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Biology of aging research goal: Defeating Death – California Life Company (Calicolabs.com), A Billion-dollar Longevity Lab, since 2013, GOOGLE cofounder and CEO Larry Page, formation of a new Alphabet entity is using consumer genetics and genealogy firm Ancestry’s forest of family trees

Reporter: Aviva Lev-Ari, PhD, RN

 

Conclusion – “Don’t smoke, and don’t go to war.”

Humans have more control over how long they live than their genes do. It’s all the other things that families share—homes and neighborhoods, culture and cuisine, access to education and health care—that make a much bigger difference in the set of numbers that might one day grace your tombstone.

Analyzing the pedigrees of more than 400 million people who lived and died in Europe and America going back to 1800 was that although longevity tends to run in families, your DNA has far less influence on how long you live than previously thought. The results, published Tuesday in the journal Genetics, is the first research to be made public from the collaboration, which ended quietly in July and whose terms remain confidential.

“The true heritability of human longevity for that cohort is likely no more than seven percent,” says Ruby. Previous estimates for how much genes explain variations in lifespan have ranged from around 15 to 30 percent. So what did Ruby uncover that previous studies had missed? Just how often amorous humans go against the old adage that “opposites attract.”

For example, you might choose a partner who also has curly hair, and if the curly-haired trait winds up being somehow associated with long lifespans, this would inflate estimates of lifespan heritability passed on to your kids. Same thing for non-genetic traits like wealth, education, and access to good health care. People tend to choose partners in their same income bracket with the same terminal degree, both of which are associated with living longer, healthier lives.

Calicolabs.com – NEWS

Genetics Society of America press release on Calico paper titled, “Estimates of the heritability of human longevity are substantially inflated due to assortative mating.”Nov 6, 2018

AbbVie and Calico Announce Extension of Groundbreaking Collaboration June 26, 2018

Calico Scientists Publish Paper in eLife Demonstrating that the Naked Mole Rat’s Risk of Death Does Not Increase With AgeJanuary 25, 2018

C4 Therapeutics and Calico Enter Strategic Partnership to Discover Novel Therapeutics Based on Targeted Protein DegradationMarch 23, 2017

Daphne Koller Named to FiercePharma’s “Fierce Women in Biopharma 2016” ListOctober 13, 2016

Calico Appoints Daphne Koller as Chief Computing OfficerAugust 17, 2016

The Jackson Laboratory and Calico to Investigate Basic Biology of AgingApril 26, 2016

David Botstein receives the Double Helix Medal from Cold Spring Harbor LaboratoryNovember 9, 2015 | Cold Spring Harbor Laboratory

AncestryDNA and Calico to Research the Genetics of Human LifespanJuly 21, 2015

Cynthia Kenyon named one of the “15 Most Amazing Women in Science Today”July 20, 2015 | Business Insider

Calico enters into agreement with the Buck Institute to conduct research into the biology of aging and to identify potential therapeutics for age-related diseasesApril 28, 2015

Calico licenses technology from acclaimed UCSF laboratoryMarch 31, 2015

Calico and QB3 announce partnership to conduct research into the biology of aging and to identify potential therapeutics for age-related diseasesMarch 24, 2015

Broad Institute and Calico announce an extensive collaboration focused on the biology of aging and therapeutic approaches to diseases of agingMarch 17, 2015

Art Levinson to receive National Medal of Technology and InnovationOctober 3, 2014

UT Southwestern researchers discover novel class of NAMPT activators for neurodegenerative disease; Calico enters into exclusive collaboration with 2M to develop UTSW technologySeptember 11, 2014

AbbVie and Calico Announce a Novel Collaboration to Accelerate the Discovery, Development, and Commercialization of New TherapiesSeptember 3, 2014

Google announces Calico, a new company focused on health and well-being (Google News)September 18, 2013

SOURCE

https://www.calicolabs.com/

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Science luminaries speak at Breakthrough Symposium – Livestream available

 

UPDATED on 11/7/2018

Angelika Amon wins 2019 Breakthrough Prize in Life Sciences

Four other MIT researchers to receive New Horizons Prizes in math and physics; two alumni win Breakthrough Prize in Fundamental Physics.

Anne Trafton | MIT News Office
October 17, 2018

Angelika Amon, an MIT professor of biology, is one of five scientists who will receive a 2019 Breakthrough Prize in Life Sciences, given for transformative advances toward understanding living systems and extending human life.

