Sarrazin, PhD, Senior Scientific Evaluator, In Vitro Diagnostic Devices, Medical Devices Bureau, Therapeutic Product Directorate, Health Canada. Patrice discusses Health Canada's perspective on genetic testing as well as policy and regulation in Canada.
Part of Dx2010, a workshop at MaRS focused on best practices and regulatory considerations for developing gene-based diagnostic and prognostic tests.
Direct To Consumer Genomics and the Future of HealthcareRyan Squire
Richard Sharp, Ph.D., Director of Bioethics Research at the Cleveland Clinic presents on direct-to-consumer genomics and the future of health care.
Dr. Sharp received his training in philosophy and medical ethics at Michigan State University.
Prior to joining the Cleveland Clinic in 2007, Dr. Sharp taught bioethics at Baylor College of Medicine and the National Institute of Environmental Health Sciences, one of the National Institutes of Health (NIH), where he directed the Program in Environmental Health Policy and Ethics.
His research examines the promotion of informed patient decision-making in clinical research, particularly research that involves genetic analyses.
Medical Utopias: The Promise of Emerging TechnologiesAlex Tang
Medical utopias are often about good health, absence of suffering, and even delaying of the aging process. The last two decades have seen a tremendous increase in emerging medical technologies to achieve these utopias. The completion of the sequencing of the human genome sets the stage for the next step of genetic and molecular advances. The increase in computing power, storage capacity, connectivity, and the Internet has opened avenues of new diagnostic and therapeutic modalities. The perfecting of sustaining cell growth in vitro and cell nucleus transfer has opened the way to cloning, stem cell harvesting, and a new field of regenerative medicine. However, these emerging technologies bring with them a large number of bioethical concerns that need to be addressed. These concerns involving tissue engineering, bioelectronics, new genetics, cloning, gene therapy, germ-line genome modifications are only the tip of the iceberg. In this paper I will reflect on three areas of concern. Firstly, the emergence of the digital patient will be considered. This digital patient will be deeply formed and informed by health information technology (IT), the social media, and issues involving privacy, confidentiality and data security. Secondly, the direct to customers (DTC) genetic screening tests will be discussed. The ethical issue of buccal swabs taken at home and be tested for genetic diseases and future prediction of other illnesses which is marketed directly to the consumers will be examined. Finally, the development of new pharmaco-therapeutics will be explored. There have been changes in the way new drugs are tested and these changes do raise some ethical concerns. The examination of these ethical issues will be done in the framework of respect for autonomy, beneficence, non-maleficence, and justice.
A look at future directions for biology. Personalized genomics is a key step in moving towards individualized medicine and preventative interventions. The traditional trial and error approach of molecular biology is being replaced by the direct design of synthetic biology. Synthetically developed energy solutions could have a substantial impact on natural resource demand.
You're driving down the highway, when suddenly you spot a police officer or a state trooper in your rearview mirror. You're driving the speed limit; your tags are up-to-date, yet you suddenly feel guilty – like you've done something wrong.
This is how the FDA makes us feel when it comes to running direct-to-consumer (DTC) advertising for medical devices and pharmaceuticals. More often than not, you aren't doing anything wrong. But your anxiety levels run high as soon as you step on the gas.
Doctors’ Views of Direct-to-Consumer Drug AdvertisingCMI_Compas
CMI/Compas Study on Doctors’ Views of Direct-to-Consumer Drug Advertising, April 2013, In Preparation for the FDA Survey of Clinicians on Direct-to-Consumer Drug Advertising
This ppt is prepared by Sandeep Kumar Maurya , m. pharma ,department of pharmaceutical sciences, dr. harisingh gour university sagar madhya pradesh.
This SlideShare covers some of genetic disorders , molecular pathology, single gene disorder type of single gene disorder and advanced level cancer , mechanism of cancer, model for cancer induction explanation.
1. Introduction of genetic disorder
2. Common genetic disorders
3. Causes of genetic disorders
4. Symptoms of genetic disorders
5. single gene disorder
6. Cancer.
8. References.
Genetic disorders occur when a mutation (a harmful change to a gene, also known as a pathogenic variant) affects your genes or when you have the wrong amount of genetic material. Genes are made of DNA (deoxyribonucleic acid), which contain instructions for cell functioning and the characteristics that make you unique.
