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Bioinformatics Tool Review: Genome Variant Analysis Tools

Posted in Big Data, BioIT: BioInformatics, BioIT: BioInformatics, NGS, Clinical & Translational, Pharmaceuticall R&D Informatics, Clinical Genomics, Cancer Informatics, Cancer Informatics, Clinical Genomics, Computational Biology/Systems and Bioinformatics, Genome Biology, Personalized and Precision Medicine & Genomic Research, Uncategorized, tagged , , , , , , , , , , , , , on October 23, 2018| Leave a Comment »


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.

Nature. 2015 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 LL1, Terczyńska-Dyla E1, Mørk N2, Scavenius C1, Enghild JJ1, Höning K3, Hornung V3,4, Christiansen M5,6, Mogensen TH2,6, Hartmann 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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Live Coverage: MedCity Converge 2018 Philadelphia: AI in Cancer and Keynote Address

Posted in Artificial Intelligence, Artificial Intelligence Applications in Health Care, Big Data, BioIT: BioInformatics, Cancer - General, Cancer and Current Therapeutics, Cancer Informatics, Cancer Vaccines: Targeting Cancer Genes for Immunotherapy, Conference Coverage with Social Media, Health Care System by Country, HealthCare IT, Immuno-Oncology & Genomics, Personalized and Precision Medicine & Genomic Research, tagged , , , , , , on July 11, 2018| Leave a Comment »


 

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/

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Medcity Converge 2018 Philadelphia: Live Coverage @pharma_BI

Posted in Artificial Intelligence Applications in Health Care, BioIT: BioInformatics, BioIT: BioInformatics, NGS, Clinical & Translational, Pharmaceuticall R&D Informatics, Clinical Genomics, Cancer Informatics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Informatics, Cancer Prevention: Research & Programs, Clinical & Translational, Clinical Diagnostics, Evidence-based decision-making, Health Economics and Outcomes Research, Healthcare costs and reimbursement, Personalized and Precision Medicine & Genomic Research, Transformative Technologies in Healthcare, tagged , , , , , , , , on July 11, 2018| Leave a Comment »


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/

 

 

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Thriving at the Survival Calls during Careers in the Digital Age – An AGE like no Other, also known as, DIGITAL

Posted in Big Data & Analytics, BioIT: BioInformatics, BioIT: BioInformatics, NGS, Clinical & Translational, Pharmaceuticall R&D Informatics, Clinical Genomics, Cancer Informatics, BioTechnology - Venture Creation, BioTechnology - Venture Creation, Venture Capital, Data Science, Digital HealthCare – biotech & internet joint ventures, Genetics & Innovations in Treatment, Genetics & Pharmaceutical, Genome Biology, Genomic Testing: Methodology for Diagnosis, Health Law & Patient Safety, HealthCare IT, LPBI Group Founder - Aviva Lev-Ari, Scientific & Biotech Conferences: Press Coverage, Scientific Publishing, Scientist: Career considerations, Statistical Methods for Research Evaluation, Women in Life Sciences on June 11, 2018| Leave a Comment »


Thriving at the Survival Calls during Careers in the Digital Age – An AGE like no Other, also known as, DIGITAL

Author and Curator: Aviva Lev-Ari, PhD, RN

 

The source for the inspiration to write this curation is described in

Survival Calls during Careers in the Digital Age

https://pharmaceuticalintelligence.com/2018/06/13/survival-calls-during-careers-in-the-digital-age/

 

In this curation, I present the following concepts in three parts:

  1. Part 1: Authenticity of Careers in the Digital Age: In Focus, the BioTechnology Sector

  2. Part 2: Top 10 books to help you survive the Digital Age

  3. Part 3: A case study on Thriving at the Survival Calls during Careers in the Digital Age: Aviva Lev-Ari, UCB, PhD’83; HUJI, MA’76 

 

Part 1: Authenticity of Careers in the Digital Age: 

In Focus, the BioTechnology Sector

 

Lisa LaMotta, Senior Editor, BioPharma Dive wrote in Conference edition | June 11, 2018

Unlike that little cancer conference in Chicago last week, the BIO International convention is not about data, but about the people who make up the biopharma industry.

The meeting brings together scientists, board members, business development heads and salespeople, from the smallest virtual biotechs to the largest of pharmas. It allows executives at fledgling biotechs to sit at the same tables as major decision-makers in the industry — even if it does look a little bit like speed dating.

But it’s not just a partnering meeting.

This year’s BIO also sought to shine a light on pressing issues facing the industry. Among those tackled included elevating the discussion on gender diversity and how to bring more women to the board level; raising awareness around suicide and the need for more mental health treatments; giving a voice to patient advocacy groups; and highlighting the need for access to treatments in developing nations.

Four days of meetings and panel discussions are unlikely to move the needle for many of these challenges, but debate can be the first step toward progress.