Amon, the Kathleen and Curtis Marble Professor in Cancer Research and a member of MIT’s Koch Institute for Integrative Cancer Research, was honored for her work in determining the consequences of aneuploidy, an abnormal chromosome number that results from mis-segregation of chromosomes during cell division.

The award, announced this morning, comes with a $3 million prize.

“Angelika Amon is an outstanding choice to receive the Breakthrough Prize,” says Tyler Jacks, director of the Koch Institute and the David H. Koch Professor of Biology. “Her work on understanding how cells control the decisions to divide and the effects of imbalances in chromosome number has helped shape how we think about normal development and disease. Angelika is a fearless investigator and a true scientist’s scientist. All of us in the Koch Institute and across MIT are thrilled by this news.”

Two MIT alumni, Charles Kane PhD ’89 and Eugene Mele PhD ’78, both professors at the University of Pennsylvania, will share a Breakthrough Prize in Fundamental Physics. Kane and Mele are being recognized for their new ideas about topology and symmetry in physics, leading to the prediction of a new class of materials that conduct electricity only on their surface.

SOURCE

http://news.mit.edu/2018/angelika-amon-breakthrough-prize-life-sciences-1017

 

Complete List of 2019 Winners Breakthrough Prize

 

Breakthrough Prize in Life Sciences Breakthrough Prize

  • C. Frank Bennett and Adrian R. Krainer – Ionis Pharmaceuticals and Cold Spring Harbor Laboratory
    Citation: For the development of an effective antisense oligonucleotide therapy for children with the neurodegenerative disease spinal muscular atrophy.
  • Angelika Amon – Massachusetts Institute of Technology and Howard Hughes Medical Institute
    Citation: For determining the consequences of aneuploidy, an abnormal chromosome number resulting from chromosome mis-segregation.
  • Xiaowei Zhuang – Harvard University and Howard Hughes Medical Institute
    Citation: For discovering hidden structures in cells by developing super-resolution imaging, a method that transcends the fundamental spatial resolution limit of light microscopy.
  • Zhijian “James” Chen – University of Texas Southwestern Medical Center and Howard Hughes Medical Institute
    Citation: For elucidating how DNA triggers immune and autoimmune responses from the interior of a cell through the discovery of the DNA-sensing enzyme cGAS.

Breakthrough Prize In Fundamental Physics

  • Charles Kane and Eugene Mele – University of Pennsylvania
    Citation: For new ideas about topology and symmetry in physics, leading to the prediction of a new class of materials that conduct electricity only on their surface.

Breakthrough Prize In Mathematics

  • Vincent Lafforgue – CNRS (National Center for Scientific Research, France) and Institut Fourier, Université Grenoble Alpes
    Citation: For ground breaking contributions to several areas of mathematics, in particular to the Langlands program in the function field case.

Special Breakthrough Prize In Fundamental Physics

  • Jocelyn Bell Burnell – University of Dundee and University of Oxford
    Citation: For fundamental contributions to the discovery of pulsars, and a lifetime of inspiring leadership in the scientific community.

 

Press Release From: Breakthrough Prize Foundation
Posted: Sunday, November 4, 2018

Winners of 2019 Breakthrough Prize Will Lead Discussions on Cutting-Edge Research with Inspiring TED-Style Talks

 

WHAT:          The 2019 Breakthrough Prize Symposium, held the day after the Breakthrough

Prize Awards ceremony, will feature both current and former laureates leading TED-style talks on cutting-edge science research initiatives and the significance and future of scientific discovery.

Topics include abnormal chromosomes and their role in cancer and potential use as a therapeutic target; exploring radio bursts and what’s going on in the stars; algebraic geometry and the Langlands Program; and discussing RNA splicing as a target for the next generation of precision medicines.

Dr. Jennifer Doudna, 2015 Breakthrough Prize Laureate and leader in the CRISPR revolution, will present “Recoding Life: The Future of Genome Editing.”

The event will conclude with three cross-disciplinary panel discussions between laureates past and present, about broad philosophical subjects around science and technology.  The topics of this year’s discussions include: ‘Is there (intelligent) life in the Universe?’; ‘What are the limits of science?’; and ‘Is time travel possible?’.