You receive half your genes from each biological parent and may inherit a gene mutation from one parent or both. Sometimes genes change due to issues within the DNA (mutations). This can raise your risk of having a genetic disorder. Some cause symptoms at birth, while others develop over time.`
Introduction of Cancer
Cancer is caused by the failure of genetic mechanisms that control the growth and proliferation of cells. In most cases, cumulative damage to multiple genes (the "multi-hit" model) via physical and chemical agents, replication errors, etc. contribute to oncogenesis. However, a person's inherited genetic background also may strongly contribute. In cancer, a single transformed cell grows to become a primary tumor, accumulates more mutations and becomes more aggressive, then metastasizes to another tissue and forms a secondary tumor. The difference between a benign tumor and a malignant one mostly involves the latter's ability to invade and metastasize to other tissues. Tumors are classified according to the embryonic origin of the tissue from which they originate. The term carcinoma is used to denote cancers of endodermal (e.g., gut epithelia cancers) or ectodermal (e.g., skin, neural epithelia) origin. Cancers of mesodermal origin (e.g., muscle, blood cells) are called sarcomas. Carcinomas make up >90% of malignant tumors.
Dawn Laney, MS, CGC, Associate Professor/Genetic Counselor.
Review of relevant definitions for Fabry disease.
Review of genetics for Fabry disease.
Review of diagnosis of Fabry disease.
Review of treatment for Fabry disease.
Review of research for Fabry disease.
Los días 11 y 12 de diciembre de 2014, la Fundación Ramón Areces celebró el Simposio Internacional 'Neuropatías periféricas hereditarias. Desde la biología a la terapéutica' en colaboración con CIBERER-ISCIII y el Centro de Investigación Príncipe Felipe. El tipo más común de estas patologías es la enfermedad de Charcot-Marie-Tooth, un trastorno neuromuscular hereditario con una prevalencia estimada de 17-40 afectados por 100.000 habitantes. Durante estos dos días, investigadores mostraron sus avances en la mejora del diagnóstico y el tratamiento y, por ende, de la aproximación clínica y la calidad de vida de las personas afectadas por estas patologías.
Tuberous sclerosis dr. amit vatkar, pediatric neurologistDr Amit Vatkar
Tuberous Sclerosis is a genetically inherited neurocutaneous syndrome can affect families in an autosomal dominant.
in this presentaion i will try and give u a review to the case and its management.
it will help u get a n outllook to diagnose a case of tuberous sclerosis
i have shown some images of the lesions present in the case to get a photographic memory.
-What are Standards of Care and why does the Mito community need such standards?
-Review the MMS's Standards of Care for Mitochondrial Disease and how they were developed.
-Outline upcoming MMS projects.
What you should know about genetic testing for mitochondrial disordersmitoaction
Amanda Balog, CGC, Senior Genetic Counselor, Mitochondrial and Metabolic Genetics, of GeneDx discusses: "What You Should Know About Genetic Testing for Mitochondrial Disorders."
Richard Frye, MD, PhD, FAAP, FAAN, CPI, will discuss:
*The enteric (gut) microbiome has an important influence on health and disease states in humans.
* The enteric microbiome influences the human host using chemical mediators, some of which can directly affect mitochondrial function
* Short chain fatty acids produced by gut bacteria not only modulate mitochondrial function and cellular regulatory pathways, but can also be used as mitochondrial fuels.
How to Build Your Mitochondrial Medical Homemitoaction
Topics include:
The importance of a medical home for a mitochondrial disease patient.
Definition of a medical home.
How to establish a medical home.
Why a medical home is an important component of good patient advocacy.
Tips on maintaining a healthy medical home relationship.
Wees will describe theses issues primarily from a pediatric perspective, but she will give adult examples as well.
Wees is a patient advocate with Empowered Medical Advocacy. She assists parents and caregivers each week in navigating toward improved quality of life for their child and their families.
Mitochondrial Medicine Society MitoAction Updates 4.1.16mitoaction
Areas of discussion include: Transplantation in Mito patients, Stroke protocol for MELAS, Standards of care for Mito patients, Centers of Excellence and the need for community involvement/input (v2 slides)
Incapacity Planning and Guardianship 2016mitoaction
As patients or caregivers, it is frightening to think about what would happen if we could not advocate for ourselves. Fortunately, there are legal documents that can be used to communicate our wishes under such circumstances. This type of legal preparation is called incapacity planning and guardianship.
