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Archive for January, 2015

3:30PM –5:15PM, January 26, 2015 – NGS Applications: Impact of Genomics on Cancer Care @Silicon Valley 2015 Personalized Medicine World Conference, Mountain View, CA

Reporter: Aviva Lev-Ari, PhD, RN

 

Real Time Conference Coverage with Social Media

@Computer History Museum by Dr. Aviva Lev-Ari, PhD, RN

3:30PM – 3:45PM Mike Pellini, Foundation Medicine (Chair)

“Comprehensive” Molecular Profiling And Big Data Is Changing The Fight Against Cancer

LIVE FROM THE PODIUM
Changing the paradigm of cancer patients treatment offerings.
why should we utilize NGS in Diagnosis? No one asks that in 2015
  • Actionable if based on Clinical Trials or the literature treatment of the mutation id efficacious.

CANCER IS A DISEASE OF THE GENOME

  • Single-marker molecular test
  • multi-gene “Hot Spot” Test
  • Comprehensive Genomic Profile – sequence all genes known to implicate Cancer – all alterations to be done within one test
  • Commercial adoption – 35000 patients
  • Oncology & Pathology: Perform Test deliver information
  • FoundationCore – Capture information in a database — who to take this information to be able to use it
  • Amount of data vast: connection of Pharma, Trials, Patients
  • Pathology: disrupt their relationship — they need be integrated
  • FDA – Impressive actions taken are very impressive
  • Payer Organization need be integrated
  • FoundationnOne – information must be transpalant: Capturing every data
  • Notification – when information is ready for patient care
  • Liquid biopsy: diagnosis of colon cancer, gastric cancer – NEW presentation of tumors an MD never seen before
  • Patient Match 35000 patient followed – within 72 hours all 28 MDs in FoundationMedicine get the genomics data, so each will see every case.

3:45PM – 4:00PM Nicholas Dracopoli, Janssen R&D

Circulating Tumor Cells: From Enumeration to Comprehensive Characterization

LIVE FROM THE PODIUM

  • Apoptosis – Patients have Outcomes Targeted Therapy vs Immunotherapy
  • Tumors have different Genotypes that evolve with Time and Treatment
  • Hallmark of Cancer Emerge over Time
  • Diagnosis & Liquid Biopsies
  • Biopsy: Tissue, invasive, freq – limited
  • analysis Protein, DNA
  • Negative Depletion to isolate CTCs – Cancer Tumor Cells
  • Fluidigm – blood cells are split into two flows cancer tumor cells normal cells
  • Genotyping and Phenotyping
  • Breast Cancer CTCs – Measuring Epithelial to Mesenchymal Transition (EMT)
  • plasticity of cells as a result of therapy
  • RNA-based Genotype
  • Capture of CTCs followed by Culture and tumorigenesis in mouse Models
  • Liquid Biopsy: Genetic and Genomics data combined
  • CTC and cfDNA: Cancer Patients has more DNA circulation, DNA is dying,
  • Progression of tumor over time: Genomics and Epithelial transition, MGH developed the technology using Fluidigm platform

4:00PM – 4:30PM   Panel, Q&A

Krishna Yeshwant Genia, Google Ventures 

LIVE APNEL DISCUSSION – moderated by Mike Pellini, FoundationOne – In 3-5 years Genomics will become Standard of care in the Developed Nations, leading with the US.  President of the US in State of the Union address supported Precision Medicine as a driver for COst containment for HealthCare. 

Krishna Yeshwant Genia, Google Ventures: Exciting time, Science in the next 5 years Immunotherapy will become standdard of Care

Science in the next 5 years Immunotherapy will become standard of Care, IT is emerging

Stefan Roever, Roche: Structural mutation in the Genome, root core mutation, cancer sequencing, cost effective, every cancer patient need to be sequenced tumor comparison, one read to sequence. Life technologies in his career,

Nicholas Dracopoli, Janssen– Testing improves, longitudinal data collection

4:45PM – 5:00PM 

Session Chair: Frank S. Ong, Illumina (Chair) 

Dennis Slamon, UCLA

Molecular Diversity of Human Breast Cancer: Clinical and Therapeutic Implications

The Past

  • The One-Size-Fits All
  • Surgery
  • Radiation
  • The Hodgkin’s Legacy – The Golden Age
  • Disease Entities – Endocrine Therapy of Breast Cancer in the 19th Century
  • 1896 – 1940
  • HER2 Alteration – Overexpression Oncoprotein – shortening survival
  • Survival: Target validation A, B – HER2 Receptor
  • Preclinical Impact of Trastuzumab on Tumor Growth: Genentech,
  • Breast Cancer Subtypes
  • Breast Cancer adjuvant Chemotherapy: Treatment evolution:  Drug survival 34% 6years, only surgery 26% in 12 years 50% in 6 years
  • Multiple sites within one tumor – Actionable Impact only by identification of mutations, target therapy without increased tocisity

5:00PM – 5:15PM Tom Caskey, Baylor College of Medicine

Executive Care for Genetic Disease Prevention

  • Young Presidents Organization – to participate
  • Genetic Screening: New-born
  • Prediction of disease: Genomics, familial risk
  • Disease areas: Familial Disorders, CVD, neurological
  • Coronary Disease: Carotid Syndrome, Obesity,hearing deficiency, eye condition: Macular degeneration, retinitis pigmentosa
  • Diabetes 2 and retinopathy
  • Prostate cancer pathology
  • thyroid cancer
  • Hairy cell leukemia
  • Lipomatosis – not available in the literature as causing disease
  • Myotonic Dystrophy – pre-symptomatic allele
  • Metabolome
  • Report goes out to the Doctors: Bioinformaticals identified RISK.