For a detailed schedule of the program, visit https://breakthroughprize2019.berkeley.edu/  

WHEN:        Monday, November 5, 2018

                     Pauley Ballroom, MLK Student Union

UC Berkeley

The presentations will be streamed live via YouTube (see program for URLs) and Facebook Live. 

Breakthrough Prize Laureate Talks

9:30AM – 5:00PM PST

Evening Cross-Disciplinary Panel

5:30PM – 7:00 PM PST

 

SCHEDULE

 

BREAKTHROUGH PRIZE LAUREATE TALKS

 (9:30AM – 5:00PM PST)

10:30 AM – Abnormal Chromosome Number: it’s Role in Cancer and Potential as a Therapeutic

Angelika Amon, 2019 Laureate

10:55 AM – Envisaging the Emergence of Quantum Topological Matter     

Charles Kane, 2019 Laureate

 

11:20 AM – Recoding Life: The Future of Genome Editing              

Jennifer Doudna, 2015 Laureate

11:45 AM – Some Open Problems in Algebraic Geometry and the Langlands Program

Vincent Lafforgue, 2019 Laureate

12:10 PM – RNA Splicing as a Target for the Next Generation of Precision Medicines       

Adrian R. Krainer, 2019 Laureate

1:35 PM – Biomaterials and How They Will Change our Lives        

Robert Langer, 2014 Laureate

2:00 PM – Imaging the Invisible in Living Organisms –– Current State of the Art and Future         

Xiaowei Zhuang, 2019 Laureate

2:25 PM – The Winding Road from Topological Insulators  

Gene Mele, 2019 Laureate

2:50 PM – Inflammation 2030 – Modern Disease Caused by an Old Flame 

James Chen, 2019 Laureate

3:45 PM – Seeking a Computer-free Proof of the 4-Color Theorem

Ian Agol, 2016 Laureate

4:10 PM – Genetic Medicines: Present and Future   

Frank Bennett, 2019 Laureate

5:00 PM – Radio Bursts!  What’s Going on Amongst the Stars?

Jocelyn Bell Burnell, 2018 Laureate

BREAKTHROUGH PRIZE PANEL DISCUSSIONS

(5:30 – 7:00PM PST)

Is there (intelligent) life in the Universe?

Featuring Jocelyn Bell, Astronomy, 2018 Laureate; John Hardy, Neuroscience, 2017 Laureate; and Kim Nasmyth, Molecular Biology, 2018 Laureate

Astronomers have been looking for life beyond Earth for decades, but have so far found nothing. But the recent discovery that almost all stars probably host planets may have changed the game. How likely are we to find primitive life? How hard is it to get from cells to brains? And why have we not seen evidence of civilizations?

What are the limits of science?

Featuring Andrei Linde, Theoretical Physics, Cosmology – 2012 Laureate; Gary Ruvkun, Molecular Biology, Genetics, 2015 Laureate; and  Xiaowei Zhuang, Biophysics, 2019 Laureate

 

Science has shown us a universe more and more distant from our familiar world: at microscopic and cosmic scales, at the dawn of time and remote stages of evolutionary history. But is this process limitless? What are the furthest and smallest physical and biological objects we can see? Can we ever know what happened at the moment of the Big Bang? And how far back can we retrace the origin of life on Earth?

Is time travel possible?

Nima Arkani-Hamed, Theoretical Physics, 2012 Laureate; Daniel Harlow, Theoretical Physics,  2019 Laureate; Daniel Jafferis, Theoretical Physics,  2019 Laureate; and Aron Wall, Theoretical Physics, 2019 Laureate

 

Time travel is a staple of science fiction, but how does mainstream science see it? Is it forbidden by the laws of physics? And if not, could it ever be a practical possibility? And do scientists even agree about what time is?

MEDIA OPPORTUNITIES: All events are free and open to the media, but seating is limited. Please RSVP to Kristen Bothwell /kbothwell@rubenstein.com / 212-843-9227; or Emily Gest / egest@rubenstein.com / 917-690-7823.

The Breakthrough Prize Symposium partners include Stanford University, the University of California, San Francisco, and the University of California, Berkeley.

The Breakthrough Prize in Life Sciences honors transformative advances toward understanding living systems and extending human life. The Breakthrough Prize in Mathematics honors the world’s best mathematicians who have contributed to major advances in the field. The Breakthrough Prize in Fundamental Physics recognizes major insights into the deepest questions of the Universe.