I attended the meetings on June 4,5,6, 2018 and covered in Real Time the sessions I attended. On the link below, Tweets, Re-Tweets and Likes mirrors the feelings and the opinions of the attendees as expressed in real time using the Twitter.com platform. This BioTechnology events manifested the AUTHENTICITY of Careers in the Digital Age – An AGE like no Other, also known as, DIGITAL.

The entire event is covered on twitter.com by the following hash tag and two handles:

 

I covered the events on two tracks via two Twitter handles, each handle has its own followers:

The official LPBI Group Twitter.com account

The Aviva Lev-Ari, PhD, RN Twitter.com account

Track A:

  • Original Tweets by @Pharma_BI and by @AVIVA1950 for #BIO2018 @IAmBiotech @BIOConvention – BIO 2018, Boston, June 4-7, 2018, BCEC

Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2018/06/11/original-tweets-by-pharma_bi-and-by-aviva1950-from-bio2018-iambiotech-bioconvention-bio-2018-boston-june-4-7-2018-bcec/

 

  • Reactions to Original Tweets by @Pharma_BI and by @AVIVA1950 from #BIO2018

Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2018/06/12/reactions-to-original-tweets-by-pharma_bi-and-by-aviva1950-from-bio2018/

Track B:

  • Re-Tweets and Likes by @Pharma_BI and by @AVIVA1950 from #BIO2018 @IAmBiotech @BIOConvention – BIO 2018, Boston, June 4-7, 2018, BCEC

Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2018/06/11/re-tweets-and-likes-by-pharma_bi-aviva1950-from-bio2018-iambiotech-bioconvention-bio-2018-boston-june-4-7-2018-bcec/

Part 2: Top 10 books to help you survive the digital age

From Philip K Dick’s obtuse robots to Mark O’Connell’s guide to transhumanism, novelist Julian Gough picks essential reading for a helter skelter world

Here are 10 of the books that did help me [novelist Julian Gough]: they might also help you understand, and survive, our complicated, stressful, digital age.

  1. Marshall McLuhan Unbound by Marshall McLuhan (2005)
    The visionary Canadian media analyst predicted the internet, and coined the phrase the Global Village, in the early 1960s. His dense, complex, intriguing books explore how changes in technology change us. This book presents his most important essays as 20 slim pamphlets in a handsome, profoundly physical, defiantly non-digital slipcase.
  2. Ubik by Philip K Dick (1969)
    Pure pulp SF pleasure; a deep book disguised as a dumb one. Dick shows us, not a dystopia, but a believably shabby, amusingly human future. The everyman hero, Joe Chip, wakes up and argues with his robot toaster, which refuses to toast until he sticks a coin in the slot. Joe can’t do this, because he’s broke. He then has a stand-up row with his robot front door, which won’t open, because he owes it money too … Technology changes: being human, and broke, doesn’t. Warning: Dick wrote Ubik at speed, on speed. But embedded in the pulpy prose are diamonds of imagery that will stay with you for ever.
  3. The Singularity Is Near by Ray Kurzweil (2005)
    This book is what Silicon Valley has instead of a bible. It’s a visionary work that predicts a technological transformation of the world in our lifetime. Kurzweil argues that computer intelligence will soon outperform human thought. We will then encode our minds, upload them, and become one with our technology, achieving the Singularity. At which point, the curve of technological progress starts to go straight up. Ultimately – omnipotent, no longer mortal, no longer flesh – we transform all the matter in the universe into consciousness; into us.
  4. To Be a Machine by Mark O’Connell (2017)
    This response to Kurzweil won this year’s Wellcome prize. It’s a short, punchy tour of transhumanism: the attempt to meld our minds with machines, to transcend biology and escape death. He meets some of the main players, and many on the fringes, and listens to them, quizzically. It is a deliberately, defiantly human book, operating in that very modern zone between sarcasm and irony, where humans thrive and computers crash.
  5. A Visit from the Goon Squad by Jennifer Egan (2011)
    This intricately structured, incredibly clever novel moves from the 60s right through to a future maybe 15 years from now. It steps so lightly into that future you hardly notice the transition. It has sex and drugs and rock’n’roll, solar farms, social media scams and a stunningly moving chapter written as a PowerPoint presentation. It’s a masterpiece. Life will be like this.
  6. What Technology Wants by Kevin Kelly (2010)
    Kelly argues that we scruffy biological humans are no longer driving technological progress. Instead, the technium, “the greater, global, massively interconnected system of technology vibrating around us”, is now driving its own progress, faster and faster, and we are just caught up in its slipstream. As we accelerate down the technological waterslide, there is no stopping now … Kelly’s vision of the future is scary, but it’s fun, and there is still a place for us in it.
  7. The Meme Machine by Susan Blackmore (1999)
    Blackmore expands powerfully and convincingly on Richard Dawkins’s original concept of the meme. She makes a forceful case that technology, religion, fashion, art and even our personalities are made of memes – ideas that replicate, mutate and thus evolve over time. We are their replicators (if you buy my novel, you’ve replicated its memes); but memes drive our behaviour just as we drive theirs. It’s a fascinating book that will flip your world upside down.
  8. Neuromancer by William Gibson (1984)
    In the early 1980s, Gibson watched kids leaning into the screens as they played arcade games. They wanted to be inside the machines, he realised, and they preferred the games to reality. In this novel, Gibson invented the term cyberspace; sparked the cyberpunk movement (to his chagrin); and vividly imagined the jittery, multi-screened, anxious, technological reality that his book would help call into being.
  9. You Are Not a Gadget: A Manifesto by Jaron Lanier (2010)
    Lanier, an intense, brilliant, dreadlocked artist, musician and computer scientist, helped to develop virtual reality. His influential essay Digital Maoism described early the downsides of online collective action. And he is deeply aware that design choices made by (mainly white, young, male) software engineers can shape human behaviour globally. He argues, urgently, that we need to question those choices, now, because once they are locked in, all of humanity must move along those tracks, and we may not like where they take us. Events since 2010 have proved him right. His manifesto is a passionate argument in favour of the individual voice, the individual gesture.
  10. All About Love: New Visions by bell hooks (2000)
    Not, perhaps, an immediately obvious influence on a near-future techno-thriller in which military drones chase a woman and her son through Las Vegas. But hooks’s magnificent exploration and celebration of love, first published 18 years ago, will be far more useful to us, in our alienated digital future, than the 10,000 books of technobabble published this year. All About Love is an intensely practical roadmap, from where we are now to where we could be. When Naomi and Colt find themselves on the run through a militarised American wilderness of spirit, when GPS fails them, bell hooks is their secret guide.