@PMWCintl 

#PMWC15

#startup #biotech #pharmanews @BiotechNews

@BloombergNews

@CancerNews

#Cancer Therapy

#science  #innovation @BloombergTV

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2:15PM – 3:o0PM, January 26, 2015 – Impact of Genomics on Cancer Care @Silicon Valley 2015 Personalized Medicine World Conference, Mountain View, CA

Reporter: Aviva Lev-Ari, PhD, RN

 

Real Time Conference Coverage with Social Media

@Computer History Museum by Dr. Aviva Lev-Ari, PhD, RN

Session Chair: Frank S. Ong, Illumina (Chair)

2:15PM – 2:30PM  Kim Popovits, Genomic Health

Transforming the Cancer Patient Journey with Actionable Genomic Information

LIVE from the Podium

  • Proprietary technology for DIagnosis – new workflow
  • Genome profile – no need to wait 3 months to next CT to see shrinkage of Tumor
  • Mutation Pane for patients that drug did not shrinking the tumor
  • multiple genes, higher Tumor burden
  • leveraging Genomic Health’s Leading Brand and Channel to Capture

2:30PM – 2:45PM Janusz Dutkowski, Data4Cure

LIVE from the PODIUM

  • Two goals vs many predictions
  • Universe of Data: Predictions still dat poor, linear,
  • biological complexity
  • Cancer genome interpretation
  • Genome analysis – data boosted
  • Actionable Drivers: algorithms
  • common and rare variants
  • Molecular hierarchy: Pathways, genes, complex, processes
  • Multiscale cancer maps – Context matter
  • GBM Biomarkers – Brain Tumors
  • Human knowledge is critical: Scientists and Clinicians
  • Learn, collaborate, apply, share, collaborate, laern share — biological knowledge iteration

Personal Systems Interpretation: a Multidimensional View Into Cancer

2:45PM – 3:00PM Martin Naley, Cure Forward

The Coming Genomics Boom: Will Patients Be The Catalyst?

LIVE FROM THE PODIUM

  • Will the patient be the Catalyst? Genomics Boom gained Presidents support
  • Introduction to services
  • development of personal genome sequencing 23andMe
  • Precision medicine – Dana Farber — EVERY PATIENT ENTERING WITH CANCER DIAGNOSIS, RECEIVE A GENOME SEQUENCES
  • Oncology trial statistics – 85% participate, 88% reports experience is positive
  • Clinical Trials have difficulty filling up the Trials

Eric Topol, The Patient will see you NOW!!

  • shred the snare

Trial comes to the Patient

  • CureForward: Donate data, match, assist patients
  • diagnostics test providers

Comments from the Audience

interpretation of the biology remains a major challenge in the field, the advances represent technology, sequencing efficacy, mapping with reduced error –that development is not coupled with a parallel advancing of the ability to translate the Genomics research into the discipline of Biology beyond concordance, affinity and statistical correlations. The Biology Departments need to be brought closer to the Genomics Centers.

 @PMWCintl 

#PMWC15

#startup #biotech #pharmanews @BiotechNews

@BloombergNews

@CancerNews

#Cancer Therapy

#science  #innovation @BloombergTV

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1:00PM – 2:00PM, January 26, 2015 – Clinical Methodologies of NGS – LIVE @Silicon Valley 2015 Personalized Medicine World Conference, Mountain View, CA

Real Time Conference Coverage with Social Media

@Computer History Museum by Dr. Aviva Lev-Ari, PhD, RN

1:00PM – 1:15PM Mike Snyder, Stanford (Chair)

Analyzing Complex Diseases Using Integrative Omics Technologies

LIVE FROM THE PODIUM

Complex Disease

  • Highest prevalence: Diabetes and Autism as examples
  • Personal “Omics” Profiling – Molecualr measurement: Microbiome, metabolomics via Urine
  • Principles
  • Genome Sequence(Illumina, Complete Genomics): Predict Diabetes
  • Life Time change if the Genome sequencing find risk for diabetes
  • Metabolic Disorder can be familial
  • Molecules and Biochemical Pathways that change during acquisition of Diabetes: Insulin, Biosynthetic pathway
  • Microbiome is important for health: implicated in IBD: Crohn’s and Enterical Colitis
  • in Nasal microbes: Streptococcus pneumonie
  • Stool microbiome: during fever Respiratory infection: Gut microbiome changes
  • 70 Prediabetics: Personal Omics profile – data sensors:
  • other data types sensors: Insulin Resistance –>>> obesity — Diabetes
  • AUTISM: protein in patients –
  • Cetificate in Genomics

 

1:15PM – 1:30PM Patrick Roche, HTG Molecular -mRNA and MiRNA

NGS-based Molecular Profiling from a Single FFPE Section

LIVE from the PODIUM

Molecular Profiling is slow: the alternative is

HTGEdge CHemistry

  • Nuclease protection – HTG EdgeSeq – No DNA or RNA: extraction of RNS for adoptors like Illumina Sequencer
  • HTG and NGS – Edge Chemistry is optimized for NGS workflow
  • miRNA Asssay – Whole Transcriptome (HTG EdgeSeq WTA
  • Reproducability Tissue microarrays (TNAs)
  • Lung Fusions Assay: Measure expression of HERs microarrays
  • Fusion Measurement Techniques
  • Cellline carrying – Lung Fusion – HTG EdgeSeq: ALK, ROS1, RET, NTRK1 Fusion
  • Analytics Software: Rearrange for 5’/3′ length
  • HERs insertion
  • Comprehensive Molecular Profiling: The Product
  • Profile expression of 2500 cancer related genes
  • Oncology Biomarker Panel:
  • COmprehensive molecular profiling

 

1:30PM – 1:45PM Michael Ball, GenoLogics

The Impact of Informatics on Clinical NGS Services

LIVE from the PODIUM

  • Informatics market is $Billion
  • 23andMe
  • Informatics
  • Operations in multiple locations
  • From Start Up to Genome Factory
  • ClarityLIMS
  • 8 weeks kickoff to production
  • Future is in the CLOUD
  • Informatics: prevention of errors

 

1:45PM – 2:00PM Jason Merker, Stanford University School of Medicine

Using Genome Sequencing in the Clinical Setting

LIVE from the PODIUM

  • WOrlflow: Stanford CLinical Genomics Service
  • MD order a test
  • Genetics Counsellor counsalt
  • question posed to patient and treating team
  • insurance authorisation
  • biobanking
  • results of Illumina sequencer
  • Data analysis (MedGAP)
  • variants analysis
  • curation meeting
  • genomics Review Group
  • Genomics Review Board – Bioethic/legal, additional genetics expertise
  • FINAL report generation: coverage of metrics, meeting with genetic COunselor
  • Multidisciplinary team – more precise clinical genetic care
  • GS is a test for AUNEXPALINED GENETIC DISEASES
  • potential methodology improvements
  • CNV and other SV detection

 

2:00PM – 2:15PM John Ryals, Metabolon, Inc. CLIA

Getting More from NGS: Metabolomics as a First-line Phenotyping Tool

LIVE FROM THE PODIUM

Where knowing COmes to Life?

