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Archive for the ‘Cancer Informatics’ Category


Bioinformatics Tool Review: Genome Variant Analysis Tools

Curator: Stephen J. Williams, Ph.D.

Updated 11/15/2018

The following post will be an ongoing curation of reviews of gene variant bioinformatic software.

 

The Ensembl Variant Effect Predictor.

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.

Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4.

Author information

1

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. wm2@ebi.ac.uk.

2

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

3

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. fiona@ebi.ac.uk.

Abstract

The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.

 

Rare diseases can be difficult to diagnose due to low incidence and incomplete penetrance of implicated alleles however variant analysis of whole genome sequencing can identify underlying genetic events responsible for the disease (Nature, 2015).  However, a large cohort is required for many WGS association studies in order to produce enough statistical power for interpretation (see post and here).  To this effect major sequencing projects have been initiated worldwide including:

A more thorough curation of sequencing projects can be seen in the following post:

Icelandic Population Genomic Study Results by deCODE Genetics come to Fruition: Curation of Current genomic studies

 

And although sequencing costs have dramatically been reduced over the years, the costs to determine the functional consequences of such variants remains high, as thorough basic research studies must be conducted to validate the interpretation of variant data with respect to the underlying disease, as only a small fraction of variants from a genome sequencing project will encode for a functional protein.  Correct annotation of sequences and variants, identification of correct corresponding reference genes or transcripts in GENCODE or RefSeq respectively offer compelling challenges to the proper identification of sequenced variants as potential functional variants.

To this effect, the authors developed the Ensembl Variant Effect Predictor (VEP), which is a software suite that performs annotations and analysis of most types of genomic variation in coding and non-coding regions of the genome.

Summary of Features

  • Annotation: VEP can annotate two broad categories of genomic variants
    • Sequence variants with specific and defined changes: indels, base substitutions, SNVs, tandem repeats
    • Larger structural variants > 50 nucleotides
  • Species and assembly/genomic database support: VEP can analyze data from any species with assembled genome sequence and annotated gene set. VEP supports chromosome assemblies such as the latest GRCh38, FASTA, as well as transcripts from RefSeq as well as user-derived sequences
  • Transcript Annotation: VEP includes a wide variety of gene and transcript related information including NCBI Gene ID, Gene Symbol, Transcript ID, NCBI RefSeq ID, exon/intron information, and cross reference to other databases such as UniProt
  • Protein Annotation: Protein-related fields include Protein ID, RefSeq ID, SwissProt, UniParc ID, reference codons and amino acids, SIFT pathogenicity score, protein domains
  • Noncoding Annotation: VEP reports variants in noncoding regions including genomic regulatory regions, intronic regions, transcription binding motifs. Data from ENCODE, BLUEPRINT, and NIH Epigenetics RoadMap are used for primary annotation.  Plugins to the Perl coding are also available to link other databases which annotate noncoding sequence features.
  • Frequency, phenotype, and citation annotation: VEP searches Ensembl databases containing a large amount of germline variant information and checks variants against the dbSNP single nucleotide polymorphism database. VEP integrates with mutational databases such as COSMIC, the Human Gene Mutation Database, and structural and copy number variants from Database of Genomic Variants.  Allele Frequencies are reported from 1000 Genomes and NHLBI and integrates with PubMed for literature annotation.  Phenotype information is from OMIM, Orphanet, GWAS and clinical information of variants from ClinVar.
  • Flexible Input and Output Formats: VEP supports input data format called “variant call format” or VCP, a standard in next-gen sequencing. VEP has the ability to process variant identifiers from other database formats.  Output formats are tab deliminated and give the user choices in presentation of results (HTML or text based)
  • Choice of user interface
    • Online tool (VEP Web): simple point and click; incorporates Instant VEP Functionality and copy and paste features. Results can be stored online in cloud storage on Ensembl.
    • VEP script: VEP is available as a downloadable PERL script (see below for link) and can process large amounts of data rapidly. This interface is powerfully flexible with the ability to integrate multiple plugins available from Ensembl and GitHub.  The ability to alter the PERL code and add plugins and code functions allows the flexibility to modify any feature of VEP.
    • VEP REST API: provides robust computational access to any programming language and returns basic variant annotation. Can make use of external plugins.

 

 

Watch Video on VES Instructional Webinar: https://youtu.be/7Fs7MHfXjWk

Watch Video on VES Web Version training on How to Analyze Your Sequence in VEP

 

 

Availability of data and materials

The dataset supporting the conclusions of this article is available from Illumina’s Platinum Genomes [93] and using the Ensembl release 75 gene set. Pre-built data sets are available for all Ensembl and Ensembl Genomes species [94]. They can also be downloaded automatically during set up whilst installing the VEP.

 

References

Large-scale discovery of novel genetic causes of developmental disorders.

Deciphering Developmental Disorders Study.

Nature2015 Mar 12;519(7542):223-8. doi: 10.1038/nature14135. PMID:25533962

Updated 11/15/2018

 

Research Points to Caution in Use of Variant Effect Prediction Bioinformatic Tools

Although we have the ability to use high throughput sequencing to identify allelic variants occurring in rare disease, correlation of these variants with the underlying disease is often difficult due to a few concerns:

  • For rare sporadic diseases, classical gene/variant association studies have proven difficult to perform (Meyts et al. 2016)
  • As Whole Exome Sequencing (WES) returns a considerable number of variants, how to differentiate the normal allelic variation found in the human population from disease-causing pathogenic alleles
  • For rare diseases, pathogenic allele frequencies are generally low

Therefore, for these rare pathogenic alleles, the use of bioinformatics tools in order to predict the resulting changes in gene function may provide insight into disease etiology when validation of these allelic changes might be experimentally difficult.

In a 2017 Genes & Immunity paper, Line Lykke Andersen and Rune Hartmann tested the reliability of various bioinformatic software to predict the functional consequence of variants of six different genes involved in interferon induction and sixteen allelic variants of the IFNLR1 gene.  These variants were found in cohorts of patients presenting with herpes simplex encephalitis (HSE). Most of the adult population is seropositive for Herpes Simplex Virus (HSV) however a minor fraction (1 in 250,000 individuals per year) of HSV infected individuals will develop HSE (Hjalmarsson et al., 2007).  It has been suggested that HSE occurs in individuals with rare primary immunodeficiencies caused by gene defects affecting innate immunity through reduced production of interferons (IFN) (Zhang et al., Lim et al.).

 

References

Meyts I, Bosch B, Bolze A, Boisson B, Itan Y, Belkadi A, et al. Exome and genome sequencing for inborn errors of immunity. J Allergy Clin Immunol. 2016;138:957–69.

Hjalmarsson A, Blomqvist P, Skoldenberg B. Herpes simplex encephalitis in Sweden, 1990-2001: incidence, morbidity, and mortality. Clin Infect Dis. 2007;45:875–80.

Zhang SY, Jouanguy E, Ugolini S, Smahi A, Elain G, Romero P, et al. TLR3 deficiency in patients with herpes simplex encephalitis. Science. 2007;317:1522–7.