SOURCE

https://www.theguardian.com/books/2018/may/30/top-10-books-to-help-you-survive-the-digital-age?utm_source=esp&utm_medium=Email&utm_campaign=Bookmarks+-+Collections+2017&utm_term=277690&subid=25658468&CMP=bookmarks_collection

Part 3: A case study on Thriving at the Survival Calls during Careers in the Digital Age:  Aviva Lev-Ari, UCB, PhD’83; HUJI, MA’76

 

On June 10, 2018

 

Following, is a case study about an alumna of HUJI and UC, Berkeley as an inspirational role model. An alumna’s profile in context of dynamic careers in the digital age. It has great timeliness and relevance to graduate students, PhD level at UC Berkeley and beyond, to all other top tier universities in the US and Europe. As presented in the following curations:

Professional Self Re-Invention: From Academia to Industry – Opportunities for PhDs in the Business Sector of the Economy

https://pharmaceuticalintelligence.com/2018/05/22/professional-self-re-invention-from-academia-to-industry-opportunities-for-phds-in-the-business-sector-of-the-economy/

 

Pioneering implementations of analytics to business decision making: contributions to domain knowledge conceptualization, research design, methodology development, data modeling and statistical data analysis: Aviva Lev-Ari, UCB, PhD’83; HUJI, MA’76 

https://pharmaceuticalintelligence.com/2018/05/28/pioneering-implementations-of-analytics-to-business-decision-making-contributions-to-domain-knowledge-conceptualization-research-design-methodology-development-data-modeling-and-statistical-data-a/

 

This alumna is Editor-in-Chief of a Journal that has other 173 articles on Scientist: Career Considerations 

https://pharmaceuticalintelligence.com/category/scientist-career-considerations/

 

In a 5/22/2018 article, Ways to Pursue Science Careers in Business After a PhD by Ankita Gurao,

https://bitesizebio.com/38498/ways-to-pursue-the-business-of-science-after-a-ph-d/?utm_source=facebook&utm_medium=social&utm_campaign=SocialWarfare

Unemployment figures of PhDs by field of science are included, Ankita Gurao identifies the following four alternative careers for PhDs in the non-academic world:

  1. Science Writer/Journalist/Communicator
  2. Science Management
  3. Science Administration
  4. Science Entrepreneurship

My career, as presented in Reflections on a Four-phase Career: Aviva Lev-Ari, PhD, RN, March 2018

https://pharmaceuticalintelligence.com/2018/03/06/reflections-on-a-four-phase-career-aviva-lev-ari-phd-rn-march-2018/

has the following phases:

  • Phase 1: Research, 1973 – 1983
  • Phase 2: Corporate Applied Research in the US, 1985 – 2005
  • Phase 3: Career Reinvention in Health Care, 2005 – 2012
  • Phase 4: Electronic Scientific Publishing, 4/2012 to present

These four phases are easily mapped to the four alternative careers for PhDs in the non-academic world. One can draw parallel lines between the four career opportunities A,B,C,D, above, and each one of the four phases in my own career.

Namely, I have identified A,B,C,D as early as 1985, and pursued each of them in several institutional settings, as follows:

A. Science Writer/Journalist/Communicator – see link above for Phase 4: Electronic Scientific Publishing, 4/2012 to present 

B. Science Management – see link above for Phase 2: Corporate Applied Research in the US, 1985 – 2005 and Phase 3: Career Reinvention in Health Care, 2005 – 2012 

C. Science Administration – see link above for Phase 2: Corporate Applied Research in the US, 1985 – 2005and Phase 4: Electronic Scientific Publishing, 4/2012 to present 

D. Science Entrepreneurship – see link above for Phase 4: Electronic Scientific Publishing, 4/2012 to present  

Impressions of My Days at Berkeley in Recollections: Part 1 and 2, below.