  • Discovery HD4 platform launched in 4/2014
  • 200 molecules are derived from bacterial metabolism
  • Metabolon’s proprietaty technologydevelopment
  • Human Metabolome Individually
  • Metabolon GWAS Study- Nature 477, 54-60 (2011)
  • 145 Associations
  • Conclusiono: Genetic Origins of Individual Variations in Metabolosm

200 patients – blood and urine tests

70 unaffected cases

Correct Disease assessment

  • Patient 11315: thymidine – Maple Syrup Urine Disease mutation on an ENZYME
  • Metabolic signatures in Patients: Gzene Penetrations
  • case 3905 – Fructose intollerence vs sorbitol Case 3958: Urea Case 3976: Liver – shows tylenol toxicite

@PMWCintl 

#PMWC15

#startup #biotech #pharmanews @BiotechNews

@BloombergNews

@CancerNews

#Cancer Therapy

#science  #innovation @BloombergTV

Read Full Post »

10:30AM-12PM, January 26, 2015  – NGS Applications: Impact of Genomics on Cancer Care – LIVE @Silicon Valley 2015 Personalized Medicine World Conference, Mountain View, CA

Reporter: Aviva Lev-Ari, PhD, RN

Real Time Conference Coverage with Social Media

@Computer History Museum by Dr. Aviva Lev-Ari, PhD, RN

Session Chair: Frank S. Ong, Illumina (Chair)

LIVE FROM THE PODIUM

Changing aspects of Genomics

10:30AM – 10:45AM John Leite, Illumina

The Path to Adoption of NGS for Clinical Oncology Management

  • Research – Computing Discovery
  • Translation
  • Clinical

Knowledge GAP CRISIS – Omics vs Paths

  • testing
  • reimbursement – How will NGS help profitability by lowering the Cost of Testing
  • Enabling Oncology applications – COmplete clinical SOlutions
  • TRADITIONAL APPROACH: One drug—>> COmpanion Test (single target) –>>> Patients
  • PRECISION ONCOLOGY — PHARMA ALLIANACE WITH AZ, JENSEN, — UNIVERSAL SOLUTION REQUIRES COLLABORATIONS WITH CANCER TREATMENT CENTERS
  • Clinical NGS Standard – Suite of standards: SAmple processing, content, sequencing
  • Performance evaluation: Change in management behavior, how tests are ordered, cost to be low

10:45AM – 11:00AM Mike Nolan, Thermo Fisher

Collaboration in an Ecosystem

Pioneering the Path to Precision Oncology Through Next-Generation Sequencing

LIVE from the PODIUM
ThermoScientific – a Leader in NGS
  • Ion Torrent NGS Cancer Research Tools
  • 75% of Cancer patients are treated in the community
  • >600 types of tests for clinical Research labs
  • Global OncoNetwork COnsorsium
  • Development of Regulated NGS Oncology SolutionsL From Academic Center to the Clinic
  • Oncomine: Cancer Research Panel
  • NCI Match Trial –
  • New LiquidBiopsy – NGS Workflow — ONE blood cell
  • Leading the way in NGS Oncology Genomics

11:00AM – 11:15AM Brad Gray, NanoString Technologies

Improving Cancer Care Through Localized Tumor Profiling

LIVE from the PODIUM

  • Improving Cancer Care Through localized Tumor Profiling
  • Cancer Translational Paradox: tumor goes smaller with Therapy
  • Automated workflow – NanoString Advantage: Localized profiling –>>Locatiles
  • Molecular RNA – NOT Sequencing: nCOUNTER: Powerful CHemistry, simple Workflow
  • nanoString: 2008 gene expression, gene fusion, multiple proteins
  • 600 Peer review papers published using this technology
  • 50% – install based in CHina
  • major Pharma
  • Clinical Diagnostics: Pfizer
  • DIagnostics Lab: Washington Univeristy, St. Louis – Breast Cancer Assay
  • Companion Diagnostics: BioPharma: Celgene – Lymphoma, Leukhemia
  • Prosigna: Informing Breast Cancer Treatment Decisions – 30 Worlworld
  • Companion DIagnostics: Celgene Collaboration Clinical Labs offer Prosigna Testing – Celgene is funding the development
  • 250 days from when a paper was published to having a test to deliver
  • Multiplex gene expression and high growth Companion Diagnostics

 

11:15AM – 11:30AM Mark Erlander, Trovagene CLIA, NASDAQ

Quantitative Detection of Cancer Mutations in Liquid Biopsy Samples

LIVE FROM THE PODIUM

  • Circulating Tumor DNA (ctDNA): Main advantages
  • Detection of mutation genetics
  • Metastatic Cancer: Monitoring Mutation Level
  • Platforme: DCP – Precision Cancer Monitoring
  • Samples in Urine and Plasma: Proprietary Mutant Allele Enrichment Method
  • how to measure changes: in plasma circulating DNA in less quantity – In urine better for harvesting DNA
  • Prospective blinded study of BRAF V600E Mutation
  • Detection in Cell-Free DNA of Patients with Systemic Historic ctDNA Improve Genotyping Over Tissue Biopsies in Histiocyctic
  • Correction between Longitudinal ctDNA and Radiographic Response
  • colonorectal: Urine pationet and Plasma circualting Metastesis cells from the LIVER
  • high concordance between Urine and Palsma ctDNA : Monitoring During and Post Surgery of KRAS
  • Pancreatic Cancer, collaboration with Copenhagen University: IF KRAS IS HIGH SURVIVAL WILL BE LOW — surgery intervention is critical for survival
  • NSCLC – Lung Cancer: EGFR – Cost of Biopsy for Lung Cancer $1400, healthcare cost burden – test of urine – lower the burden of Cost