Lim HK, Seppanen M, Hautala T, Ciancanelli MJ, Itan Y, Lafaille FG, et al. TLR3 deficiency in herpes simplex encephalitis: high allelic heterogeneity and recurrence risk. Neurology. 2014;83:1888–97.

 

Genes Immun. 2017 Dec 4. doi: 10.1038/s41435-017-0002-z.

Frequently used bioinformatics tools overestimate the damaging effect of allelic variants.

Andersen LL1Terczyńska-Dyla E1Mørk N2Scavenius C1Enghild JJ1Höning K3Hornung V3,4Christiansen M5,6Mogensen TH2,6Hartmann R7.

 

Abstract

We selected two sets of naturally occurring human missense allelic variants within innate immune genes. The first set represented eleven non-synonymous variants in six different genes involved in interferon (IFN) induction, present in a cohort of patients suffering from herpes simplex encephalitis (HSE) and the second set represented sixteen allelic variants of the IFNLR1 gene. We recreated the variants in vitro and tested their effect on protein function in a HEK293T cell based assay. We then used an array of 14 available bioinformatics tools to predict the effect of these variants upon protein function. To our surprise two of the most commonly used tools, CADD and SIFT, produced a high rate of false positives, whereas SNPs&GO exhibited the lowest rate of false positives in our test. As the problem in our test in general was false positive variants, inclusion of mutation significance cutoff (MSC) did not improve accuracy.

Methodology

  1. Identification of rare variants
  2. Genomes of nineteen Dutch patients with a history of HSE sequenced by WES and identification of novel HSE causing variants determined by filtering the single nucleotide polymorphisms (SNPs) that had a frequency below 1% in the NHBLI Exome Sequencing Project Exome Variant Server and the 1000 Genomes Project and were present within 204 genes involved in the immune response to HSV.
  3. Identified variants (204) manually evaluated for involvement of IFN induction based on IDBase and KEGG pathway database analysis.
  4. In-silico predictions: Variants classified by the in silico variant pathogenicity prediction programs: SIFT, Mutation Assessor, FATHMM, PROVEAN, SNAP2, PolyPhen2, PhD-SNP, SNP&GO, FATHMM-MKL, MutationTaster2, PredictSNP, Condel, MetaSNP, and CADD. Each program returned prediction scores measuring likelihood of a variant either being ‘deleterious’ or ‘neutral’. Prediction accuracy measured as

ACC = (true positive+true negative)/(true positive+true negative+false positive+false negative)

 

  1. Validation of prediction software/tools

In order to validate the predictive value of the software, HEK293T cells, deficient in IRF3, MAVS, and IKKe/TBK1, were cotransfected with the nine variants of the aforementioned genes and a luciferase reporter under control of the IFN-b promoter and luciferase activity measured as an indicator of IFN signaling function.  Western blot was performed to confirm the expression of the constructs.

 

Results

Table 2 Summary of the
bioinformatic predictions
HSE variants IFNLR1 variants Overall ACC
TN TP FN FP Total ACC TN TP FN FP Total ACC
Uniform cutoff
SIFT 4 1 0 4 9 0.56 8 1 0 7 16 0.56 0.56
Mutation assessor 6 1 0 2 9 0.78 9 1 0 6 16 0.63 0.68
FATHMM 7 1 0 1 9 0.89 0.89
PROVEAN 8 1 0 0 9 1.00 11 1 0 4 16 0.75 0.84
SNAP2 5 1 0 3 9 0.67 8 0 1 7 16 0.50 0.56
PolyPhen2 6 1 0 2 9 0.78 12 1 0 3 16 0.81 0.80
PhD-SNP 7 1 0 1 9 0.89 11 1 0 4 16 0.75 0.80
SNPs&GO 8 1 0 0 9 1.00 14 1 0 1 16 0.94 0.96
FATHMM MKL 4 1 0 4 9 0.56 13 0 1 2 16 0.81 0.72
MutationTaster2 4 0 1 4 9 0.44 14 0 1 1 16 0.88 0.72
PredictSNP 6 1 0 2 9 0.78 11 1 0 4 16 0.75 0.76
Condel 6 1 0 2 9 0.78 0.78
Meta-SNP 8 1 0 0 9 1.00 11 1 0 4 16 0.75 0.84
CADD 2 1 0 6 9 0.33 8 0 1 7 16 0.50 0.44
MSC 95% cutoff
SIFT 5 1 0 3 9 0.67 8 1 0 8 16 0.50 0.56
PolyPhen2 6 1 0 2 9 0.78 13 1 0 3 16 0.81 0.80
CADD 4 1 0 4 9 0.56 7 0 1 9 16 0.44 0.48

 

Note: TN: true negative, TP: true positive, FN: false negative, FP: false positive, ACC: accuracy

Functional testing (data obtained from reporter construct experiments) were considered as the correct outcome.

Three prediction tools (PROVEAN, SNP&GO, and MetaSNP correctly predicted the effect of all nine variants tested.

 

Other articles related to Genomics and Bioinformatics on this online Open Access Journal Include:

Finding the Genetic Links in Common Disease: Caveats of Whole Genome Sequencing Studies

 

Large-scale sequencing does not support the idea that lower-frequency variants have a major role in predisposition to type 2 diabetes

 

US Personalized Cancer Genome Sequencing Market Outlook 2018 –

 

Icelandic Population Genomic Study Results by deCODE Genetics come to Fruition: Curation of Current genomic studies

 

 

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Single-cell Genomics: Directions in Computational and Systems Biology – Contributions of Prof. Aviv Regev @Broad Institute of MIT and Harvard, Cochair, the Human Cell Atlas Organizing Committee with Sarah Teichmann of the Wellcome Trust Sanger Institute

 

Curator: Aviva Lev-Ari, PhD, RN

 

Dana Pe’er, PhD, now chair of computational and systems biology at the Sloan Kettering Institute at the Memorial Sloan Kettering Cancer Center and a member of the Human Cell Atlas Organizing Committee,

what really sets Regev apart is the elegance of her work. Regev, says Pe’er, “has a rare, innate ability of seeing complex biology and simplifying it and formalizing it into beautiful, abstract, describable principles.”

Dr. Aviv Regev, an MIT biology professor who is also chair of the faculty of the Broad and director of its Klarman Cell Observatory and Cell Circuits Program, was reviewing a newly published white paper detailing how the Human Cell Atlas is expected to change the way we diagnose, monitor, and treat disease at a gathering of international scientists at Israel’s Weizmann Institute of Science, 10/2017.

For Regev, the importance of the Human Cell Atlas goes beyond its promise to revolutionize biology and medicine. As she once put it, without an atlas of our cells, “we don’t really know what we’re made of.”

Regev, turned to a technique known as RNA interference (she now uses CRISPR), which allowed her to systematically shut genes down. Then she looked at which genes were expressed to determine how the cells’ response changed in each case. Her team singled out 100 different genes that were involved in regulating the response to the pathogens—some of which weren’t previously known to be involved in immune function. The study, published in Science, generated headlines.