For more information on the Breakthrough Prize, visit https://breakthroughprize.org.

// end //

SOURCE

http://spaceref.com/news/viewpr.html?pid=53322


Patent on Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription was awarded to UC, Berkeley on October 30, 2018

  •  site-specific modification of a target DNA and/or a polypeptide associated with the target DNA, a DNA-targeting RNA
  •  genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Reporter: Aviva Lev-Ari, PhD, RN

 

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United States Patent 10,113,167
Doudna ,   et al. October 30, 2018

Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription 

AbstractThe present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.


Inventors: Doudna; Jennifer A. (Berkeley, CA), Jinek; Martin (Berkeley, CA), Chylinski; Krzysztof (Vienna, AT), Charpentier; Emmanuelle (Braunschweig, DE)
Applicant:
Name City State Country Type

The Regents of the University of California
University of Vienna
Charpentier; Emmanuelle
Oakland
Vienna
Braunschweig
CA
N/A
N/A
US
AT
DE
Assignee: The Regents of the University of California (Oakland, CA)
University of Vienna (Vienna, AT)
Charpentier; Emmanuelle (Braunschweig, DE)
Family ID: 1000003617643
Appl. No.: 15/138,604
Filed: April 26, 2016

SOURCE

http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.htm&r=1&f=G&l=50&s1=10113167.PN.&OS=PN/10113167&RS=PN/10113167

SAVE

UC Berkeley team awarded second CRISPR-Cas9 patent

 

“Today’s news … represents yet another validation of the historic and field-changing breakthrough invented by scientists Jennifer Doudna, Emmanuelle Charpentier, and their team… The patent announced today specifically highlights the CRISPR-Cas9 invention’s ability to edit DNA in any setting, including within animal and human cells. It also highlights its utility in several formats across both dual-RNA and single-RNA configurations, useful for therapy for genetic diseases and for improving food security.”
— Edward Penhoet, special adviser to the UC Berkeley chancellor, tells Axios

The details: According to the patent, the compositions can be used in animal or human cells, and can work as either 2 separate pieces of RNA or a single piece of RNA.

  • Penhoet says the new patent covers 2 RNA components that together form the “DNA-targeting-RNA,” with one that targets the particular sequence of DNA needed to be edited and the other that binds with the Cas9 protein.
  • This follows another patent given to UC Berkeley in June on methods to use CRISPR-cas9.
  • The patents cover the composites used by CRISPR-Cas9 within human, plant, animal and bacteria cells.
  • Both allow the use of strands of RNA “that can be shorter than naturally-occurring RNA components. This allows them to be more easily used and, therefore, is a form often preferred,” Penhoet says.

Go deeper:

SOURCE

https://www.axios.com/uc-berkeley-awarded-crispr-cas9-gene-edit-patent-5a533f22-929d-4e7d-83fe-0a73ebeb4538.html


NHLBI decision to halt Heart Stem-Cell Study (CONCERT-HF trial) due to concerns about Anversa’s Animal Studies, not due to any Data generated by the Clinical trial itself, no compromised patient safety by trial

Reporter: Aviva Lev-Ari, PhD, RN

Doubts about Anversa’s work arose in the early 2000s after other researchers failed to replicate his findings and questioned whether cardiac stem cells existed2,3,4.

Paper of Former HMS Prof. Withdrawn, Clinical Trial Paused after Harvard Requests Retractions

https://www.thecrimson.com/article/2018/10/31/medical-school-paper-retracted/

NHLBI NEWS

Statement

Statement on NHLBI decision to pause the CONCERT-HF trial

The National Heart, Lung, and Blood Institute (NHLBI), part of the National Institutes of Health, is pausing the CONCERT-HF trialexternal link, which involves patients with chronic heart failure. Recent calls for the retraction of journal articles in related fields of cell therapy research have raised concerns about the scientific foundations of this trial.  While none of the articles in question derive from the CONCERT-HF trial itself, the NHLBI convened CONCERT-HF’s Data and Safety Monitoring Board (DSMB) out of an abundance of caution to ensure the study continues to meet the highest standards for participant safety and scientific integrity. Informed by the DSMB recommendations of October 25, 2018, the NHLBI is pausing the trial. While the DSMB did not have any participant safety concerns, this pause enables the DSMB to complete its review.