These lecture slides, by Dr Sidra Arshad, offer a quick overview of the physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar lead (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
6. Describe the flow of current around the heart during the cardiac cycle
7. Discuss the placement and polarity of the leads of electrocardiograph
8. Describe the normal electrocardiograms recorded from the limb leads and explain the physiological basis of the different records that are obtained
9. Define mean electrical vector (axis) of the heart and give the normal range
10. Define the mean QRS vector
11. Describe the axes of leads (hexagonal reference system)
12. Comprehend the vectorial analysis of the normal ECG
13. Determine the mean electrical axis of the ventricular QRS and appreciate the mean axis deviation
14. Explain the concepts of current of injury, J point, and their significance
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
4. Electrocardiogram, StatPearls - https://www.ncbi.nlm.nih.gov/books/NBK549803/
5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. Chapter 3, Cardiology Explained, https://www.ncbi.nlm.nih.gov/books/NBK2214/
7. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
- Video recording of this lecture in English language: https://youtu.be/kqbnxVAZs-0
- Video recording of this lecture in Arabic language: https://youtu.be/SINlygW1Mpc
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
Rasamanikya is a excellent preparation in the field of Rasashastra, it is used in various Kushtha Roga, Shwasa, Vicharchika, Bhagandara, Vatarakta, and Phiranga Roga. In this article Preparation& Comparative analytical profile for both Formulationon i.e Rasamanikya prepared by Kushmanda swarasa & Churnodhaka Shodita Haratala. The study aims to provide insights into the comparative efficacy and analytical aspects of these formulations for enhanced therapeutic outcomes.
Basavarajeeyam is an important text for ayurvedic physician belonging to andhra pradehs. It is a popular compendium in various parts of our country as well as in andhra pradesh. The content of the text was presented in sanskrit and telugu language (Bilingual). One of the most famous book in ayurvedic pharmaceutics and therapeutics. This book contains 25 chapters called as prakaranas. Many rasaoushadis were explained, pioneer of dhatu druti, nadi pareeksha, mutra pareeksha etc. Belongs to the period of 15-16 century. New diseases like upadamsha, phiranga rogas are explained.
Here is the updated list of Top Best Ayurvedic medicine for Gas and Indigestion and those are Gas-O-Go Syp for Dyspepsia | Lavizyme Syrup for Acidity | Yumzyme Hepatoprotective Capsules etc
micro teaching on communication m.sc nursing.pdfAnurag Sharma
Microteaching is a unique model of practice teaching. It is a viable instrument for the. desired change in the teaching behavior or the behavior potential which, in specified types of real. classroom situations, tends to facilitate the achievement of specified types of objectives.
1. Interpreting Genetic Testing
Richard G. Boles, M.D.
Medical Director, Courtagen Life Sciences, Inc.
Associate Professor of Pediatrics, Keck School of Medicine at USC
Division of Medical Genetics, Children’s Hospital Los Angeles
September 13, 2013
2. Disclosure: I wear many hats.
09/13/13 Company Confidential 2
Medical Director of Courtagen Life Sciences Inc.
• Test development
• Test interpretation
• Marketing
Researcher with NIH and foundation funding
• Studying sequence variation that predispose
towards functional disease
• Treatment protocols
Clinician treating patients
• Functional disease (CVS, autism, etc.)
• Genetic/metabolic disorders
• General pediatrics
3. Mitochondrial Genetics
The Basics
37 genes
-Maternal inheritance
1,013 genes
-Autosomal recessive
-Autosomal dominant
-X-linked
Nuclear DNAMitochondrial DNA
5. Courtagen Next Generation Sequencing
09/13/13 Company Confidential 5
Novel Assay Design
• Uses a combination of PCR and Probe based approaches to selectively enrich
pseudogene free DNA
• 2 x 250bp reads assists in reducing mis-mapping to pseudogenes
• Average variant depth of coverage greater than 200X
• Sequence data analyzed using Courtagen’s proprietary bioinformatics analysis
program (Ziphyr®)
• Non-synonymous variants reviewed and scored for correlation with the clinical
phenotype of each patient.
• Variants suspected to be related to disease are confirmed by Sanger sequencing
On target readsPseudogene depletion step
.