 

11:30AM – 11:45AM Tom Willis, Sequenta

Immune Response Profiling: Actionable Insights Through Next-Gen Sequencing

LIVE from the PODIUM

  • The Immune System is involved in almost every aspect of Human Health
  • Immune System Diversity is created through DNA Recombination: T and B cells
  • NGSis used for DNA Recombination of T and B Cells
  • Application system of bar codes for every cell sequence – cataloguing
  • Clinical validation – ClonoSIGHT for Lymphoid Cancers – CLL
  • 1 Million patients a year — WHO will benefit?? – Clinical Needs for Testing
  • Using ClonoSIGHT to measure MRD – Monitoring after Transplant
  • bar code of cancer cells using ClonoSIGHT to revolutionize MRD Testing
  • Opportunity to Guide Therapy in Hematology: Multiple Myeloma

 

11:45 Audience Q&A

 

@PMWCintl 

#PMWC15

#startup #biotech #pharmanews @BiotechNews

@BloombergNews

@CancerNews

#Cancer Therapy

#science  #innovation @BloombergTV

 

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9AM-10AM, January 26, 2015 – Newborn & Prenatal Diagnosis – LIVE @Silicon Valley 2015 Personalized Medicine World Conference, Mountain View, CA

Reporter: Aviva Lev-Ari, PhD, RN

 

Real Time Conference Coverage with Social Media

@Computer History Museum by Dr. Aviva Lev-Ari, PhD, RN

Session Chair: Susan Gross, Natera (chair)

 

9:00AM – 9:15AM Dennis Lo, Li Ka Shing Institute

Noninvasive Prenatal Testing: What’s Next?

LIVE FROM THE PODIUM

Fragment size vs Frequency  – Size Analysis of Mitrochondrial DNA – for Size-based Molecular Diagnosis , bioanalyzer: Maternal DNA (long) and Fetal (Short) for Plasma DNA size distribution on Chromosome 13

  • Sex Hormone – Congenital – Adreneal steroidogenesis  – Prenatal virility of a fetal fetus – targeting sequencing
  • Father, Mother, homozygos, Mutant Gene vs Normal Gene: Mathernal plasma analysis, if Mother is Heterozygote – proband mutation identified, Maternal plasma targeted MPS: Gene to CHromosome to Fetal Chromosome
  • Maternal Plasma SNPs analysis Mother: A, Father AG
  • Fetal DNA Fraction 14% in first trimester: Maternal blood cell
  • Fetal DNA Fraction 34% – Post delivery plasma
  • Noval DIagnosis : Preeclamsia, non-invasive

 

9:15AM – 9:30AM Susan Gross, Natera

Identifying Constellations in Cell-Free DNA

LIVE from the Podium

  • Traditional Approaches: Counting CirculatingSNPs – 20,000 SNPs – Prenatal Screening
  • NonInvasive Pre: Clinical business develop a DB
  • False Negatives (abnormal) and False Positive (normal)
  • Mother has abnormal x chromosome: Vanishing Twin
  • Constellation DNA Platform from a Global Footprint: Cancer Liquid Biopsy

 

9:30AM – 9:45AM Vince Ramey, DNAnexus

Addressing Operational Challenges of Prenatal Testing such as Scalability and Global Data Access

NGS Test Volume and Delivery: Landscapeand Forecast

  • forecasting regulatory requirements
  • DNAnexus – Founded in 2009: Security, Speed, Control –CLOUD-BASED PLATFORM for clinical data for sequencing
  • they sit between the sequencer and Natera
  • Cloud based genome informatics
  • Clinical Testing Operating Needs: LIMS Integration, Reproduction of Results, Scalable Test Workload
  • Decentralized sequencing, Centralized DAta Management, Globally Scale your Enterprise

 

9:45AM -10AM Ramji Srinivasan, Counsyl

Next Generation Counseling: Reinventing Results Delivery

  • Understanding the results
  • Patients need to get the results
  • Seeing the Expert
  • accessible, credible, timely, scalable,33 board-certified Genetics Counseling
  • PROCESS: Online Delivery flow: patient notified results are ready, Patient schedule first session, patient schedule session to discuss the results
  • Online _ MD Flow: MD sees log, MD order Lab
  • NEW WORL FLOW – automatic e-mail notification is sent with results ready
  • patients view educator videos and schedule consult
  • patient recieves follow up
  • Scale, enhance aptient dedication, flexible for new test data, less time on paper work more with patients

 

@PMWCintl 

#PMWC15

#startup #biotech #pharmanews @BiotechNews

@BloombergNews

@CancerNews

#Cancer Therapy

#science  #innovation @BloombergTV

 

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7:55AM – 9AM, January 26, 2015 –  Introduction and Overview – LIVE @Silicon Valley 2015 Personalized Medicine World Conference, Mountain View, CA

Real Time Conference Coverage with Social Media

@Computer History Museum by Dr. Aviva Lev-Ari, PhD, RN

7:55AM –Ralph Snyderman, Duke University 

Ralph Snyderman, M.D., Chancellor Emeritus, Duke University

 

Ralph Snyderman, MD is Chancellor Emeritus, Duke University and James B. Duke Professor of Medicine in the Duke University School of Medicine. He served as Chancellor for Health Affairs and Dean of the School of Medicine at Duke University from 1989 to July 2004 and led the transition of this excellent medical center into an internationally recognized leader of academic medicine. He oversaw the development of the Duke University Health System, one of the most successful integrated academic health systems in the country, and served as its first President and Chief Executive Officer. Dr. Snyderman has played a leading role in the conception and development of Personalized Health Care, an evolving model of national health care delivery. He was amongst the first to envision and articulate the need to move the current focus of health care from the treatment of disease-events to personalized, predictive, preventive, and participatory care that is focused on the patient. Dr. Snyderman is the recipient of numerous awards recognizing his contributions to research and to developing more rationale models of health care. In 2012, he received the David E. Rogers Award from the Association of American Medical Colleges who referred to Snyderman as “the father of personalized medicine.”