The safety of all clinical trial participants is paramount to NHLBI. NHLBI will honor its commitment to CONCERT-HF participants and continue the follow-up protocol during this pause for all participants who have already been treated in the study. Participants are being notified of the status of the trial and how to request additional information.

The CONCERT-HF trial seeks to determine whether c-kit+ cells, either alone or in combination with mesenchymal stem cells derived from the bone marrow, are safe and benefit patients with chronic heart failure, who have very limited treatment options. Despite significant medical and surgical advances, patients with heart failure continue to experience a low quality of life and about half of them will die within five years of receiving a diagnosis.

The scientific basis of CONCERT-HF is supported by a body of evidence in several preclinical models in a number of studies in a variety of laboratories and was reviewed by a Protocol Review Committee (PRC) independent of the trial. The cell therapies that CONCERT-HF is testing are under an investigational new drug (IND) designation which is overseen by the U.S. Food and Drug Administration (FDA). The cells are produced by an accredited laboratory independent of the clinical sites. In addition, as part of standard oversight of clinical trials, the DSMB routinely reviews and monitors CONCERT-HF to ensure participant safety and that the study continues to ask compelling scientific questions with implications for patient care.

The DSMB’s review will be conducted as expeditiously as possible and will inform NHLBI’s future actions that will ensure the highest standards of participant safety and scientific integrity.

SOURCE

https://www.nhlbi.nih.gov/news/2018/statement-nhlbi-decision-pause-concert-hf-trial

References

  1. Quaini, F. et al. N. Engl. J. Med. 346, 5–15 (2002).
  1. Murry, C. E. et al. Nature 428, 664–668 (2004).
  1. Balsam, L. B. Nature 428, 668–673 (2004).
  1. Nygren, J. M. et al. Nature Med. 10, 494–501 (2004).

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Bioinformatics Tool Review: Genome Variant Analysis Tools

Curator: Stephen J. Williams, Ph.D.

 

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

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

 

 


Cardiac Medical Devices Pioneer, Earl E. Bakken, Medtronic Co-founder, the developer of the first external, battery-powered, transistorized pacemaker, died at 94 on 10/21/2018 in Hawaii

Reporter: Aviva Lev-Ari, PhD, RN

 

Earl Bakken was born to Florence and Osval Bakken on January 10, 1924, in Minneapolis. After serving as a radar instructor in World War II, Bakken earned a degree in electrical engineering at the University of Minnesota.

In the late 1950’s, Bakken developed the first external, wearable, battery-powered, transistorized heart pacemaker, and commercialized the first implantable pacemaker in 1960. Medtronic grew rapidly from there; today its medical products and devices improve the lives of two people every second.

Earl with five-year-old pacemaker recipient Lyla Koch in 1984

Image Sourcehttp://www.medtronic.com/us-en/about/news/celebrating-earl-bakken.html

CELEBRATING EARL BAKKEN

Legendary Medtronic co-founder passes away in Hawaii.

Earl Bakken, Co-founder, Medtronic, died at 94

Image Sourcehttp://www.medtronic.com/us-en/about/news/celebrating-earl-bakken.html

The business struggled, but while servicing medical equipment, Bakken and Hermundslie built relationships with doctors at university hospitals in Minneapolis. There they met C. Walton Lillehei, a young staff surgeon who would later become famous for pioneering open-heart surgery. Following a blackout in the Twin Cities that caused the death of an infant, Lillehei asked Bakken to come up with a solution. He responded by adapting a circuit described in Popular Electronics magazine to create the first external wearable, battery-powered pacemaker, replacing the large, alternating current-powered pacemakers that were in use at the time.

The original Medtronic "Garage Gang" poses in front of Medtronic Operational Headquarters in Fridley, Minnesota.

The Garage Gang

Standing: Dale Blosberg, Norman Hagfors, Earl Hatten. Seated: John Bravis, Earl Bakken, Louis Leisch

They expanded services to other medical technology. Then in 1960, the first implantable pacemaker was implanted in a human patient. Bakken and Hermundslie reached a licensing agreement with the inventors, giving their small company exclusive manufacturing and marketing rights to the device, and Medtronic took off.

“Earl always had a vision of healthcare of not being about devices, about drugs, but about restoring people to full health,” said former Medtronic CEO Bill George. “And so from the very start he was focused on not implanting a device, but enabling people to live a full active life and he delivered that point of view to all Medtronic employees through The Mission.