Turnaround = Weeks not Months
6. Why order a Genetic Test?
09/13/13 Company Confidential 6
• Establish/prove an exact diagnosis
– Justify existing mitochondrial treatments/precautions
– Limit further diagnostic testing
– Finally, an answer
• Determine the mode of inheritance
• Help guide therapy
– Which cofactors are likely to work?
– Suggest new/different therapies
• An investment in further knowledge
– Delayed diagnoses/recommendations
8. Clinical History
09/13/13 Company Confidential 8
• Autism – early infancy
– Lost language skills acquired at 18 months.
– Diagnosed with “autism” at age 2 yrs
• Cyclic vomiting syndrome – age 6 years
– Episodes of nausea, vomiting and lethargy lasting from a few days
to a week or more
• Rhabdomyolysis – age 11 years
– Hospitalized twice, maximum CK = 100K; precipitated by anesthesia
(dental) and influenza B
• Complex regional pain syndrome – age 12 yrs
– Episodes in which right foot becomes cold, purple, tender,
allodynia, unable to bear weight; wheelchair bound for months
• Other chronic intermittent symptoms
– Headache, muscle pain, constipation, photophobia, ptosis, tics,
hours-long episodes of hiccups.
• Severe exercise intolerance
10. Genomics
09/13/13 Company Confidential 10
• NextGen sequencing of the 1,100 gene MitoCarta - 200-fold
– L340F change in the CHAT gene encoding choline O-acetyltransferase gene,
the enzyme catalyzes the synthesis of acetylcholine from choline and acetyl-
CoA in cholinergic neurons
– Variant is highly conserved, predicted as deleterious by MutationTaster,
SIFT, and PolyPhen2. Prevalence: 1 in 200
• Good genotype-phenotype match
– Cognitive decline is a prominent factor in this patient's disease
– Poorly tolerates anticholinergic medications
– One CHAT mutation was found in another patient with a similar phenotype
of pseudoobstruction, POTS, chronic fatigue, dysautonomia, autistic
spectrum disorder, and exaggerated anticholinergic effects to medications
11. CHoline O-AcetylTransferase
Haploinsufficiency as a Novel Treatable Disorder
09/13/13 Company Confidential 11
• Four cases, each with apparent maternal inheritance, biochemical data
demonstrating mitochondrial dysfunction, and typical symptomatology
of neurological disease, pain, fatigue, and GI dysmotility.
• Additional manifestations are distinct:
– Episodic mental status changes w/o known triggers
– POTS/dysautonomia
– Severe reactions to anticholinergic medications
• Parasympathetic deficiency by LifeShirt (- 3 to 4 SD)
• Anecdotal, yet dramatic, improvement with donepezil (Aricept)
• Digenic: mtDNA + CHAT “polymorphism”
12. nucSEEK
TM
Case Report
09/13/13 Company Confidential 12
• 17-year-old female. Presents with “functional” disease:
– Chronic pain: migraine, myalgia, joints, abdomen (“functional”)
– Depression, anxiety, and panic
– Chronic fatigue syndrome
– Tinnitus, POTS, other dysautonomic symptoms
• Apparent maternal inheritance:
– Brother is the proband, presented at age 8 years with ketotic hypoglycemia,
chronic pain “cramps”, and tinnitus.
– Mother with migraine, fibromyalgia, depression, parasthesia
– Functional symptoms is maternal aunt, uncle, and grandmother
• Biochemical testing: minimal due to HMO, anion gap metabolic acidosis/ketosis,
high urine carnitine and blood C8
• Substantial improvement on 600 mg BID of coenzyme Q10, B100, and sertraline
(Zoloft)
13. H599R in the SCN4A Gene
09/13/13 Company Confidential 13
• The variant found in this patient is predicted to be deleterious
– very-highly evolutionarily conserved
– per computer algorithms
– rare, present in 1 out of 670 people.
• Encodes the alpha subunit of the voltage-gated, type IV sodium channel, which is
expressed in skeletal muscle.
• Along with other proteins in its category, these proteins are responsible for the
generation and propagation of action potentials in neurons and muscle.
• Mutations in this gene have been linked to hyperkalemic periodic paralysis (type 2),
myasthenic syndrome (acetazolamide-responsive), myotonia congenita atypical
(acetazolamide-responsive) and paramyotonia congenita
• All are autosomal dominant conditions.
• Phenotypic variability is considerable. Some patients manifest as muscle stiffness or
cramps.