  • Recollections: Part 1 – My days at Berkeley, 9/1978 – 12/1983 –About my doctoral advisor, Allan Pred, other professors and other peers

https://pharmaceuticalintelligence.com/2018/03/15/recollections-my-days-at-berkeley-9-1978-12-1983-about-my-doctoral-advisor-allan-pred-other-professors-and-other-peer/

  • Recollections: Part 2 – “While Rolling” is preceded by “While Enrolling” Autobiographical Alumna Recollections of Berkeley – Aviva Lev-Ari, PhD’83

https://pharmaceuticalintelligence.com/2018/05/24/recollections-part-2-while-rolling-is-preceded-by-while-enrolling-autobiographical-alumna-recollections-of-berkeley-aviva-lev-ari-phd83/

The topic of Careers in the Digital Age is closely related to my profile, see chiefly: Four-phase Career, Reflections, Recollections Parts 1 & 2 and information from other biographical sources, below.

Other sources for my biography

 

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Bio-IT World Announces 2018 Best Of Show Award Winners – May 17, 2018

Posted in BioIT: BioInformatics, Conference Coverage with Social Media on May 17, 2018| Leave a Comment »


Bio-IT World Announces 2018 Best Of Show Award Winners

Reporter: Aviva Lev-Ari, PhD, RN

 3h3 hours ago

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Aviva Lev-Ari Retweeted Mary-Ann Moore

Bravo

Aviva Lev-Ari added,

“This company has been pushing the boundaries for the past 10 years in life sciences. With their new product they have brought natural language to the masses.” – judges. Congratulations …
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    Award-winning Science Writer; Columnist, New York Times; Author of She Has Her Mother’s Laugh, 2018) Up to 30 top contributed the largest to

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    Plenary Keynote Presentation: Height and Intelligence: Exploring the Complexity and Controversy of Heredity

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    2018 BioIT AWARDS Judges’ Prize WINNER Alexion Pharmaceuticala nominated by EPAM Systems – SmartPanel: Rare DIsease Diagnostics – Algorithm Competition – automate from MDs Notes

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    Bio-IT World Personalized & Translational Medicine WINNER @MGH NeuroBank Patient-Centric Platform Clinical Research

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    Bio-IT World IT OINfrastructure- WINNER Celgene

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    Bio-IT World Clinical & Health IT – WINNER TakedaPharmaceutical Nominated by Deloitte

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    Bio-IT World Best Practices Awards – WINNER AstraZeneca, Nominated by Genedata IMED BioTech Unit

  8.  6h6 hours ago

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    Franklin Award goes to Desmond G. Higgins, PhD, Professor, Biochemistry, University College Dublin Conway Institute of Biomolecular & Biomedical Research

  9.  6h6 hours ago

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    @BenjaminFranklin and @JWBizzaro, Managing Director, .org Presented Award to @DesmondGHiggins

May 16, 2018 | BOSTON—Bio-IT World announced the 2018 winners of the Best of Show Awards Program to a packed audience at the Bio-IT World Conference & Expo. The awards program recognizes the best of the innovative product solutions for the life sciences industry on display at the Bio-IT World conference in Boston.

“It’s always a treat to explore what’s new in our industry,” said Bio-IT World Editor, Allison Proffitt. “The innovation on display by Bio-IT World exhibitors never disappoints, and we are excited to shine a spotlight on the best life sciences has to offer.”

The Best of Show program relies on a panel of expert judges from academia and industry who screen eligible new products and hear presentations from a list of finalists on site. This year our judges considered 46 new products and viewed presentations on site from 18 finalists.

The judges named winners in six categories this year: Data Integration & Management; Analysis & Data Computing; Genomic Data Services; Data Visualization & Exploration; Storage Infrastructure & Hardware; and the Judges’ Prize. Attendees also voted on the People’s Choice Award, selecting products that they believe measurably improve workflow or capacity, enabling better research.

The 2018 judging panel included Joe Cerro, BostonCIO; Chris Dwan, Bridgeplate; Richard Holland, New Forest Ventures; Eleanor Howe, Diamond Age Data Science; Phillips Kuhl, Cambridge Healthtech Institute; Steve Marshall, Marshall Data Solutions; Michael Miller, Genentech; Art Morales, Analgesic Solutions; Nanguneri Nirmala, Tufts University School of Medicine; Alexander Sherman, Massachusetts General Hospital; Subi Subramanian, Vertex Pharmaceuticals; Bill Van Etten, BioTeam; and Proffitt.

 

2018 Bio-IT World Best of Show Winners

 

People’s Choice

OnRamp BioInformatics, Inc.
ROSALIND
onramp.bio/meet-rosalind

OnRamp BioInformatics provides ROSALIND™, the first-ever genomics analysis platform specifically designed for life science researchers to analyze and interpret datasets, while freeing up more time for bioinformaticians. Named in honor of pioneering researcher Rosalind Franklin, who made a major contribution to the discovery of the double-helix structure of DNA with her famous photograph 51, OnRamp’s ROSALIND platform aims to simplify the practice of genomic data interpretation.