The project, the Human Cell Atlas, aims to create a reference map that categorizes all the approximately 37 trillion cells that make up a human. The Human Cell Atlas is often compared to the Human Genome Project, the monumental scientific collaboration that gave us a complete readout of human DNA, or what might be considered the unabridged cookbook for human life. In a sense, the atlas is a continuation of that project’s work. But while the same DNA cookbook is found in every cell, each cell type reads only some of the recipes—that is, it expresses only certain genes, following their DNA instructions to produce the proteins that carry out a cell’s activities. The promise of the Human Cell Atlas is to reveal which specific genes are expressed in every cell type, and where the cells expressing those genes can be found.

Regev says,

The final product, will amount to nothing less than a “periodic table of our cells,” a tool that is designed not to answer one specific question but to make countless new discoveries possible.

Sequencing the RNA of the cells she’s studying can tell her only so much. To understand how the circuits change under different circumstances, Regev subjects cells to different stimuli, such as hormones or pathogens, to see how the resulting protein signals change.

“the modeling step”—creating algorithms that try to decipher the most likely sequence of molecular events following a stimulus. And just as someone might study a computer by cutting out circuits and seeing how that changes the machine’s operation, Regev tests her model by seeing if it can predict what will happen when she silences specific genes and then exposes the cells to the same stimulus.

By sequencing the RNA of individual cancer cells in recent years—“Every cell is an experiment now,” she says—she has found remarkable differences between the cells of a single tumor, even when they have the same mutations. (Last year that work led to Memorial Sloan Kettering’s Paul Marks Prize for Cancer Research.) She found that while some cancers are thought to develop resistance to therapy, a subset of melanoma cells were resistant from the start. And she discovered that two types of brain cancer, oligodendroglioma and astrocytoma, harbor the same cancer stem cells, which could have important implications for how they’re treated.

As a 2017 overview of the Human Cell Atlas by the project’s organizing committee noted, an atlas “is a map that aims to show the relationships among its elements.” Just as corresponding coastlines seen in an atlas of Earth offer visual evidence of continental drift, compiling all the data about our cells in one place could reveal relationships among cells, tissues, and organs, including some that are entirely unexpected. And just as the periodic table made it possible to predict the existence of elements yet to be observed, the Human Cell Atlas, Regev says, could help us predict the existence of cells that haven’t been found.

This year alone it will fund 85 Human Cell Atlas grants. Early results are already pouring in.

  • In March, Swedish researchers working on cells related to human development announced they had sequenced 250,000 individual cells.
  • In May, a team at the Broad made a data set of more than 500,000 immune cells available on a preview site.

The goal, Regev says, is for researchers everywhere to be able to use the open-source platform of the Human Cell Atlas to perform joint analyses.

Eric Lander, PhDthe founding director and president of the Broad Institute and a member of the Human Cell Atlas Organizing Committee, likens it to genomics.

“People thought at the beginning they might use genomics for this application or that application,” he says. “Nothing has failed to be transformed by genomics, and nothing will fail to be transformed by having a cell atlas.”

“How did we ever imagine we were going to solve a problem without single-cell resolution?”

SOURCE

https://www.technologyreview.com/s/611786/the-cartographer-of-cells/?utm_source=MIT+Technology+Review&utm_campaign=Alumni-Newsletter_Sep-Oct-2018&utm_medium=email

Other related articles published in this Open Access Online Scientific Journal include the following:

 

University of California Santa Cruz’s Genomics Institute will create a Map of Human Genetic Variations

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2015/01/13/university-of-california-santa-cruzs-genomics-institute-will-create-a-map-of-human-genetic-variations/

 

Recognitions for Contributions in Genomics by Dan David Prize Awards

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2017/07/31/recognitions-for-contributions-in-genomics-by-dan-david-prize-awards/

 

ENCODE (Encyclopedia of DNA Elements) program: ‘Tragic’ Sequestration Impact on NHGRI Programs

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/09/18/encode-encyclopedia-of-dna-elements-program-tragic-sequestration-impact-on-nhgri-programs/

 

Single-cell Sequencing

Genomic Diagnostics: Three Techniques to Perform Single Cell Gene Expression and Genome Sequencing Single Molecule DNA Sequencing

Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2017/07/04/genomic-diagnostics-three-techniques-to-perform-single-cell-gene-expression-and-genome-sequencing-single-molecule-dna-sequencing/

 

LIVE – Real Time – 16th Annual Cancer Research Symposium, Koch Institute, Friday, June 16, 9AM – 5PM, Kresge Auditorium, MIT – See, Aviv Regev

REAL TIME PRESS COVERAGE & Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2017/03/13/16th-annual-cancer-research-symposium-koch-institute-friday-june-16-9am-5pm-kresge-auditorium-mit/

 

LIVE 11/3/2015 1:30PM @The 15th Annual EmTech MIT – MIT Media Lab: Top 10 Breakthrough Technologies & 2015 Innovators Under 35 – See, Gilead Evrony

REAL TIME PRESS COVERAGE & Reporter: Aviva Lev-Ari, PhD, RN
https://pharmaceuticalintelligence.com/2015/11/03/live-1132015-130pm-the-15th-annual-emtech-mit-mit-media-lab-top-10-breakthrough-technologies-2015-innovators-under-35/

 

Cellular Guillotine Created for Studying Single-Cell Wound Repair

Reporter: Irina Robu, PhD

https://pharmaceuticalintelligence.com/2017/06/29/cellular-guillotine-created-for-studying-single-cell-wound-repair/

 

New subgroups of ILC immune cells discovered through single-cell RNA sequencing

Reporter: Stephen J Williams, PhD

https://pharmaceuticalintelligence.com/2016/02/17/new-subgroups-of-ilc-immune-cells-discovered-through-single-cell-rna-sequencing-from-karolinska-institute/

 

#JPM16: Illumina’s CEO on new genotyping array called Infinium XT and Bio-Rad Partnership for single-cell sequencing workflow

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2016/01/12/jpm16-illuminas-ceo-on-new-genotyping-array-called-infinium-xt-and-bio-rad-partnership-for-single-cell-sequencing-workflow/

 

Juno Acquires AbVitro for $125M: high-throughput and single-cell sequencing capabilities for Immune-Oncology Drug Discovery

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2016/01/12/juno-acquires-abvitro-for-125m-high-throughput-and-single-cell-sequencing-capabilities-for-immune-oncology-drug-discovery/

 

NIH to Award Up to $12M to Fund DNA, RNA Sequencing Research: single-cell genomics,  sample preparation,  transcriptomics and epigenomics, and  genome-wide functional analysis.

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2015/10/27/nih-to-award-up-to-12m-to-fund-dna-rna-sequencing-research-single-cell-genomics-sample-preparation-transcriptomics-and-epigenomics-and-genome-wide-functional-analysis/

 

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

https://pharmaceuticalintelligence.com/2012/08/07/genome-wide-single-cell-analysis-of-recombination-activity-and-de-novo-mutation-rates-in-human-sperm/

REFERENCES to Original studies

In Science, 2018

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

 See all authors and affiliations

Science  21 Apr 2017:
Vol. 356, Issue 6335, eaah4573
DOI: 10.1126/science.aah4573
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

See all authors and affiliations

Science  26 Apr 2018:
eaar3131
DOI: 10.1126/science.aar3131

In Nature, 2018 and 2017

How to build a human cell atlas

Aviv Regev is a maven of hard-core biological analyses. Now she is part of an effort to map every cell in the human body.