• On retrospect, the patient, her two siblings and their mother suffer from muscle
cramps, especially her brother, and especially in the toes.
• Acetazolamide treatment is generally effective in this condition. In this patient:
– reduced pain in abdomen and joints
– Less depression and anxiety
• Her mother carries the mutation by Sanger; testing in other relatives is pending.
17. Genotype-Phenotype
Correlation in Mitochondrial Disease
• A single condition can be caused by mutation in a large
number, perhaps hundreds, of genes.
• A single family segregating an identified mutation can present
with very-different disease manifestations in each affected
relative.
• mtSEEK: NextGen sequencing of the 37 mtDNA genes
and control region
• nucSEEK: NextGen sequencing of the 1,197 nuclear-
coded genes involved in energy metabolism:
09/13/13 17
What genotype-phenotype correlation!
crazy20nancy20straight20jacket.jpg
18. Molecular (DNA) Diagnosis
• Mitochondrial DNA (mtDNA)
– Standard mtDNA analysis
• PCR for common point mutations (3243A>G, 8344A>G,
8993T>G or C)
• PCR or Southern blotting for large rearrangements
– Full mtDNA sequencing
• Nuclear DNA testing
– Single gene (MNGIE)
– Small Panel (few-several genes: e.g. COX deficiency, mtDNA
depletion,)
– Mito-exome (1,100 genes)
– Exome (22,000 genes)
– Genome (all of the DNA)
19. Our Approach – Sequence ‘Em All!
09/13/13 Company Confidential 19
mtSEEK
TM
NextGen sequencing of the 37 mtDNA genes and control region
nucSEEK
TM
NextGen sequencing of the 1,197 nuclear-coded genes involved
in energy metabolism
• MitoCarta (1013 genes)
• Peroxisomal genes
• Cytosolic “metabolic” genes
• Phenocopies
20. 20
Bioinformatics – Simplifying the Data
• Sequences are compared to the human genome reference sequence.
• Each sequence will produce about 3,000 variants
• The data are filtered for:
• coverage (how many times each base was measured) - removing
variants that have not been sequenced enough times to provide
confidence in the result
• variants located in the intron regions
• variants that are synonymous – change a nucleotide, but do not
result in an amino acid change
producing about 300 variants per nucSEEK sequence
• Final filter: all common variants present in 1% or greater of the
population are removed – leaving about 30 variants per sequence that
may have some association with disease.
21. 21
Bioinformatics – Interpreting the Data
• Sequence variants are evaluated for predicted pathology =
the likelihood that a variant adversely affects protein function:
• prevalence – how frequent the variant is in humans
• conservation – how common mutation is in other species
• protein function – predicted by 3 computer algorithms
• Suspected mode of inheritance: dominant, recessive, unknown
versus the number of probable mutations found.
• The patient’s phenotype – clinical manifestations.
• Any laboratory or other data provided.
24. Report Classifications
Negative: No variants were detected that are suspected to be associated with the patient’s
disease.
Likely Negative: One or more variants were identified that are likely not associated with the
patient’s disease. However, one or more variants were identified for which further testing may
be indicated. Parental testing, clinical correlation, or further biochemical, imaging, or other tests
may alter the test interpretation.
Uncertain. Variant of Uncertain Significance (VUS): One or more variants were
detected for which clinical significance is uncertain. Parental testing, clinical correlation, or
further imaging, biochemical, or other tests are likely indicated.
Likely positive: One or more variants were found that are likely associated with the
patient’s disease. While these variants have not previously been reported in the scientific
literature as being associated with disease, based on our current interpretation algorithm, these
variants are predicted to be damaging to protein structure and function. Parental testing, clinical
correlation, or further imaging, biochemical, or other tests are likely indicated.
Positive: One or more genetic variants were identified that have been previously associated
with disease or are very likely pathogenic based on their predicted effect on protein structure.
09/13/13 Company Confidential 24
28. Who Is Really “Normal”?
09/13/13 28
One Negative Control Subject had an Abnormal Interpretation:
•CPOX: coproporphyrinogen oxidase
•Sixth enzyme of the heme biosynthetic pathway
•Cause of hereditary coproporphyria (HCP)
•Autosomal dominant
•Hepatic, neurological and psychiatric disease, like acute intermittent porphyria PLUS skin
rash
•not reported in the 1,000 Genomes Database), high evolutionary conservation (at least
as distant as zebrafish), and 3/3 computer algorithms of protein function.