ROSALIND puts the researcher into the driver’s seat of data analysis and democratizes bioinformatics by broadly expanding access to genomic and proteomic technologies for cancer research, precision medicine and sustainable agriculture.

While many open-source tools remain the lifeline of genomic analysis, a simplified and innovative user experience for the biologist can empower them to run their own analyses, while utilizing these tools without the need for typing any command-line instructions.

ROSALIND is powered in partnership with Google Cloud and features scalable compute power and economical cloud-based storage. ROSALIND is a swarming docker-based genomic analysis solution incorporating the industry’s most trusted open-source tools and algorithms, with an angular front-end and secure RESTful API. ROSALIND is also deployable on-premise.

We believe that by empowering biologists with an intuitive and comprehensive platform to explore their data and collaborate with colleagues and bioinformaticians, we can help accelerate our industry and the widespread adoption of genomic technologies by dramatically lowering costs, taking out complexity and, ultimately, putting more focus back on what to do with results, not how to get to them.

 

Data Integration & Management

The Hyve BV
RADAR-base
radar-cns.org

Developed in the framework of the IMI RADAR-CNS project, RADAR-base is an open source platform designed to securely collect, store and share readings from wearable devices and smartphone sensors to enable remote monitoring. The RADAR-base platform consists of three major categories of components:

Data ingestion: Recognizing and registering data-sources (including smartphones and wearable devices), collecting the data via a direct Bluetooth connection or through a 3rd party API and streaming in near real time to the server (green box in the figure). Using Apache Kafka, the collected data is streamed to dedicated topics in real-time where the data is optimally schematized using Apache Avro;

Data storage and management: Consists of two centralized storage systems behind an authorized security layer. A cold-storage based on HDFS that is scalable and fault-tolerant focusing on storing large volumes of high frequency raw-data, and a hot-storage based on MongoDB storing aggregated data to provide a near real-time overview of the raw-data. (blue box in the figure);

Data sharing: Visualizing aggregated data in a live dashboard and exporting raw data for further analyses in various formats including AVRO, JSON and CSV (yellow box in the figure).

The platform is highly secured by a centralized management system of users and their authorities, participants, allowed devices and their specifications. RADAR-Base platform is distributed as Docker containers with associated scripts and configuration files to enable easy installation.

 

Analysis & Data Computing

Sinequa
Sinequa ES v10
sinequa.com

The Sinequa Cognitive Search and Analytics platform handles all structured and unstructured data sources and uses Natural Language Processing (NLP), statistical analysis and Machine Learning (ML) in order to create an enriched “Logical Data Warehouse” (LDW). This LDW is optimized for performance in delivering rapid responses to users’ information needs. Users can ask questions in their native language or ask that relevant information be “pushed” to them in a timely fashion when it emerges.

More than 180 connectors ready for use “out of the box” make the process of connecting multiple data sources fast and seamless. Company and industry-specific dictionaries and ontologies can be easily integrated, putting specific knowledge “under the hood” of the Sinequa platform, making it an intelligent partner for anyone in search of relevant subject information.

 

Genomic Data Services

Diploid
Moon 1.0
diploid.com/moon

Moon is the first software to autonomously diagnose rare diseases from WES/WGS data. By applying AI to the domain of rare disease diagnostics, Moon brings speed and scalability to the genome interpretation process.

The software only requires the patient’s gender, age of onset and his/her symptoms – in addition to the genetic data. Moon then goes from whole genome variant data (VCF) to pinpointing the causal variant in less than 5 minutes.

The software highlights one or a few variants that could explain the patient’s phenotype. For every variant, Moon displays an extensive list of annotations that it mined from the literature, allowing geneticists to easily verify decisions from the AI algorithms. Moon’s speed does not only save a lot of time and money, it also saves lives: Moon has already proven its utility in the NICU at Rady Children’s Hospital (San Diego): https://goo.gl/7TDrQD.

Unfortunately, about 50% of rare disease patients remain undiagnosed, even after whole genome sequencing and expert interpretation. Most hospitals don’t have the resources to keep analyzing negative cases even though new correlations between genes and disorders are published every day. Moon changes all this: as the software autonomously mines the literature and analyses samples, it can reanalyze older, negative cases in the background. Only when new information that might lead to a diagnosis becomes available, the assigned geneticist is notified. That way, hospitals can frequently reanalyze thousands of cases with minimal labor, providing a perspective to undiagnosed patients.

 

Data Visualization & Exploration

Nanome
NanoPro
nanome.ai/

Nanome is helping to improve the drug discovery process through intuitive virtual reality interfaces. They developed applications for experimentation, collaboration, and learning at the nano-scale leveraging leading VR hardware like the Oculus Rift and HTC Vive to create immersive virtual workspaces wherein users can visualize, design, and simulate molecules, proteins, and more. To try the next generation of tools for small molecule design and macromolecular exploration, stop by the Nanome Booth: #711.