  1. Research | 

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  6. Amendments and Corrections | 

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  10. Comments and Opinion | 

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5:00 – 5:45 PM Early Diagnosis Through Predictive Biomarkers, NonInvasive Testing

Reporter: Stephen J. Williams, Ph.D.

 

Diagnosing cancer early is often the difference between survival and death. Hear from experts regarding the new and emerging technologies that form the next generation of cancer diagnostics.

Moderator: Heather Rose, Director of Licensing, Thomas Jefferson University
Speakers:
Bonnie Anderson, Chairman and CEO, Veracyte @BonnieAndDx
Kevin Hrusovsky, Founder and Chairman, Powering Precision Health @KevinHrusovsky

Bonnie Anderson and Veracyte produces genomic tests for thyroid and other cancer diagnosis.  Kevin Hrusovksy and Precision Health uses peer reviewed evidence based medicine to affect precision medicine decision.

Bonnie: aim to get a truth of diagnosis.  Getting tumor tissue is paramount as well as properly preserved tissue.  They use deep RNA sequencing  and machine learning  in their clinically approved tests.

Kevin: Serial biospace entrepreneur.  Two diseases, cancer and neurologic, have been diseases which have been hardest to get reproducible and validated biomarkers of early disease.  He concentrates on protein biomarkers.

Heather:  FDA has recently approved drugs for early disease intervention.  However the use of biomarkers can go beyond patient stratification in clinical trials.

Kevin: 15 approved drugs for MS but the markers are scans looking for brain atrophy which is too late of an endpoint.  So we need biomarkers of early disease progression.  We can use those early biomarkers of disease progression so pharma can target those early biomarkers and or use those early biomarkers of disease progression  for endpoint

Bonnie: exciting time in the early diagnostics field. She prefers transcriptomics to DNA based methods such as WES or WGS (whole exome or whole genome sequencing).  It was critical to show data on the cost savings imparted by their transcriptomic based thryoid cancer diagnostic test for payers to consider this test eligible for reimbursement.

Kevin: There has been 20 million  CAT scans for  cancer but it is estimated 90% of these scans led to misdiagnosis. Biomarker  development  has revolutionized diagnostics in this disease area.  They have developed a breakthrough panel of ten protein biomarkers in serum which he estimates may replace 5 million mammograms.

All panelists agreed on the importance of regulatory compliance and the focus of new research should be on early detection.  In addition they believe that Dr. Gotlieb’s appointment to the FDA is a positive for the biomarker development field, as Dr. Gotlieb understands the potential and importance of early detection and prevention of disease.  Kevin also felt Dr. Gotlieb understands the importance of incorporating biomarkers as endpoints in clinical trials.  Over 750 phase 1,2, and 3 clinical trials use biomarker endpoints but the pharma companies still need to prove the biomarkers clinical relevance to the FDA.They also agreed it would be helpful to involve advocacy groups in putting more pressure on the healthcare providers and policy makers on this importance of diagnostics as a preventative measure.

In addition, the discovery and use of biomarkers as disease endpoints has led to a resurgence of Alzheimer’s disease drug development by companies which have previously given up on these type of neurodegenerative diseases.

Kevin feels proteomics offers great advantages over DNA-based diagnostics, especially in cancer such as ovarian cancer, where a high degree of specificity for a diagnostic test is required to ascertain if a woman should undergo prophylactic oophorectomy.  He suggests that a new blood-based protein biomarker panel is being developed for early detection of some forms of ovarian cancer.

Please follow on Twitter using the following #hash tags and @pharma_BI

#MCConverge

#cancertreatment

#healthIT

#innovation

#precisionmedicine

#healthcaremodels

#personalizedmedicine

#healthcaredata

And at the following handles:

@pharma_BI

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Please see related articles on Live Coverage of Previous Meetings on this Open Access Journal

LIVE – Real Time – 16th Annual Cancer Research Symposium, Koch Institute, Friday, June 16, 9AM – 5PM, Kresge Auditorium, MIT

Real Time Coverage and eProceedings of Presentations on 11/16 – 11/17, 2016, The 12th Annual Personalized Medicine Conference, HARVARD MEDICAL SCHOOL, Joseph B. Martin Conference Center, 77 Avenue Louis Pasteur, Boston

Tweets Impression Analytics, Re-Tweets, Tweets and Likes by @AVIVA1950 and @pharma_BI for 2018 BioIT, Boston, 5/15 – 5/17, 2018

BIO 2018! June 4-7, 2018 at Boston Convention & Exhibition Center

https://pharmaceuticalintelligence.com/press-coverage/

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Reporter: Stephen J. Williams, PhD

10:00-10:45 AM The Davids vs. the Cancer Goliath Part 1

Startups from diagnostics, biopharma, medtech, digital health and emerging tech will have 8 minutes to articulate their visions on how they aim to tame the beast.

Start Time End Time Company
10:00 10:08 Belong.Life
10:09 10:17 Care+Wear
10:18 10:26 OncoPower
10:27 10:35 PolyAurum LLC
10:36 10:44 Seeker Health

Speakers:
Karthik Koduru, MD, Co-Founder and Chief Oncologist, OncoPower
Eliran Malki, Co-Founder and CEO, Belong.Life
Chaitenya Razdan, Co-founder and CEO, Care+Wear @_crazdan
Debra Shipley Travers, President & CEO, PolyAurum LLC @polyaurum
Sandra Shpilberg, Founder and CEO, Seeker Health @sandrashpilberg

Belong Life

  • 10,000 cancer patients a month helping patients navigate cancer care with Belong App
  • Belong Eco system includes all their practitioners and using a trigger based content delivery (posts, articles etc)
  • most important taking unstructured health data (images, social activity, patient compilance) and converting to structured data

Care+Wear

personally design picc line cover for oncology patients

partners include NBA Major league baseball, Oscar de la Renta,

designs easy access pic line gowns and shirts

OncoPower :Digital Health in a Blockchain Ecosystem

problems associated with patient adherence and developed a product to address this

  1. OncoPower Blockchain: HIPAA compliant using the coin Oncopower security token to incentiavize patients and oncologists to consult with each other or oncologists with tumor boards; this is not an initial coin offering

PolyArum

  • spinout from UPENN; developing a nanoparticle based radiation therapy; glioblastoma muse model showed great response with gold based nanoparticle and radiation
  • they see enhanced tumor penetration, and retention of the gold nanoparticles
  • however most nanoparticles need to be a large size greater than 5 nm to see effect so they used a polymer based particle; see good uptake but excretion past a week so need to re-dose with Au nanoparticles
  • they are looking for capital and expect to start trials in 2020

Seeker Health

  • tying to improve the efficiency of clinical trial enrollment
  • using social networks to find the patients to enroll in clinical trials
  • steps they use 1) find patients on Facebook, Google, Twitter 2) engage patient screen 3) screening at clinical sites
  • Seeker Portal is a patient management system: patients referred to a clinical site now can be tracked

11:00- 11:45 AM Breakout: How to Scale Precision Medicine

The potential for precision medicine is real, but is limited by access to patient datasets. How are government entities, hospitals and startups bringing the promise of precision medicine to the masses of oncology patients