29. Case Report, 3-year-old girl
• GI dysmotility – on full TPN cannot tolerate
any enteral intake, including jejunal drips
• Chronic pain – severe leg pain and
headache
• Chronic fatigue – sleeping 22 hours a day
• Hypoglyemia, even on 24-hour drip
feedings
• Episodic right arm limpness
• Anemia – received multiple blood
transfusions
• Dysautonomia: tachycardia, temperature
instability, hypoxia, neurogenic bladder
• Rotenone-sensitive NADH-cytochrome c
reductase deficiency = 7%.
09/13/13 29
30. nucSEEK Case Report 2
• TRAP1: A 3-year-old girl presented with multiple manifestations of
functional disease, including gastrointestinal dysmotility requiring
TPN, chronic fatigue, and chronic pain in many locations.
• Sequencing revealed a predicted deleterious variant, I235V, in the
TNF receptor-associated protein 1 (TRAP1), a mitochondrial
chaperone involved in antioxidant defense.
• This patient is one of 12 cases identified by Courtagen to date who
have previously unidentified disease associated with mutations in
the TRAP1 ATPase domain, all of which have a triad of dysmotility,
pain and fatigue, with normal intelligence.
• Chronic pain improved greatly on antioxidant therapy.
30
31. nucSEEK Case Report 3
• SHMT1: A 4–year-old female presented with ataxia and
developmental regression.
• Sequencing revealed the presence of a novel homozygous
predicted deleterious variant, E344Q, in the serine
hydroxymethyltransferase 1 (SHMT1) gene, within the folate
metabolism pathway.
• Treatment with folinic acid and glycine resulted in
improvement of her gross motor, fine motor and expressive
language skills.
31
32. nucSEEK Case Report 4
• COQ2: A newborn girl presented with severe dilated
cardiomyopathy and hypotonia.
• Sequencing identified a homozygous variant, V393A, in the
COQ2 gene. While she was empirically started on CoQ10 by
her physician early on, this diagnosis resulted in the dosage
being increased many fold.
• Her cardiac function has improved substantially, and no
longer requires transplantation.
32
33. nucSEEK Case Report 5
• CHRNA4: A 14-year-old male presented with abnormal
movements that were described as tics.
• nucSEEKTM
revealed a predicted deleterious mutation, E92Q,
in the nicotinic cholinergic receptor (CHRNA4).
• Treatment was altered to address seizures, resulting in
substantial clinical improvement.
33
34. nucSEEKTM
Case Report 6
• IARS2: A couple who had lost a child to Leigh disease were
expecting and requested prenatal testing.
• Two deleterious-predicted mutations in IARS2 (W607X,
E708K) were identified in the deceased child, one inherited
from each parent. Although no defects have been reported
in IARS2, other tRNA synthetase genes are implicated in
Leigh’s disease.
• The couple underwent prenatal testing, revealing the fetus
to be heterozygous for IARS2 and thus predicted to be
healthy.
34
35. nucSEEKTM
Case Report 7
• PNKD: A 6-year-old boy was referred for intermittent ataxia,
diarrhea, exercise intolerance and speech articulation difficulties.
• Sequencing identified the predicted deleterious mutation G89R in
the paroxysmal nonkinesigenic dyskinesia (PNKD) gene, associated
with the rare AD movement disorder. On retrospective inquiry, he
and his mother were noted to have dyskinesia. Counseling
regarding the benign nature of this condition and disease triggers
was helpful to the family, and the boy’s manifestations have
improved. This mutation differs from the 2 classic mutations
previously reported, and with a phenotype dominated with ataxia,
not dyskinesia or dystonia, this family represents an undescribed
variant of the disorder.
• An unrelated case of a novel PNKD mutation with ataxia and
dystonia was identified by our laboratory as well.