A lifelong aspiration came true for Bakken in 2013, when Medtronic Philanthropy launched The Bakken Invitation to honor people who received medical devices, and who made an impact on the lives of others, through service and volunteerism. Bakken, who in his later years became a medical device patient, with a pacemaker, coronary stents and insulin pump, was fond of asking patients what they planned to do with their gift of “extra life.” Each year Bakken met with the honorees. “Their stories are a powerful reminder that we can all give back-no matter our current situation,” he said after meeting them in 2014.

Earl poses with recipients of the Bakken Invitation in 2013.Earl with Bakken Invitation recipients in 2013

Every year in December, Medtronic employees gather to mark another Bakken inspiration — the employee holiday program. The company invites patients from all over the world to share their stories of how medical technology has improved their lives. Hundreds of employees fill the Medtronic conservatory for the event, while thousands of others listen or watch via Medtronic TV.


Three Scenarios for the Scaling up Potential of LPBI Group’s BioMed e-Series: Lights on Intellectual Property Growth Capacity and the Business Potential of the Venture

Author: Aviva Lev-Ari, PhD, RN

 

From: Aviva Lev-Ari <avivalev-ari@alum.berkeley.edu>

Date: October 20, 2018 at 10:36:21 AM EDT

To: Gail Thornton <gailsthornton@yahoo.com>, “Dr. Larry Bernstein” <larry.bernstein@gmail.com>, Stephen J Williams <sjwilliamspa@comcast.net>

Cc: Marcus Feldman <mfeldman@stanford.edu>, rmandahl@gmail.com, Justin MDMEPhD <jdpmdphd@gmail.com>, Tilda Barliya <tildabarliya@gmail.com>, “Dr. Irina Robu, PhD” <irina.stefania@gmail.com>, “Dr. Raphael Nir” <rnir@sbhsciences.com>, “Dr. Dror Nir” <drornir0305@gmail.com>, Dee Sag <demet.sag@gmail.com>, Sudipta Saha <sudiptasaha1977@gmail.com>

Subject: Re: Dr. Laura Carfang from SurvivingBreastCancer.org interested in your Voices project

 

Dr. Larry, Dr. Williams, Gail

 

I wish to thank Dr. Williams for exposing to SurvivingBreastCancer.org

Our Series E: Parient-centered Medicine, Volume One: Voices of Patients, an e-Book on patients personal experiences with invasive surgical procedures, chiefly, cancerous organ excision and open heart surgery.

This Volume one is unique and please all read again the Preface, Introduction, Summary and Epilogue. Read in the follwoing link:

https://pharmaceuticalintelligence.com/biomed-e-books/series-e-titles-in-the-strategic-plan-for-2014-1015/2014-the-patients-voice-personal-experience-with-invasive-medical-procedures/

and

Co-Editors: Dr. Larry H. Bernstein and Gail Thornton

 

As Editor-in-Chief, I made the selection of the editors and envisioned the following unique features of this e-book:

  • Commissioned Gail to conduct interviews with Patients and to author articles that provide primary patients accounts. One article of Gail is on a cardiac patient, the rest on several cancer types, non on Breast Cancer
  • Gail, as Volume Co-Editors suggested to conduct interviews with Hospital CEOs around the Globe, I.e., Singapore, Switzerland, US: CA, NJ
  • Commissioned Dr. Larry to contribute articles on “The MD as a Cancer Patient”
  • Identified another “MD as a cancer patient”, Finding My Voice: A Laryngectomee’s Story
  • Identified two authors, for cardiac patients experience, one with open heart surgery, the other about a cardiac medical device in usage

As such, Series E: Volume One is a very distinctive e-Book. Gail Thornton and myself discussed marketing the e-Book in Cancer Treatment Centers in the US. The e-Book is priced for patients as e-readers ($49, 824 pages vs $75 or $115 for volumes of 2,000 – 3,000 pages or more)

I personally, planned this volume to be an e-Book widely marketed and read by the public at large. The other 15 volumes are of interest to the public, they are primarily for the Heath Care sector professionals, policy makers in Heath Care, Science and Research Administrators, Scientists, the entire GLOBAL and American Medical community.

Our BioMed e-Series Plan: SIXTEEN volumes to be completed in July 2019 and reach the Milestone of EXIT and ownership transfer in 12/2019 to 12/2020, time frame.