Moderator: Sandeep Burugupalli, Senior Manager, Real World Data Innovation, Pfizer @sandeepburug
Speakers:
Ingo ​Chakravarty, President and CEO, Navican @IngoChakravarty
Eugean Jiwanmall, Senior Research Analyst for Medical Policy & Technology Evaluation , Independence Blue Cross @IBX
Andrew Norden, M.D., Chief Medical Officer, Cota @ANordenMD
Ankur Parikh M.D, Medical Director of Precision Medicine, Cancer Treatment Centers of America @CancerCenter

Ingo: data is not ordered, only half of patients are tracked in some database, reimbursement a challenge

Eugean: identifying mutations as patients getting more comprehensive genomic coverage, clinical trials are expanding more rapidly as seen in 2018 ASCO

Ingo: general principals related to health outcomes or policy or reimbursement.. human studies are paramount but payers may not allowing for general principals (i.e. an Alk mutation in lung cancer and crizotanib treatment may be covered but maybe not for glioblastoma or another cancer containing similar ALK mutation; payers still depend on clinical trial results)

Andrew: using gene panels and NGS but only want to look for actionable targets; they establish an expert panel which reviews these NGS sequence results to determine actionable mutations

Ankur:  they have molecular tumor boards but still if want to prescribe off label and can’t find a clinical trial there is no reimbursement

Andrew: going beyond actionable mutations, although many are doing WES (whole exome sequencing) can we use machine learning to see if there are actionable data from a WES

Ingo: we forget in datasets is that patients have needs today and we need those payment systems and structures today

Eugean: problem is the start from cost (where the cost starts at and was it truly medically necessary)

Norden: there are not enough data sharing to make a decision; an enormous amount of effort to get businesses and technical limitations in data sharing; possibly there are policies needed to be put in place to assimilate datasets and promote collaborations

Ingo: need to take out the middle men between sequencing of patient tumor and treatment decision; middle men are taking out value out of the ‘supply chain’;

Andrew: PATIENTS DON’T OWN their DATA but MOST clinicians agree THEY SHOULD

Ankur: patients are willing to share data but the HIPAA compliance is a barrier

 

11:50- 12:30 AM Fireside Chat with Michael Pellini, M.D.

Building a Precision Medicine Business from the Ground Up: An Operating and Venture Perspective

Dr. Pellini has spent more than 20 years working on the operating side of four companies, each of which has pushed the boundaries of the standard of care. He will describe his most recent experience at Foundation Medicine, at the forefront of precision medicine, and how that experience can be leveraged on the venture side, where he now evaluates new healthcare technologies.

Speaker:
Michael Pellini, M.D., Managing Partner, Section 32 and Chairman, Foundation Medicine @MichaelPellini

Roche just bought Foundation Medicine for $2.5 billion.  They negotiated over 7 months but aside from critics they felt it was a great deal because it gives them, as a diagnostic venture, the international reach and biotech expertise.  Foundation Medicine offered Roche expertise on the diagnostic space including ability to navigate payers and regulatory aspects of the diagnostic business.  He feels it benefits all aspects of patient care and the work they do with other companies.

Moderatore: Roche is doing multiple deals to ‘own’ a disease state.

Dr. Pellini:  Roche is closing a deal with Flatiron just like how Merck closed deals with genomics companies.  He feels best to build the best company on a stand alone basis and provide for patients, then good things will happen.  However the problem of achieving scale for Precision Medicine is reimbursement by payers.  They still have to keep collecting data and evolving services to suit pharma.  They didn’t know if there model would work but when he met with FDA in 2011 they worked with Precision Medicine, said collect the data and we will keep working with you,

However the payers aren’t contributing to the effort.  They need to assist some of the young companies that can’t raise the billion dollars needed for all the evidence that payers require.  Precision Medicine still have problems, even though they have collected tremendous amounts of data and raised significant money.  From the private payer perspective there is no clear roadmap for success.

They recognized that the payers would be difficult but they had a plan but won’t invest in companies that don’t have a plan for getting reimbursement from payers.

Moderator: What is section 32?

Pellini:  Their investment arm invests in the spectrum of precision healtcare companies including tech companies.  They started with a digital path imaging system that went from looking through a scope and now looking at a monitor with software integrated with medical records. Section 32 has $130 million under management and may go to $400 Million but they want to stay small.

Pellini: we get 4-5 AI pitches a week.

Moderator: Are you interested in companion diagnostics?

Pellini:  There may be 24 expected 2018 drug approvals and 35% of them have a companion diagnostic (CDX) with them.  however going out ten years 70% may have a CDX associated with them.  Payers need to work with companies to figure out how to pay with these CDXs.

 

 

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Live Coverage: MedCity Converge 2018 Philadelphia: AI in Cancer and Keynote Address

Reporter: Stephen J. Williams, PhD

8:30 AM -9:15

Practical Applications of AI in Cancer

We are far from machine learning dictating clinical decision making, but AI has important niche applications in oncology. Hear from a panel of innovative startups and established life science players about how machine learning and AI can transform different aspects in healthcare, be it in patient recruitment, data analysis, drug discovery or care delivery.

Moderator: Ayan Bhattacharya, Advanced Analytics Specialist Leader, Deloitte Consulting LLP
Speakers:
Wout Brusselaers, CEO and Co-Founder, Deep 6 AI @woutbrusselaers ‏
Tufia Haddad, M.D., Chair of Breast Medical Oncology and Department of Oncology Chair of IT, Mayo Clinic
Carla Leibowitz, Head of Corporate Development, Arterys @carlaleibowitz
John Quackenbush, Ph.D., Professor and Director of the Center for Cancer Computational Biology, Dana-Farber Cancer Institute

Ayan: working at IBM and Thompon Rueters with structured datasets and having gone through his own cancer battle, he is now working in healthcare AI which has an unstructured dataset(s)

Carla: collecting medical images over the world, mainly tumor and calculating tumor volumetrics

Tufia: drug resistant breast cancer clinician but interested in AI and healthcareIT at Mayo

John: taking large scale datasets but a machine learning skeptic

moderator: how has imaging evolved?

Carla: ten times images but not ten times radiologists so stressed field needs help with image analysis; they have seen measuring lung tumor volumetrics as a therapeutic diagnostic has worked

moderator: how has AI affected patient recruitment?

Tufia: majority of patients are receiving great care but AI can offer profiles and determine which patients can benefit from tertiary care;

John: 1980 paper on no free lunch theorem; great enthusiasm about optimization algortihisms fell short in application; can extract great information from e.g. images

moderator: how is AI for healthcare delivery working at mayo?