There you’ll have the ability to:

  • Import molecular structures from a local machine or an online database such as RCSB or DrugBank.
  • – Manipulate molecular structures by literally grabbing, rotating, or enlarging the area of interest with their hands.
  • – Apply different representations to their selection of Atoms, Residues, Chains, or Proteins such as Stick, Wire, Ball & Stick, or Van der Waals.
  • – Measure distances and angles between atoms.
  • – Mutate amino acids and cycle through rotamer libraries.
  • – Design small molecules by building with any element from the periodic table.
  • – Minimize manipulated molecules to prevent clashes and provide a local energy minimum conformation.
  • – Duplicate or Split any selected area of your structure to modify or export independently.
  • – Export your molecular structures to PDB.
  • – Join a virtual reality session as a guest with or without virtual reality hardware.
  • – Present and collaborate in the same virtual environment with colleagues to demonstrate proposals or compare before and after results.

 

Storage Infrastructure & Hardware

PetaGene
PetaSuite Cloud Edition – Version 1.2
petagene.com

Launching at Bio-IT World 2018, PetaSuite Cloud Edition (CE) combines two innovations: (i) the ability for a user’s software tools and pipelines to seamlessly integrate with a wide variety of cloud platforms without modification, and (ii) significantly improved, high-performance, scalable PetaSuite genomic compression technology.

For example, users can now directly run, without modification, their custom BWA-mem, GATK, Python, Java, shell scripts, and other POSIX-based software/pipelines streaming directly to/from AWS, Google Cloud, Azure, and private cloud storage, as though they were local filestores. PetaSuite CE supports each platform’s object encryption during transfer and at rest. User applications can connect to multiple cloud platforms, buckets and regions as desired, transparently, and on demand, in user-mode, without needing to modify their pipelines, setup mounts, or have administrator privileges.

Whether running on bare-metal, in VMs, or within Docker containers, for public, private or hybrid cloud, PetaSuite CE enables organizations to unlock the power of distributed object storage seamlessly from their POSIX-compliant tools and pipelines.

PetaSuite CE is built from the ground-up for the extremely high performance streaming and random-access workloads demanded by genomics applications. The integrated, transparent PetaGene compression has been significantly improved to deliver even faster compression and greater reductions of up to 6x of both BAM and FASTQ.GZ files, enabling large costs savings in cloud storage and data transfer times. Moreover, PetaGene compression can also preserve the MD5 checksum of the original BAM or FASTQ.GZ file and not just the internal raw SAM/FASTQ data.

 

Judges’ Prize

Linguamatics
iScite 2.0
iscite.com

Linguamatics iScite, a Software-as-a-Service search application, puts the power of text analytics directly into scientists’ hands.

Award-winning Natural Language Processing
Researchers can extract and analyze relevant data to rapidly answer business-critical questions. iScite utilizes Linguamatics’ award-winning Natural Language Processing (NLP) based blend of analytical methods. By understanding the semantics and structure of text, iScite handles the variety of ways people express the same information, ensuring searches are comprehensive and accurate.

Easy to use on any device
iScite’s intuitive HTML interface includes a simple search box and auto-complete suggestions. The innovative answer-routing engine lets users answer simple or complex questions using puzzle-piece building blocks – simplifying access to powerful queries that extract concepts, relationships, numerical data such as drug dosages, mutations and more.

Get answers to questions, not just documents
Data sources include Linguamatics’ cloud-hosted content. MEDLINE, Clinical Trials.gov, FDA Drug Labels, PubMed Central, and Patent Abstracts are annotated with curated terminologies for diseases, drugs, genes and organizations. Scientists can answer questions such as:

  • What genes are involved in breast cancer?
  • What protocol designs have been used for immuno-oncology trials?
  • What are the adverse events for kinase inhibitors?

Actionable results
Results are presented in structured form, with bar chart facets for dynamic, visual results-filtering, a document viewer that highlights key terms and relationships, and relevant link-outs. Users can curate, save, and export their results.

iScite allows users across drug discovery and development to cut through the vast information landscape and discover the most valuable insights.

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Bio-IT World Announces 2018 Best Practices Awards Winners | May 17, 2018

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2018 CHI’s BioIT World conference THURSDAY, MAY 17 | 8:00 – 9:45 AM – Awards and Keynote

Posted in BioIT: BioInformatics, Conference Coverage with Social Media on May 17, 2018| Leave a Comment »


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2018 CHI’s BioIT World conference & Expo, May 15 – 17, 2018, Boston, MA – Seaport World Trade Center

2018 CHI’s BioIT World conference & Expo, May 15 – 17, 2018, Boston, MA – Seaport World Trade Center

http://www.bio-itworldexpo.com/

LPBI Group will cover Track 7: NGS in Real Time for #BioIT18

@pharma_BI

@AVIVA1950

Aviva Lev-Ari, PhD, RN will be in attendance

 

 

 

THURSDAY, MAY 17 | 8:00 – 9:45 AM

8:00 Organizer Remarks

Cindy Crowninshield, RDN, LDN, HHC, Senior Conference Director/Team Lead, Cambridge Healthtech Institute

 Kanda Software8:05 Awards Program Introduction

Alex Karpovsky, CEO, Kanda Software Inc.