LIVE

Secepbility to disease: Biomarkers for molecular basis of inheritance.based on DISRUPTIVE TECHNOLOGIES AND INNOVATIONS. NEW form of healthcare RISK SECEPTABILITY can be tracked over time, technologies and inovations — From disease to predictive and precision Medicine. THE RIGHR DRUD for the right patient at the right time

8:00AM Peter Donnelly, Oxford University PMWC 2015 UK Introduction and Overview

Peter Donnelly, Director of the Wellcome Trust Centre for Human Genetics, Oxford University

Peter Donnelly is Director of the Wellcome Trust Centre for Human Genetics and Professor of Statistical Science at the University of Oxford. He grew up in Australia and on graduating from the University of Queensland he studied for a doctorate in Oxford as a Rhodes Scholar. He held professorships at the Universities of London and Chicago before returning to Oxford in 1996. Peter’s early research work concerned the development of stochastic models in population genetics, including the coalescent, and then the development of statistical methods for genetic and genomic data. His group developed several widely-used statistical algorithms, including STRUCTURE and PHASE, and, in collaboration with colleagues in Oxford, IMPUTE. His current research focuses on understanding the genetic basis of human diseases, human demographic history, bacterial evolution and infection, and the mechanisms involved in mammalian recombination. Peter played a major role in the HapMap project, and more recently, he chaired the Wellcome Trust Case Control Consortium (WTCCC) and its successor, WTCCC2, a large international collaboration studying the genetic basis of more than 20 common human diseases and conditions in over 60,000 people. He also leads WGS500, an Oxford collaboration with Illumina to sequence 500 individuals with a range of clinical conditions, to assess the short-term potential for whole genome sequencing in clinical medicine. Peter is a Fellow of the Royal Society and of the Academy of Medical Sciences. LIVE – Chair of the WELLCOME TRUST.

In April 2015 same conference in Oxford, UK. Sequencing 100,000 patients in the British Universal Health System by 2017.

8:05AM Amir Dan Rubin, Stanford Health Care Stanford Health Care Delivery Innovation

Amir Dan Rubin, President & CEO, Stanford Health Care

Amir Dan Rubin serves as President and CEO of Stanford Hospital & Clinics in Palo Alto. He previously served as COO for the UCLA Hospital System, responsible for the operations of the Ronald Reagan UCLA Medical Center, Mattel Children’s Hospital at UCLA, the Resnick Neuropsychiatric Hospital at UCLA, Santa Monica-UCLA Medical Center and Orthopedic Hospital, among others. Prior to UCLA, Amir served as COO for Stony Brook University Hospital where he was involved in efforts to improve quality, operations, and the patient experience. Prior to Stony Brook, Amir served as a VP of Operations for Memorial Hermann Hospital in Houston, and before that he was Director of Business Development for the corporate parent of the Memorial Hermann Healthcare System.

 LIVE from the Podium

How Stanford Healthcare system integrates: Science, Compassion one patient at a time. Innovations in the PM area: Monoclonal antibodies, Deep sequencing in blood circulation tumor cells, using biomarkers vs other diagnostics more invasive. Clinical Care: transforming Coordinated Care, Bashboard for the physician to know what to order.

C-i-Care – platform for patients decision support tools, Neuro HealthCare and Genomics is an example for precision medicine

Virtual Care Innovation – platforms for Personalized and MOBILE care, On-line telecom visit with MDs.

8:15AM Craig Venter, JCVI

Craig Venter, Ph.D., Founder & CEO, JCVI

J. Craig Venter is regarded as one of the most forward-looking scientists of the 21st century for his progressive innovations and contributions to genomic research. He is the founder and president of the J. Craig Venter Institute and J. Craig Venter Science Foundation as well as the founder and chairman of the Institute for Genomic Research (TIGR). Dr. Venter has played a vital role in the expeditious sequencing and analysis of the human genome using the methodology of “shotgun sequencing”. His accomplishments in the development of methods for decoding genetic sequences, notably expressed-sequence tags (ESTs), not only helped identify new genes and explore their functions, but also provided a foundation for understanding the relationships between species and the biology of microbes.

LIVE from the Podium

Human Longevity: combining Phynotype with Genotype information for purposes of Predictions. Digitization of the genotype information, many species, bacterias to eurucyrte cell based systems. Syntathising chromosones – synthesize, DNA is a SOftware of life, change in code means change in life.

Interpretation of the Humane Genome is very important in parallel to obtaining more species having a sequenced genome. Inexpensive sequencing solutions, boxes of Sequencers – HLI in LaJolla, Clinical Center and Sequencing Center, Collaboration with Google in Mountain View.

Global Sequencing PacBio Assembly and Scaling. Haploid cells for genome, Sequencing of isolated sperm cells to identify COMPOUND HETEROZYGOTS — compound mutation architecture. WGS in Cancer CAre – Success in Grug: Herceptin, XAKORI, KALYDECO.

HUMAN MICROBIOMES – Metabolomics – GE 7T Whole body MRI – new MRI Imaging algorithms to understand predictions – Brain mapping for Decoding the Brain

Human Phenotyping: collecting data in Brazil.Integrating data better. DB Size: Raw vs Features. Multi-task learning