Tufia: for every hour with patient two hours of data mining. for care delivery hope to use the systems to leverage the cognitive systems to do the data mining

John: problem with irreproducible research which makes a poor dataset:  also these care packages are based on population data not personalized datasets; challenges to AI is moving correlation to causation

Carla: algorithisms from on healthcare network is not good enough, Google tried and it failed

John: curation very important; good annotation is needed; needed to go in and develop, with curators, a systematic way to curate medial records; need standardization and reproducibility; applications in radiometrics can be different based on different data collection machines; developed a machine learning model site where investigators can compare models on a hub; also need to communicate with patients on healthcare information and quality information

Ayan: Australia and Canada has done the most concerning AI and lifescience, healthcare space; AI in most cases is cognitive learning: really two types of companies 1) the Microsofts, Googles, and 2) the startups that may be more pure AI

 

Final Notes: We are at a point where collecting massive amounts of healthcare related data is simple, rapid, and shareable.  However challenges exist in quality of datasets, proper curation and annotation, need for collaboration across all healthcare stakeholders including patients, and dissemination of useful and accurate information

 

9:15 AM–9:45 AM

Opening Keynote: Dr. Joshua Brody, Medical Oncologist, Mount Sinai Health System

The Promise and Hype of Immunotherapy

Immunotherapy is revolutionizing oncology care across various types of cancers, but it is also necessary to sort the hype from the reality. In his keynote, Dr. Brody will delve into the history of this new therapy mode and how it has transformed the treatment of lymphoma and other diseases. He will address the hype surrounding it, why so many still don’t respond to the treatment regimen and chart the way forward—one that can lead to more elegant immunotherapy combination paths and better outcomes for patients.

Speaker:
Joshua Brody, M.D., Assistant Professor, Mount Sinai School of Medicine @joshuabrodyMD

Director Lymphoma therapy at Mt. Sinai

  • lymphoma a cancer with high PD-L1 expression
  • hodgkin’s lymphoma best responder to PD1 therapy (nivolumab) but hepatic adverse effects
  • CAR-T (chimeric BCR and TCR); a long process which includes apheresis, selection CD3/CD28 cells; viral transfection of the chimeric; purification
  • complete remissions of B cell lymphomas (NCI trial) and long term remissions past 18 months
  • side effects like cytokine release (has been controlled); encephalopathy (he uses a hand writing test to see progression of adverse effect)

Vaccines

  •  teaching the immune cells as PD1 inhibition exhausting T cells so a vaccine boost could be an adjuvant to PD1 or checkpoint therapy
  • using Flt3L primed in-situ vaccine (using a Toll like receptor agonist can recruit the dendritic cells to the tumor and then activation of T cell response);  therefore vaccine does not need to be produced ex vivo; months after the vaccine the tumor still in remission
  • versus rituximab, which can target many healthy B cells this in-situ vaccine strategy is very specific for the tumorigenic B cells
  • HoWEVER they did see resistant tumor cells which did not overexpress PD-L1 but they did discover a novel checkpoint (cannot be disclosed at this point)

 

 

 

 

 

 

 

 

 

Please follow on Twitter using the following #hashtags and @pharma_BI

#MCConverge

#AI

#cancertreatment

#immunotherapy

#healthIT

#innovation

#precisionmedicine

#healthcaremodels

#personalizedmedicine

#healthcaredata

And at the following handles:

@pharma_BI

@medcitynews

 

Please see related articles on Live Coverage of Previous Meetings on this Open Access Journal

LIVE – Real Time – 16th Annual Cancer Research Symposium, Koch Institute, Friday, June 16, 9AM – 5PM, Kresge Auditorium, MIT

Real Time Coverage and eProceedings of Presentations on 11/16 – 11/17, 2016, The 12th Annual Personalized Medicine Conference, HARVARD MEDICAL SCHOOL, Joseph B. Martin Conference Center, 77 Avenue Louis Pasteur, Boston

Tweets Impression Analytics, Re-Tweets, Tweets and Likes by @AVIVA1950 and @pharma_BI for 2018 BioIT, Boston, 5/15 – 5/17, 2018

BIO 2018! June 4-7, 2018 at Boston Convention & Exhibition Center

https://pharmaceuticalintelligence.com/press-coverage/

Read Full Post »


Medcity Converge 2018 Philadelphia: Live Coverage @pharma_BI

Stephen J. Williams: Reporter

MedCity CONVERGE is a two-day executive summit that gathers innovative thought leaders from across all healthcare sectors to provide actionable insight on where oncology innovation is heading.

On July 11-12, 2018 in Philadelphia, MedCity CONVERGE will gather technology disruptors, payers, providers, life science companies, venture capitalists and more to discuss how AI, Big Data and Precision Medicine are changing the game in cancer. See agenda.

The conference highlights innovation and best practices across the continuum—from research to technological innovation to transformations of treatment and care delivery, and most importantly, patient empowerment—from some of the country’s most innovative healthcare organizations managing the disease.

Meaningful networking opportunities abound, with executives driving the innovation from diverse entities: leading hospital systems, medical device firms, biotech, pharma, emerging technology startups and health IT, as well as the investment community.

Day 1: Wednesday, July 11, 2018

7:30 AM

2nd Floor – Paris Foyer

Registration + Breakfast

8:15 AM–8:30 AM

Paris Ballroom

Welcome Remarks: Arundhati Parmar, VP and Editor-in-Chief, MedCity News

8:30 AM–9:15 AM

Paris Ballroom

Practical Applications of AI in Cancer

We are far from machine learning dictating clinical decision making, but AI has important niche applications in oncology. Hear from a panel of innovative startups and established life science players about how machine learning and AI can transform different aspects in healthcare, be it in patient recruitment, data analysis, drug discovery or care delivery.

Moderator: Ayan Bhattacharya, Advanced Analytics Specialist Leader, Deloitte Consulting LLP
Speakers:
Wout Brusselaers, CEO and Co-Founder, Deep 6 AI @woutbrusselaers ‏
Tufia Haddad, M.D., Chair of Breast Medical Oncology and Department of Oncology Chair of IT, Mayo Clinic
Carla Leibowitz, Head of Corporate Development, Arterys @carlaleibowitz
John Quackenbush, Ph.D., Professor and Director of the Center for Cancer Computational Biology, Dana-Farber Cancer Institute

9:15 AM–9:45 AM

Paris Ballroom

Opening Keynote: Dr. Joshua Brody, Medical Oncologist, Mount Sinai Health System

The Promise and Hype of Immunotherapy

Immunotherapy is revolutionizing oncology care across various types of cancers, but it is also necessary to sort the hype from the reality. In his keynote, Dr. Brody will delve into the history of this new therapy mode and how it has transformed the treatment of lymphoma and other diseases. He will address the hype surrounding it, why so many still don’t respond to the treatment regimen and chart the way forward—one that can lead to more elegant immunotherapy combination paths and better outcomes for patients.

Speaker:
Joshua Brody, M.D., Assistant Professor, Mount Sinai School of Medicine @joshuabrodyMD

9:45 AM–10:00 AM

Paris Foyer

Networking Break + Showcase

10:00 AM–10:45 AM

Paris Ballroom

The Davids vs. the Cancer Goliath Part 1

Startups from diagnostics, biopharma, medtech, digital health and emerging tech will have 8 minutes to articulate their visions on how they aim to tame the beast.