8:10 Benjamin Franklin Awards and Laureate Presentation
J.W. Bizzaro, Managing Director, Bioinformatics.org 

Desmond G. Higgins, PhD, Professor, Biochemistry, University College Dublin Conway Institute of Biomolecular & Biomedical Research – FOR CONTRIBUTIONS to Open Access Softward for Genome Sequences FASTP, FASTN, FASTA, BLAST – development on word processors – Time O(L to the N) – & Seq – 2406 years to complete sequencing

Progressive Alignment: 1984 – 1988, Desmond G. Higgins and SHarp, 1988,1989

BEFORE WWW

  • 1984 Nucleotide Sequences – Part I – GenBank EMBL
  • Journal of Biological Chemistry
  • Condition of Publication in Journal – submit SEQUENCES in three copies before for the Nucleotide Sequences Book
  • Michael Ashbutner – The EBI – Open Access to Genome Sequences – Hixton Hall
  • EMBL – European Bioinformatics Institute
  • Dublin Conway Institute – Mainframe computer moving to PCs
  • PCs – Clustal1 – Clustal4, 1988, Paul Sharp, Dublin
  • 1992 – Interner distribution – Clustal V 1992: EMBL Heidelberg, Rainer Fuchs Alan Bleasby
  • Clustal W, Clustal X, 1994 – 2007
  • Clustal W and Clustal 2.0, 2007
  • Top 30 papers on ISI up to 2015: Citation is a measure of ACTIVITY not of IMPORTANCE
  • 2008 Plan: Start from scratch
  • Clustal Omega – Release 4/2011
  • http://ebi.ac.uk/Tools

 

8:35 Bio-IT World Best Practices Awards
Allison Proffitt, Editorial Director, Bio-IT World

8:50 Keynote Introduction

  • Fastest Lowest Cost of WGA in Fire Cloud —
  • Genomics Analytics GATK4 of Intel
  • 5X in 1/3 the Time
  • AI in Genomics with GATK4 – GREATER Accuracy and Performance – Tensorflow

Michael McManus, Principal Solution Architect, Sales Marketing Group, Intel Corporation

9:00 Plenary Keynote Presentation: Height and Intelligence: Exploring the Complexity and Controversy of Heredity

Carl Zimmer

Award-winning Science Writer; Columnist, New York Times; Author of She Has Her Mother’s Laugh (coming May 2018)

Heredity has long been one of the foundations of society–but also the justification for some of the worst crimes in history. It has only been in the past century that scientists have begun to work out some of its molecular details. But the mysteries and controversies over heredity have proved remarkably durable. In my talk, I’ll explore the history and current research into heredity of two traits–height and intelligence. They may seem at first to be polar opposites, but it turns out they actually share some remarkable similarities.

Carl Zimmer is the author of 13 books about science. His newest book is She Has Her Mother’s Laugh: The Power, Perversions, and Potential of Heredity. His column, “Matter,” appears each week in the New York Times. Zimmer’s writing has earned a number of awards, including the 2016 Stephen Jay Gould Prize, awarded by the Society for the Study of Evolution to recognize individuals whose sustained efforts have advanced public understanding of evolutionary science. In 2017, he won an Online Journalism Award for his series of articles in which he explored his genome. A professor adjunct at Yale University, Zimmer is a familiar voice on programs such as Radiolab. He lives in Connecticut with his wife Grace and their children, Charlotte and Veronica. He is, to his knowledge, the only writer after whom a species of tapeworm has been named.

  • Galton,
  • Herditary Genius: Laws and Consequences, 1869
  • Twins: Hereditary & the Environment: Monozygotic twins vs Dizygotic twins, and adopted twins into different families
  • Laron Syndrome – very low stature
  • Growth Hormone – AIP gene
  • Joel Hirschhorn, Broad Institute
  • 3290 – 2018 700,00 people
  • Jonathan Pitcher – Polygenic to Omnigenic
  • Average Women’s Height (cm): Canada 157.6 CM [163.9 in 2018 vs Barbas 152.1 {169.2 in 2018]
  • Eugenics, Henry Goddard (advocated Sterilization) studied feable minded childrenVineland Training School, NJ
  • Binet – Intelligence Test related to Age
  • Feable mindedness related to hereditery: Emma Wolverton – Case study in Inheritance Kallikak Family
  • Das Erbe, 1935
  • Ian Deary, Univ of Edinburgh, 90s Correlation between IQ and mental processes
  • Sniekers, et al, Natural Genetics 49.7 – 52 Genes tied to Human Intelligence NYT, 05/22/2017
  • Up to 30 top SNPs contributed the largest to IQ Scores
  • Ancestry.com – Million of Gemone Profiles
  • DNALand.com
  • Lower Iodine – lower IQ, added Iodine to water then crops pregnant women increase IQ by 16 points.
  • Height – complex: DIet weight more protein, healthier pregnancy