An Integrative Approach to Medicine – Data vs Knowledge — == — Prediction

8:30 AM Ron Davis, Stanford

Ron Davis, Ph.D., Director, Stanford Genome Technology Center

Dr. Ron Davis developed the R-loop technique of electron microscopy for mapping coding RNA’s which led to the discovery of RNA splicing. Dr. Davis was the first to demonstrate the use of restriction endonucleases for joining DNA fragments. Dr. Davis was a co-collaborator in the development of the first DNA microarray for gene expression profiling, and the gene expression profile of the first complete eukaryotic genome. He is a Professor of Biochemistry & Genetics, and Director of the Stanford Genome Technology Center at Stanford University where he is a researcher in biotechnology and molecular genetics, particularly active in human and yeast genomics and the development of new technologies in genomics, with over 30 biotechnology patents.”
LIVE FROM THE PODIUM
From Stanford Medical Center – Department of Genomics – Stanford Genome Technology Center: BIOCHEMISTRY — NANO-FABRICATION: high sensitivity, low cost, Direct Electrical Detection:
  • DNA Detection on CMOS – developed in 2000 exported to Ion Terrron in 2010
  • Megnetic Nanoparticle Protein RealTime assay – developed in 2005 exported to MagArray
  • Coaxial Nano Magnets – Magnetic beads
  • Horizontal Nanoneedle Arrray – Atomic Layer Deposition of Many Compounds – VO2 Temperature Transition

synthetic Biology for Natural Products Replace Antibodies

  • natural products have high affinitu to proteins: Affinity-based Immuno-sensor – Quantum Biosensor: Spectroscopy in nanoscale based on trunsduction of quantum tunneling current: metal electrolyte
  • Wearable diagnostic device for real-time biomarker monitoring

8:45AM George Church, Harvard Medical School

George Church, Ph.D., Co-developer, Human Genome Project

George Church, Ph.D. Professor of Genetics, Harvard Medical School and Professor of Health Sciences & Technology, Harvard and MIT with Walter Gilbert. He developed the first direct genomic sequencing method in 1984 and helped initiate the Human Genome Project in 1984 while he was a Research Scientist at newly-formed Biogen Inc. He invented the broadly-applied concepts of molecular multiplexing and tags,homologous recombination methods,and DNA array synthesizers. Technology transfer of automated sequencing & software to Genome Therapeutics Corp. resulted in the first commercial genome sequence, (the human pathogen, Helicobacter pylori) in 1994. He initiated the Personal Genome Project (PGP) in 2005 and research on synthetic biology. He is director of the U.S. Department of Energy Center on Bioenergy at Harvard & MIT and director of the National Institutes of Health (NHGRI) Center of Excellence in Genomic Science at Harvard, MIT & Washington University. He has been advisor to 22 companies, most recently co-founding (with Joseph Jacobson, Jay Keasling, and Drew Endy) Codon Devices, a biotech startup dedicated to synthetic biology and (with Chris Somerville) founding LS9, which is focused on biofuels. He is a senior editor for Nature EMBO Molecular Systems Biology.

LIVE from the PODIUM

Synthetic Biology Originator – Testing Human Genome Interpretation

  • Moore’s Law on decrease the cost of sequencing a Genome while error rate decrease exponential as well.
  • NextGen CROSPR, Caribou Biosciences, addgene, egenesis, editas, Sigma/CRISPR
  • Hope from Pig to Organs
  • CRISPR –>> Human Organoids-on-ChipsL Wyss Institute: PAtients Mutations -> normal hiPSC–>> Cardiomyocytes – morphology abnormality –.. Targeted & Genome-wide
  • NIST +FDA Genomeinabottle.org and PersonalGenomes.org – Cohorts consented to sequencing og Genomes
  • Age NAD loss reversal via CRISPR TFAM activation
  • VPR Activation- multiplexed Activation of endo
  • epigenetics and CRISPR: FISSEQ 3D RNA – Fluorescent in situ sequencing – FISH Sequencin – Automated FISSEQ – Fibronecting nRNA – multiple identifiable reads
  • Super -resolution DNA: multiple
  • Expansion microscopy
  • In situ multiplex Proteomix
  • Genome Engineering Demos – 4Mbp Genomically Recorded Organism (GRO)
  • REGENESIS

 

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#PMWC15

#startup #biotech #pharmanews @BiotechNews

@BloombergNews

@CancerNews

#Cancer Therapy

#science  #innovation @BloombergTV

 

 

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Hamburg, Snyderman to Address Timely Issues in Personalized Medicine at 2015 Personalized Medicine World Conference in Silicon Valley

Reporter: Aviva Lev-Ari, PhD, RN

 

 

margaret_hamburg1

Margaret Hamburg, M.D.

FDA Commissioner

 

 

ralph_snyderman

 

 

 

Ralph Snyderman, M.D.

Duke University Professor of Medicine

 

Hamburg will discuss:

  • FDA’s efforts to promote personalized medicine
  • FDA’s proposed framework to regulate laboratory-developed tests (LDTs)

On day two of the conference, PMC President Edward Abrahams will moderate the session titled “Risk, Reward and Innovation: The Economic Feasibility of Personalized Medicine” that will consider pricing options.

More than 100 additional speakers include George Church, Leroy Hood, Ira Klein, Michael Pellini, Kim Popovits, Craig Ventner, Jay Wohlgemuth and Anne Wojcicki, to name a few.

For the complete program go to: http://2015sv.pmwcintl.com/program.php

We look forward to seeing you in Mountain View. Don’t forget to visit us at PMC’s booth.

 

REGISTRATION

<http://pmwcintl.us3.list-manage.com/track/click?u=ae5d3f754afc0381fd85a57af&id=d6f4c4b92d&e=a27adfd7ff>

 

Contact information: team@pmwcintl.com

 

Announcement

LEADERS IN PHARMACEUTICAL BUSINESS INTELLIGENCE

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will cover the event for the Media

Dr. Aviva Lev-Ari will be in attendance on January 26, 2015, 8:00AM to January 28, 2015, 3:30PM

Covering the Event in REALTIME using Social Media

 

 @PMWCintl 

#PMWC15

#startup #biotech #pharmanews @BiotechNews

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@CancerNews

#Cancer Therapy

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Dr. Lev-Ari, Top Contributor on Biotech Groups on LinkedIn 

http://www.linkedin.com/in/avivalevari

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Evolution and Medicine

Reporter and Curator: Larry H. Bernstein, MD, FCAP 

 

http://paleoaerie.org/2015/01/21/what-has-evolution-done-for-me-lately/

Excerpt of article

Cancer is an inescapable fact of life. All of us with either die from it or know someone who will. Cancer is so prevalent because it isn’t a disease in the way a flu or a cold is. No outside force or germ is needed to cause cancer (although it can). It arises from the very way we are put together.  Most of the genes that are needed for multicellular life have been found to be associated with cancer. Cancer is a result of our natural genetic machinery that has been built up over billions of years breaking down over time.