Start Time End Time Company
10:00 10:08 Belong.Life
10:09 10:17 Care+Wear
10:18 10:26 OncoPower
10:27 10:35 PolyAurum LLC
10:36 10:44 Seeker Health

Speakers:
Karthik Koduru, MD, Co-Founder and Chief Oncologist, OncoPower
Eliran Malki, Co-Founder and CEO, Belong.Life
Chaitenya Razdan, Co-founder and CEO, Care+Wear @_crazdan
Debra Shipley Travers, President & CEO, PolyAurum LLC @polyaurum
Sandra Shpilberg, Founder and CEO, Seeker Health @sandrashpilberg

10:45 AM–11:00 AM

Paris Foyer

Networking Break + Showcase

11:00 AM–11:45 AM

Montpellier – 3rd Floor

Breakout: Biopharma Gets Its Feet Wet in Digital Health

In the last few years, biotech and pharma companies have been leveraging digital health tools in everything from oncology trials, medication adherence to patient engagement. What are the lessons learned?

Moderator: Anthony Green, Ph.D., Vice President, Technology Commercialization Group, Ben Franklin Technology Partners
Speakers:
Derek Bowen, VP of Business Development & Strategy, Blackfynn, Inc.
Gyan Kapur, Vice President, Activate Venture Partners
Tom Kottler, Co-Founder & CEO, HealthPrize Technologies @HealthPrize

11:00 AM–11:45 AM

Paris Ballroom

Breakout: How to Scale Precision Medicine

The potential for precision medicine is real, but is limited by access to patient datasets. How are government entities, hospitals and startups bringing the promise of precision medicine to the masses of oncology patients

Moderator: Sandeep Burugupalli, Senior Manager, Real World Data Innovation, Pfizer @sandeepburug
Speakers:
Ingo ​Chakravarty, President and CEO, Navican @IngoChakravarty
Eugean Jiwanmall, Senior Research Analyst for Medical Policy & Technology Evaluation , Independence Blue Cross @IBX
Andrew Norden, M.D., Chief Medical Officer, Cota @ANordenMD
Ankur Parikh M.D, Medical Director of Precision Medicine, Cancer Treatment Centers of America @CancerCenter

11:50 AM–12:30 PM

Paris Ballroom

Fireside Chat with Michael Pellini, M.D.

Building a Precision Medicine Business from the Ground Up: An Operating and Venture Perspective

Dr. Pellini has spent more than 20 years working on the operating side of four companies, each of which has pushed the boundaries of the standard of care. He will describe his most recent experience at Foundation Medicine, at the forefront of precision medicine, and how that experience can be leveraged on the venture side, where he now evaluates new healthcare technologies.

Speaker:
Michael Pellini, M.D., Managing Partner, Section 32 and Chairman, Foundation Medicine @MichaelPellini

12:30 PM–1:30 PM

Chez Colette Restaurant – Lobby

Lunch Reception

1:30 PM–2:15 PM

Paris Ballroom

Clinical Trials 2.0

The randomized, controlled clinical trial is the gold standard, but it may be time for a new model. How can patient networks and new technology be leveraged to boost clinical trial recruitment and manage clinical trials more efficiently?

Moderator: John Reites, Chief Product Officer, Thread @johnreites
Speakers:
Andrew Chapman M.D., Chief of Cancer Services , Sidney Kimmel Cancer Center, Thomas Jefferson University Hospital
Michelle Longmire, M.D., Founder, Medable @LongmireMD
Sameek Roychowdhury MD, PhD, Medical Oncologist and Researcher, Ohio State University Comprehensive Cancer Center @OSUCCC_James

2:20 PM–3:00 PM

Paris Ballroom

CONVERGEnce on Steroids: Why Comcast and Independence Blue Cross?

This year has seen a great deal of convergence in health care.  One of the most innovative collaborations announced was that of Cable and Media giant Comcast Corporation and health plan Independence Blue Cross.  This fireside chat will explore what the joint venture is all about, the backstory of how this unlikely partnership came to be, and what it might mean for our industry.

sponsored by Independence Blue Cross

Moderator: Tom Olenzak, Managing Director Strategic Innovation Portfolio, Independence Blue Cross @IBX
Speakers:
Marc Siry, VP, Strategic Development, Comcast
Michael Vennera, SVP, Chief Information Officer, Independence Blue Cross

3:00 PM–3:15 PM

Paris Foyer

Networking Break + Showcase

3:15 PM–4:00 PM

Montpellier – 3rd Floor

Breakout: Charting the Way Forward in Gene and Cell Therapy

There is a boom underway in cell and gene therapies that are being wielded to tackle cancer and other diseases at the cellular level. FDA has approved a few drugs in the space. These innovations raise important questions about patient access, patient safety, and personalized medicine. Hear from interesting startups and experts about the future of gene therapy.

Moderator: Alaric DeArment, Senior Reporter, MedCity News
Speakers:
Amy DuRoss, CEO, Vineti
Andre Goy, M.D., Chairman and Director of John Theurer Cancer Center , Hackensack University Medical Center

3:15 PM–4:00 PM

Paris Ballroom

Breakout: What’s A Good Model for Value-Based Care in Oncology?

How do you implement a value-based care model in oncology? Medicare has created a bundled payment model in oncology and there are lessons to be learned from that and other programs. Listen to two presentations from experts in the field.

Moderator: Mahek Shah, M.D., Senior Researcher, Harvard Business School @Mahek_MD
Speakers:
Charles Saunders M.D., CEO, Integra Connect
Mari Vandenburgh, Director of Value-Based Reimbursement Operations, Highmark @Highmark

4:00 PM–4:10 PM

Paris Foyer

Networking Break + Showcase

4:10 PM–4:55 PM

Montpellier – 3rd Floor

Breakout: Trends in Oncology Investing

A panel of investors interested in therapeutics, diagnostics, digital health and emerging technology will discuss what is hot in cancer investing.

Moderator: Stephanie Baum, Director of Special Projects, MedCity News @StephLBaum
Speakers:
Karen Griffith Gryga, Chief Investment Officer, Dreamit Ventures @karengg 
Stacey Seltzer, Partner, Aisling Capital
David Shaywitz, M.D., Ph.D., Senior Partner, Takeda Ventures

4:10 PM–4:55 PM

Paris Ballroom

Breakout: What Patients Want and Need On Their Journey

Cancer patients are living with an existential threat every day. A panel of patients and experts in oncology care management will discuss what’s needed to make the journey for oncology patients a bit more bearable.

sponsored by CEO Council for Growth

Moderator: Amanda Woodworth, M.D., Director of Breast Health, Drexel University College of Medicine
Speakers:
Kezia Fitzgerald, Chief Innovation Officer & Co-Founder, CareAline® Products, LLC
Sara Hayes, Senior Director of Community Development, Health Union @SaraHayes_HU
Katrece Nolen, Cancer Survivor and Founder, Find Cancer Help @KatreceNolen
John Simpkins, Administrative DirectorService Line Director of the Cancer Center, Children’s Hospital of Philadelphia

5:00 PM–5:45 PM

Paris Ballroom

Early Diagnosis Through Predictive Biomarkers, NonInvasive Testing

Diagnosing cancer early is often the difference between survival and death. Hear from experts regarding the new and emerging technologies that form the next generation of cancer diagnostics.