35
36. Known Conditions Identified
• ACAD9: acyl-CoA dehydrogenase family, member 9
• ALDH5A1: aldehyde dehydrogenase 5 family, member A1 (succinic semialdehyde dehydrogenase)
• ATP7B: ATPase, Cu++ transporting, beta polypeptide (Wilson)
• CLCN2: chloride channel, voltage-sensitive 2
• COQ2: coenzyme Q2 homolog, prenyltransferase
• GARS: glycyl-tRNA synthetase
• KIF1B: kinesin family member 1B
• MFN2: mitofusin 2 (2 families)
• NDUFA1: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1
• NRXN1: neurexin 1 (2 families)
• PNKD: paroxysmal nonkinesigenic dyskinesia (2 families)
• RRM2B: ribonucleotide reductase M2 B
• SCN1A: sodium channel, voltage-gated, type I, alpha subunit
• SCN2A: sodium channel, voltage-gated, type II, alpha subunit
• SCN4A: The gene encodes the alpha subunit of the voltage-gated, type IV sodium channel
• SPAST: Spastin
• SPTLC2: serine palmitoyltransferase, long chain base subunit 2 (hereditary sensory neuropathy type 1C)
• TPH2: tryptophan hydroxylase 2
• UBE3A: ubiquitin protein ligase E3A (Angelman)
09/13/13 36
37. > 1 Conserved Variants in
a Folate-Related Gene
• GLDC, MTRR, SHMT2: Developmental delay, hypotonia, and skeletal muscle weakness
• ALDH1L2, GLDC: Encephalopathy (seizure disorder, mental retardation, and cerebral palsy), optic
atrophy, hearing loss, GI dysmotility and dysautonomia
• GLDC, SHMT1: Autism
• MTHFD2, MTRR: Sudden-onset OCD, motor tics, and IgA deficiency
• ALDH1L1, ALDH1L2: Severe irritability, hypersensitivity, growth issue, twin also affected, severe
PANS, immunodeficiency
• ALDH1L1, GLDC: Autism, macrocephaly, and PANS
• FPGS, MTHFD2L: Myopathy with muscle biopsy suggestive of mitochondrial myopathy
• ALDH1L1, FPGS: Tics, OCD
• ALDH1L1, ALDH1L2, FPGS (x2): Severe primordial growth retardation, in-utero stroke, and
functional disease
• ALDH1L1, MTHFD1L: Seizures, hypotonia, large bowel dysmotility and optic neuropathy
• GLDC, SLC25A32: Multiple functional/dysautonomic symptomatology, including chronic pain and
post-prandial nausea
• ALDH1L1, MTHFD1L: Cyclic vomiting
• ALDH1L2, GLDC, MTHFS: Obsessive compulsive disorder and tic disorder
• MTHFD1L, SHMT1: Tic disorder and obsessive compulsive disorder
09/13/13 37
38.
39. Case Report – Dylan, age 6
PLCG2
• Angioedema
• Chronic pain
• Pancytopenia
• Chronic fatigue
• Immunodeficiency
• Renal disease (stones and acidosis)
• Severe GI dysmotility requiring TPN
• Multiple endocrinopathies, incl diabetes
• Muscle biopsy c/w mitochondrial disease.
• Exome sequencing at UCLA: PLCG2 mutation causing
phospholipase C, gamma 2 deficiency, a disorder of
inflammation.
40. Panel versus Exome?
• Looks at many genes
• Misses the dx if you are wrong
• Many VUS
• Occasional incidentals
• Expert interpretation
• Data to mine later
• Family secrets unsafe
• Looks at “all” genes
• Misses very little, but will you
notice it?
• Buried in VUS
• Many incidentals
• Less-than-expert
• Tremendous data to mine
• Family secrets revealed
PANEL EXOME
41. Panel versus Exome?
• Looks at many genes
• Misses the dx if you are wrong
• Many VUS
• Occasional incidentals
• Expert interpretation
• Data to mine later
• Family secrets unsafe
• Looks at “all” genes
• Misses very little, but will you
notice it?
• Buried in VUS
• Many incidentals
• Less-than-expert
• Tremendous data to mine
• Family secrets revealed
PANEL EXOME
You think you know. You haven’t a clue.