CLONAL EVOLUTION OF CANCER. MEL GREAVES.HTTP://WWW.SCIENCE-CONNECTIONS.COM/TRENDS/SCIENCE_CONTENT/EVOLUTION_6.HTM

Cancer is not only a result of evolutionary processes, cancer itself follows evolutionary theory as it grows. The immune system places a selective pressure on cancer cells, keeping it in check until the cancer evolves a way to avoid it and surpass it in a process known as immunoediting. Cancers face selective pressures in the microenvironments in which they grow. Due to the fast growth of cancer cells, they suck up oxygen in the tissues, causing wildly fluctuating oxygen levels as the body tries to get oxygen to the tissues. This sort of situation is bad for normal tissues and so it is for cancer, at least until they evolve and adapt. At some point, some cancer cells will develop the ability to use what is called aerobic glycolysis to make the ATP we use for energy. Ordinarily, our cells only use glycolysis when they run out of oxygen because aerobic respiration (aka oxidative phosphorylation) is far more efficient. Cancer cells, on the other hand, learn to use glycolysis all the time, even in the presence of abundant oxygen. They may not grow as quickly when there is plenty of oxygen, but they are far better than normal cells at hypoxic, or low oxygen, conditions, which they create by virtue of their metabolism. Moreover, they are better at taking up nutrients because many of the metabolic pathways for aerobic respiration also influence nutrient uptake, so shifting those pathways to nutrient uptake rather than metabolism ensures cancer cells get first pick of any nutrients in the area. The Warburg Effect, as this is called, works by selective pressures hindering those cells that can’t do so and favoring those that can. Because cancer cells have loose genetic controls and they are constantly dividing, the cancer population can evolve, whereas the normal cells cannot.

Evolutionary theory can also be used to track cancer as it metastasizes. If a person has several tumors, it is possible to take biopsies of each one and use standard cladistic programs that are normally used to determine evolutionary relationships between organisms to find which tumor is the original tumor. If the original tumor is not one of those biopsied, it will tell you where the cancer originated within the body. You can thus track the progression of cancer throughout a person’s body. Expanding on this, one can even track the effect of cancer through its effects on how organisms interact within ecosystems, creating its own evolutionary stamp on the environment as its effects radiate throughout the ecosystem.

I’ve talked about cancer at decent length (although I could easily go one for many more pages) because it is less well publicly known than some of the other ways that evolutionary theory helps us out in medicine. The increasing resistance of bacteria and viruses to antibiotics is well known. Antibiotic resistance follows standard evolutionary processes, with the result that antibiotic resistant bacteria are expected to kill 10 million people a year by 2050.  People have to get a new flu shot every year because the flu viruses are legion and they evolve rapidly to bypass old vaccinations.  If we are to accurately predict how the viruses may adapt and properly prepare vaccines for the coming year, evolutionary theory must be taken into account. Without it, the vaccines are much less likely to be effective. Evolutionary studies have pointed out important changes in the Ebola virus and how those changes areaffecting its lethality, which will need to be taken into account for effective treatments. Tracking the origins of viruses, like the avian flu or swine flu, gives us information that will be useful in combating them or even stopping them at their source before they become a problem.

HTTP://WWW.MEDSCAPE.COM/VIEWARTICLE/756378

 

 

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The Personalized Medicine Coalition welcomes the Administration’s focus on Personalized Medicine

Reporter: Aviva Lev-Ari, PhD, RN

 

 

WASHINGTON (Jan. 21, 2015) — The Personalized Medicine Coalition issued the following statement in response to last night’s State of the Union Address.

The Personalized Medicine Coalition welcomes the Administration’s focus on personalized medicine, and is pleased that the President has announced a new “Precision Medicine Initiative.” We look forward to learning the details, and hope that the President’s plan includes needed federal policies that support personalized medicine — outlining a clear regulatory path, supporting payment policies that recognize the importance of value, and putting in place incentives for product development.

We expect the President’s plans to complement the bi-partisan 21st Century Cures Initiative now under discussion in Congress. Personalized medicine improves the quality of patient care and can lead to systemic cost savings. As the President said, the future of medicine depends on it.

President Obama on personalized medicine
State of the Union Address
Jan. 20, 2015:

“21st century businesses will rely on American science, technology, research and development. I want the country that eliminated polio and mapped the human genome to lead a new era of medicine — one that delivers the right treatment at the right time. In some patients with cystic fibrosis, this approach has reversed a disease once thought unstoppable. Tonight, I’m launching a new Precision Medicine Initiative to bring us closer to curing diseases like cancer and diabetes — and to give all of us access to the personalized information we need to keep ourselves and our families healthier.”

###


About the Personalized Medicine Coalition:

The Personalized Medicine Coalition (PMC), representing innovators, scientists, patients, providers, and payers, promotes the understanding and adoption of personalized medicine concepts, services, and products to benefit patients and the health system. For more information about PMC, visit http://www.personalizedmedicinecoalition.org.

 

Contact: Tiffany Harrington
Personalized Medicine Coalition
tharrington@personalizedmedicinecoalition.org
202-589-1755
FOR IMMEDIATE RELEASE

SOURCE

From: <eabrahams@personalizedmedicinecoalition.org>
Date: 21 Jan 2015 17:34:37 -0500
To: <avivalev-ari@alum.berkeley.edu>
Subject: PMC Releases Statement on President Obama’s “Precision Medicine Initiative”

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Point-Of-Need NGS-Based Blood-To-Result Diagnostic: DNAe Acquires nanoMR Inc.