Moderator: Heather Rose, Director of Licensing, Thomas Jefferson University
Speakers:
Bonnie Anderson, Chairman and CEO, Veracyte @BonnieAndDx
Kevin Hrusovsky, Founder and Chairman, Powering Precision Health @KevinHrusovsky

5:45 PM–7:00 PM

Paris Foyer

Networking Reception

Day 2: Thursday, July 12, 2018

7:30 AM

Paris Foyer

Breakfast + Registration

8:30 AM–8:40 AM

Paris Ballroom

Opening Remarks: Arundhati Parmar, VP and Editor-in-Chief, MedCity News

8:40 AM–9:25 AM

Paris Ballroom

The Davids vs. the Cancer Goliath Part 2

Startups from diagnostics, biopharma, medtech, digital health and emerging tech will have 8 minutes to articulate their visions on how they aim to tame the beast.

Start Time End Time Company
8:40 8:48 3Derm
8:49 8:57 CNS Pharmaceuticals
8:58 9:06 Cubismi
9:07 9:15 CytoSavvy
9:16 9:24 PotentiaMetrics

Speakers:
Liz Asai, CEO & Co-Founder, 3Derm Systems, Inc. @liz_asai
John M. Climaco, CEO, CNS Pharmaceuticals @cns_pharma 
John Freyhof, CEO, CytoSavvy
Robert Palmer, President & CEO, PotentiaMetrics @robertdpalmer 
Moira Schieke M.D., Founder, Cubismi, Adjunct Assistant Prof UW Madison @cubismi_inc

9:30 AM–10:15 AM

Paris Ballroom

Liquid Biopsy and Gene Testing vs. Reimbursement Hurdles

Genetic testing, whether broad-scale or single gene-testing, is being ordered by an increasing number of oncologists, but in many cases, patients are left to pay for these expensive tests themselves. How can this dynamic be shifted? What can be learned from the success stories?

Moderator: Shoshannah Roth, Assistant Director of Health Technology Assessment and Information Services , ECRI Institute @Ecri_Institute
Speakers:
Rob Dumanois, Manager – reimbursement strategy, Thermo Fisher Scientific
Eugean Jiwanmall, Senior Research Analyst for Medical Policy & Technology Evaluation , Independence Blue Cross @IBX
Michael Nall, President and Chief Executive Officer, Biocept

10:15 AM–10:25 AM

Paris Foyer

Networking Break + Showcase

10:25 AM–11:10 AM

Paris Ballroom

Promising Drugs, Pricing and Access

The drug pricing debate rages on. What are the solutions to continuing to foster research and innovation, while ensuring access and affordability for patients? Can biosimilars and generics be able to expand market access in the U.S.?

Moderator: Bunny Ellerin, Director, Healthcare and Pharmaceutical Management Program, Columbia Business School
Speakers:
Patrick Davish, AVP, Global & US Pricing/Market Access, Merck
Robert Dubois M.D., Chief Science Officer and Executive Vice President, National Pharmaceutical Council
Gary Kurzman, M.D., Senior Vice President and Managing Director, Healthcare, Safeguard Scientifics
Steven Lucio, Associate Vice President, Pharmacy Services, Vizient

11:10 AM–11:20 AM

Networking Break + Showcase

11:20 AM–12:05 PM

Paris Ballroom

Breaking Down Silos in Research

“Silo” is healthcare’s four-letter word. How are researchers, life science companies and others sharing information that can benefit patients more quickly? Hear from experts at institutions that are striving to tear down the walls that prevent data from flowing.

Moderator: Vini Jolly, Executive Director, Woodside Capital Partners
Speakers:
Ardy Arianpour, CEO & Co-Founder, Seqster @seqster
Lauren Becnel, Ph.D., Real World Data Lead for Oncology, Pfizer
Rakesh Mathew, Innovation, Research, & Development Lead, HealthShareExchange
David Nace M.D., Chief Medical Officer, Innovaccer

12:10 PM–12:40 PM

Paris Ballroom

Closing Keynote: Anne Stockwell, Cancer Survivor, Founder, Well Again

Finding Your Well Again
Anne Stockwell discusses her mission to help cancer survivors heal their emotional trauma and regain their balance after treatment. A multi-skilled artist as well as a three-time cancer survivor, Anne learned through experience that the emotional impact of cancer often strikes after treatment, isolating a survivor rather than lighting the way forward. Anne realized that her well-trained imagination as an artist was key to her successful reentry after cancer. Now she helps other survivors develop their own creative tools to help them find their way forward with joy.

Speaker:
Anne Stockwell, Founder and President, Well Again @annewellagain

12:40 PM–12:45 PM

Closing Remarks

 

Please follow on Twitter using the following #hashtags and @pharma_BI

#MCConverge

#cancertreatment

#healthIT

#innovation

#precisionmedicine

#healthcaremodels

#personalizedmedicine

#healthcaredata

And at the following handles:

@pharma_BI

@medcitynews

 

Please see related articles on Live Coverage of Previous Meetings on this Open Access Journal

LIVE – Real Time – 16th Annual Cancer Research Symposium, Koch Institute, Friday, June 16, 9AM – 5PM, Kresge Auditorium, MIT

Real Time Coverage and eProceedings of Presentations on 11/16 – 11/17, 2016, The 12th Annual Personalized Medicine Conference, HARVARD MEDICAL SCHOOL, Joseph B. Martin Conference Center, 77 Avenue Louis Pasteur, Boston

Tweets Impression Analytics, Re-Tweets, Tweets and Likes by @AVIVA1950 and @pharma_BI for 2018 BioIT, Boston, 5/15 – 5/17, 2018

BIO 2018! June 4-7, 2018 at Boston Convention & Exhibition Center

https://pharmaceuticalintelligence.com/press-coverage/

 

 

Read Full Post »


Centers for Medicare & Medicaid Services announced that the federal healthcare program will cover the costs of cancer gene tests that have been approved by the Food and Drug Administration

 

Reporter: Aviva Lev-Ari, PhD, RN

genetic testing just became routine care for patients with advanced cancers. And that means precision medicine has finally broken into the mainstream.

Any tests that gain FDA clearance in the future will automatically receive full coverage.

In 3/2018 there are three FDA approved Genetic Tests for Cancer:

UNDER development and not included in the agreement , above, includes:

  • Olivier Elemento, Director of the Caryl and Israel Englander Institute for Precision Medicine at Cornell, the team at Cornell, for example, has developed a whole exome test that compares mutations in tumors against healthy cells across 22,000 genes. To date, it’s been used to help match more than 1,000 patients in New York state with the best available treatment options.

Under the final decision, doctors are still free to order non-FDA approved tests, but coverage isn’t guaranteed; each case will be evaluated by local Medicare administrative contractors. Which means Elemento’s test could still be covered. “To me this is a vote of confidence that next generation sequencing is useful for cancer patients,” says Elemento.

So far, CMS is only covering these tests for stage three and stage four metastatic cancer sufferers. Most of them aren’t going to be cured. They might get a few more good months, maybe a year, tops.

Cancerous Genes

SOURCE

WITH MEDICARE SUPPORT, GENETIC CANCER TESTING GOES MAINSTREAM

https://www.wired.com/story/with-medicare-support-genetic-cancer-testing-goes-mainstream/?mbid=social_twitter_onsiteshare

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