42. Potentially Unwanted Findings
• “Incidental findings” = risk for unrelated disease: cancer,
neurodegeneration, sudden cardiac death, drug
interactions, anesthesia complications, others
• Variants of Unclear Significance (VUS)
Common in Mito-exome
Very common in exome
43. Potentially Unwanted Findings
• “Incidental findings” = risk for unrelated disease: cancer,
neurodegeneration, sudden cardiac death, drug
interactions, anesthesia complications, others
• Variants of Unclear Significance (VUS)
• Risks of disclosure of genetic information
• Family secrets
– Consanguinity
– Non-paternity
Common in Mito-exome
Very common in exome
44. 09/13/13 44
I never know when its going to come back
This fatigue is an internal attack
It so easily cripples me
Only no one can see
Its so hard when you easily tire
And everyone around you thinks your lazy and a liar
They cant see so they don't know
I know in my heart its real though
Its a relief to get the answer and know you're not crazy
You can finally prove you're not just lazy
Its still not easy and never will be
But maybe some day the world will see
45. “Functional” Disorders List:
• Autistic spectrum
disorders
• Chronic fatigue
syndrome
• Complex regional pain
syndrome
• Cyclic vomiting
syndrome
• Fibromyalgia
• Irritable bowel
syndrome
• Migraine
Social and language oddities,
and Restricted interests
Post-exertional fatigue for > 1 day,
and Unrefreshed sleep
Out-of-proportion pain following
tissue damage in severity and duration,
and Autonomic signs
Severe nausea, vomiting, and lethargy,
and Much reduced between cycles
Widespread pain
and Allodynia (painful response to pressure)
Abdominal discomfort less with BM,
and Constipation, diarrhea, or alternating
Headache with nausea and photophobia,
or Transient sensory loss or gain
46. Why Courtagen?
• Specificity: 99.99% Sensitivity: 99%
• Deeper investigation into sequence variants
• Far less filtering (only >3%, synonymous, non-coding or splice)
• Special commitment towards functional disease
• High sample volume with these disorders for comparison
• Ongoing data mining
• Interpretation, recommendations, treatment suggestions
• Turn-around in weeks, not months or years
• Courtagen handles obtaining authorization
• Aggressive financial assistance program
• Less “incidental findings”
09/13/13 46
47. Mito-Exome Limitations
• ~150 mitochondrial genes are yet to be discovered
• Phenocopies: 200 does not cover all
• 98% coverage is still not 100%
• Promoter and other regulatory mutations
• BioInformatic/interpretation is not perfect
• Some genes might have unrecognized dominant
mutations
• Some patients have polygenic disease
48. Ordering a Test from Courtagen
Physicians order genetic testing
Doctors fill out Courtagen’s test
request form and submit by fax
or online
Courtagen verifies Patient
Insurance Benefits
Courtagen Care Financial
Program available for qualified
patients
Confidential 48
DNA is process using the most
advanced laboratory methods in Next
Generation Sequencing
Results are analyzed by Courtagen’s
experienced bioinformatics team and
analysis pipeline
Clinical interpretation by our clinical
genomics team, led by Dr. Richard
Boles
Step 1Step 1 Step 2Step 2
Saliva collection kit is shipped
to the patient or provided in
the doctor office
Sample is collected and sent
directly to Courtagen
Physician signature and
Patient Consent signature
required
Step 3Step 3 Step 4Step 4
Report is posted to Courtagen’s
online portal for your physician
Genetic Counselors available to
address questions
49. What Do I Need To Get Started?
1. An order for the test from any physician
(e.g. “nucSEEK on Juan Garcia”).
2. Authorization from your insurance company, followed
by a financial survey completed by the family.
3. Clinical information, either a sub-specialist physician
note and/or completed checklist.
4. A collection kit will be sent by mail for the saliva
sample. Results are not affected by diet, treatment, or
time.
50. What Test?
•mtSEEKTM
– Entire mitochondrial DNA
– Maternal inheritance
•nucSEEKTM
– All 1,100 nuclear-encoded mitochondrial genes + phenocopies
– Consanguinity
•epiSEEKTM
– All 327 known genes that result in seizures
– Seizures are a prominent aspect of the phenotype
•autSEEKTM
COMING SOON
– All known genes that result in autistic spectrum disorders
– ASD is a prominent aspect of the phenotype
50
51. Panel versus Exome?
• Practical
• Non-invasive
• Rapid
• Replaces previous testing
• Cost-effective
• Covered by PPOs
• High positive rate
• Often leads to therapy
• Occasional incidentals
• Data to mine later
• Lack of understanding
– public
– clinicians
– genetic specialists
– payers
• Costs are still substantial,
but decreasing
• Occasional incidentals
• Unreasonable
expectations
SUCCESSFUL NOW REMAINING OBSTACLES
NextGen in Clinical Practice
Is the Future Here?