 

 

 

9:45 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

9:45 Book Signing

She Has Her Mother’s Laugh
Carl Zimmer, Award-winning Science Writer and Columnist, New York Times

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Vyasa Analytics Demos Deep Learning Software for Life Sciences at Bio-IT World 2018 – Vyasa’s booth (#632)

Posted in Artificial Intelligence, BioIT: BioInformatics, Intelligent Information Systems on May 10, 2018| Leave a Comment »


Vyasa Analytics Demos Deep Learning Software for Life Sciences at Bio-IT World 2018 – Vyasa’s booth (#632)

 

Reporter: Aviva Lev-Ari, PhD, RN

 

BOSTON – May 10, 2018 – Vyasa Analytics, a provider of deep learning software and analytics for life sciences and healthcare organizations, today announces three pre-built deep learning analytics modules for its Cortex software at Bio-IT World Conference & Expo. Cortex enables the secure, scalable application of deep learning-based artificial intelligence (AI) analytics to enterprise data, identifying patterns, relationships and concepts across disparate data sources.

 

The new Neural Concept Recognition, Image Analytics and ChemVector analytics modules in Cortex enable life sciences organizations to quickly and easily apply deep learning analytics to large data streams of text, images and chemical structures. Like all deep learning analytical modules in Cortex’s library, these new modules allow users to ask complex questions of their data and use the answers to gain critical insights.

 

“Life sciences and healthcare organizations are using AI tools to advance research and development and deliver better patient care. Deep learning algorithms provide a set of powerful approaches that help us apply analytics more effectively and comprehensively across large scale data sources,” said Dr. Christopher Bouton, founder and CEO of Vyasa. “The idea of AI has been around for decades, but we are now experiencing a perfect storm of GPU-based computing power, deep learning algorithm advances and highly scalable data sources that enables paradigm-shifting machine learning and analytics capabilities.”

 

Vyasa will be demoing three deep learning analytics modules for Cortex at Bio-IT World 2018 in Boston from May 15 to 17, including:

 

  • Neural Concept Recognition. This module can be trained on text concepts (e.g. drugs, diseases, pathways, conditions, side effects, genes) in structured and unstructured data. Users can ask Cortex complex questions across large scale data sets, and discover unexpected relationships between concept types. Concept recognition analytics is applicable to a wide range of use cases from competitive intelligence, to drug repurposing and EHR analytics.

 

  • Life Sciences R&D Specialized Image Analytics. Deep learning enables novel, powerful forms of image analytics, capable of being trained to detect patterns and objects in large scale image data sources. With just a few clicks in Cortex, the user can connect large streams of image data and apply analytics to those sources. Vyasa has finely-tuned this analysis for life sciences images, and it is ideal for cell assay screening, drug manufacturing and post-market screening for counterfeit packaging and tablets.
  • ChemVector de novo Compound Design. This proprietary Cortex module applies deep learning to chemical structures. Users can drag and drop one or more SDF files containing SMILES strings into Cortex, and Cortex can identify and generate novel compounds that optimize critical variables such as log-p, molecular weight and synthetic viability. ChemVector can be used with a range of other chemistry-specific analytical modules also available in Cortex.

 

 

Dr. Bouton, Vyasa’s founder and CEO, received his BA in Neuroscience (Magna Cum Laude) from Amherst College in 1996 and his Ph.D. in Molecular Neurobiology from Johns Hopkins University in 2001. Previously Dr. Bouton was the CEO of Entagen a software company founded in 2008 that provided innovative Big Data products including Extera and TripleMap. Entagen’s technologies won numerous awards including the “Innovative Technology of the Year Award for Big Data” from the Massachusetts Technology Leadership Council in 2012 and Entagen was recognized as a Gartner “Cool Vendor” in the Life Sciences in 2013. Entagen was acquired by Thomson Reuters in 2013. Dr. Bouton is an author on over a dozen scientific papers and book chapters and his work has been covered in a number of industry news articles.

 

Visit Vyasa and demo Cortex at booth #632, and watch the explainer video at www.vyasa.com.

About Vyasa Analytics

Vyasa Analytics provides deep learning software and analytics for life sciences and healthcare organizations. Cortex is Vyasa’s secure, highly scalable software platform for collaborative knowledge discovery and data analytics. Using Vyasa’s proprietary Neural Concept Recognition technology, Cortex identifies trends and patterns across disparate data sources, empowering project teams to gain insights and drive better decision making. Learn more at www.vyasa.com.

 

 

Angela Zmyslinski
Account Executive
azmyslinski@matternow.com
Office – 401-330-2800

     

SOURCE

From: Angela Zmyslinski <azmyslinski@matternow.com>

Date: Thursday, May 10, 2018 at 2:39 PM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: RE: Demo deep learning software for life sciences at Bio-IT World 2018

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