Reporter: Aviva Lev-Ari, PhD, RN

 

 

DNAe Acquires nanoMR Inc. in a Strategic Move to Own Complete Workflow for Point-Of-Need NGS-Based Blood-To-Result Diagnostic

 

Acquisition enables immediate presence in USA, a key market for bloodstream infection diagnosis and other applications

 

London, UK and Albuquerque, NM, USA 19 January 2015 – DNA Electronics Ltd (DNAe), the inventors of semiconductor DNA sequencing technology and developers of a new, revolutionary point-of-need test for blood infections, has on 15 January 2015 completed the acquisition of the entire issued share capital of nanoMR Inc. (nanoMR), an Albuquerque based developer of a novel system for rapid isolation of rare cells in the bloodstream by way of a merger under the laws of Delaware, USA. Led by Arnold Freedman and Dr. Oded Ben-Joseph, Outcome Capital, LLC acted as Exclusive Financial Advisor to nanoMR in the transaction.

 

Integration of the two organizations is effective immediately, creating an 80+ strong team with facilities in the UK and the USA that will operate under the DNAe brand. The acquisition is a key strategic milestone for DNAe, enabling the Company to integrate nanoMR’s unique immunomagnetic Pathogen Capture System (PCS) with its own Genalysis® PCR and semiconductor-based DNA sequencing technology to create a complete blood-to-result solution.

 

The PCS can target multiple rare bacterial and fungal cells  fom bloodstream infections at levels of 1 cell/mL or lower in less than 30 minutes, making it the ideal sample preparation technology for DNAe’s rapid point-of-need diagnostic tests. DNAe’s proven semiconductor DNA sequencing technology is already licensed to Thermo Fisher and is the core of the Ion Torrent™ Next Generation Sequencing (NGS) systems as well as to Geneu, a company selling the world’s first in-store DNA test for personalised skincare.

 

DNAe is developing an integrated instrument and consumable cartridge that will deliver results directly from blood in 2-3 hours. Its first diagnostic product, a test for the rapid diagnosis of bloodstream infections, will identify pathogens in the blood as well as antimicrobial resistance genes. This will allow clinicians to treat patients with appropriate medication before the onset of sepsis, saving lives and reducing the time spent in hospital.

 

Professor Chris Toumazou, Chairman and CEO of DNAe said: “The acquisition of the nanoMR technology and team underscores our commitment to developing a complete point-of-need solution for diagnosis of infectious diseases, particularly those that cause sepsis, where speed and DNA-specific information can make the difference between life and death. nanoMR brings a game-changing technology, a wealth of scientific expertise and the potential for exciting new applications to DNAe.”

 

The combined company will continue to work on nanoMR contracts including the development of PCS and assays for potential infectious agents for the US Department of Health and Human Services Biomedical Advanced Research and Development Agency (BARDA) and will further invest in the development of PCS from its US facility. The UK-based operation will focus on developing Genalysis® technology as part of an integrated system.

 

nanoMR’s CEO Victor Esch said: “By combining our PCS technology with the powerful molecular diagnostic technology developed by DNAe we are in a strong position to create a blood-to-result system with unmatched versatility and performance. DNAe is the perfect match for nanoMR and we look forward to a great future as part of the combined team.”

 

DNAe is an ambitious company led by a highly experienced management team. It has strong financial backing, including major shareholder Genting Berhad, a Malaysian-based global investor with a growing portfolio of cutting–edge healthcare companies.

 

Tan Sri Lim Kok Thay, CEO and Chairman of Genting Berhad said: “This is a major value-creating deal for DNAe. The development of these ground-breaking technologies to address the huge unmet medical need for rapid point-of-need testing for sepsis, as well as other applications, makes it a stand-out company that we are proud to support. We are convinced that the acquisition of the nanoMR technology and the drive and commitment of the management team to accelerate development towards commercialisation will make a major contribution to the improvement of patient care.”

 

About DNAe http://www.dnae.co.uk 

DNA Electronics Ltd. is commercialising its pioneering semiconductor DNA sequencing technology for healthcare applications where rapid near-patient live diagnostics is needed to provide actionable information to clinicians, saving lives by enabling the right treatment at the right time.

 

Through a non-exclusive license to Thermo Fisher, DNAe’s semiconductor sequencing technology is the core of the Ion Torrent™ Next Generation Sequencing (NGS) systems, proving its performance at the laboratory scale.

 

DNAe’s Genalysis® system is a sample-to-result genomic analysis platform based on semiconductor sequencing. Built into a compact device for use at the point-of-need, the system will diagnose accurately and rapidly what infection a patient has, providing the clinician with actionable information to help select the appropriate antibiotics to treat the disease. DNAe’s initial focus is on infectious disease diagnostics, where speed and DNA-specific information can make the difference between life and death. The Company’s first test will be a diagnostic for blood stream infections for use in the management and prevention of sepsis.

 

About nanoMR http://www.nanomr.com 

Founded in 2007 by researchers from the University of New Mexico, nanoMR is an early-stage life sciences company developing novel diagnostic systems for the rapid isolation of rare cell types, including bacterial and fungal pathogens, directly from blood and other matrices.

 

nanoMR’s products use an immunomagnetic capture process that can deliver either viable cells for phenotypic analysis, or extracted DNA for molecular analysis by different DNA-based platforms, including PCR, hybridization and DNA sequencing. The Company’s first product addresses the blood culture market, demonstrating identification of blood-borne infections in less than two hours, compared with days required for conventional blood-culture-based systems.

 

About Outcome Capital http://www.outcomecapital.com

Outcome Capital is a unique investment banking firm that provides middle-market growth companies in the life sciences, healthcare services and technology markets with a value-added client-centric approach to merger, acquisition and corporate finance advisory services. The firm utilizes it’s proven approach to value enhancement by assisting boards and management teams in  navigating both the financial and strategic markets and in implementing the best path for success.  Outcome Capital’s strength stems from its unique ability to draw on its wide range of operational, strategic and private equity experience, its expertise across the value building life-cycle and its broad industry relationships. The professionals at Outcome Capital take pride in their ability to help their clients to make well-informed strategic decisions and recognize the full value created by their vision.

 

 

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SOURCE
From: Eilon Amir <eamir@outcomecapital.com>
Date: Wed, 21 Jan 2015 14:44:46 +0000
To: ‘Aviva Lev-Ari’ <AvivaLev-Ari@alum.berkeley.edu>
Conversation: Outcome Capital Transaction
Subject: Outcome Capital Transaction

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