Dr. Lev-Ari gave Series E its Title and the Titles to Volume 1,2,3,4 in this e-Series. That was the case with all other four e-Series: 

https://pharmaceuticalintelligence.com/biomed-e-books/

  • Series A: Cardiovascular, six volumes, 

Content Consultant, Dr. J.D. Pearlman

  • Series B: Genomics, two volumes, 

Content Consultant, Prof. M.W. Feldman, Stanford University

  • Series C: Cancer, two volumes, 

Content Consultant, Dr. L.H. Bernstein

  • Series D: Metabolomics, Immunology, Infectious Diseases, 

Content Consultant, Dr. L.H. Bernstein

  • Series E: Patient-centered Medicine, four volumes

Content Consultant, Dr. L.H. Bernstein

 

This e-mail is about an organization, I.e., SurvivingBreastCancer.org expressing interest to support 

—–>>> A NEW e-BOOK, in Series E, Volume One: Patient Voices

To focus on the VOICES of Survivors of Breast Cancer as 2nd Edition to Volume One.

This volume, if produced, will be #17.

  • The initial 16-Volume BioMed Series did not plan on 2nd Editions to each Volume.

 

In light of SBC INTEREST, I see three Scenarios:

 

Scenario #1 limited LPBI Group involvement beyond LPBI Group Intellectual Property:

SurvivingBreastCancer.org (SBC) is given by fiat for being .org LPBI Group’s permission to use our methods in e-Publishing. They choose the Editor and they produce by their Editor and writers of their choice a volume IN THE IMAGE of Series E, Volume One 1st Edition. 

Here we own two IP assets

1.1 MIRROR IMAGE OF THE e-Table of Contents (eTOCs) of Volume One 1st Edition

1.2 The Curation methodology and all Formats, as perfected in 16-volume BioMed e-Series

Scenario #2 more involvement by LPBI Group

2.1 All of mentioned in #1 Scenarios

and

2.2. Dr. Williams provides SBC with a Bibliography in descending date of publishing of ALL Breast Cancer articles in the Archive of pharmaceuticalintelligence.com – all 5,400 articles in the Journal Archive are 100% IP of LPBI Group.

 

Scenario #3 LPBI Group becomes a BUSINESS PARTNER for SBC on the production of LPBI Group’s BioMed e-Series, Series E, 

Volume One 2nd Edition on VOICES of Patients of Breast Cancer Survivors

 

Other Options using LPBI Group Intellectual Property – very attractive proposition for potential transfer of ownership, aka, EXIT

  • eTOCs of Series E, Volume One, 1st Edition
  • The methodology of Curation and all Formats
  • Bibliography in descending date of Publication of articles on the CANCER TYPE from LPBI Group’s Archive of pharmaceuticalintelligence.com

Collaboration and Partnership with Patient Advocacy Foundations to support the following: Scaling up “Digital Library” Options on VOICES of Patients by TYPE of CANCER

  • Volume One 3rd Edition on VOICES of Patients of Prostate Cancer Survivors
  • Volume One 4th Edition on VOICES of Patients of Lymphomas and Leukemias
  • Volume One 5th Edition on VOICES of Patients of Lung Cancer 
  • Volume One 6th Edition on VOICES of Patients of Brain, Head and Neck Cancers
  • Volume One 7th Edition on VOICES of Patients of Pancreas, Liver and Biliary System Cancers
  • Volume One 8th Edition on VOICES of Patients of GI and Colonrectal 
  • Volume One 9th Edition on VOICES of Patients of Skin Cancers
  • Volume One 10th Edition on VOICES of Patients of Myelomas (Bone), Sarcomas and rare 
  • Connective tissue cancers
  • Volume One 11th Edition on VOICES of Patients of Kidney and Bladder Cancers and the GU system
  • Volume One 12th Edition on VOICES of Patients of Reproductive Organ Cancers: Ovarian, Cervical and Testicular 

BioMed e-Series 16 volumes could have TEN Editions each, Aviva can specify all these e-Book Titles on behalf of a Publisher(s).

  • 160 new titles. For a PUBLISHER, this is a gold mine.

SAME, as these Options for NEW Editions for Series E, Volume One, LPBI Group will draft Options for NEW Editions for

  • Series A – six volume times TEN Editions per Volume
  • Series B – two volumes times TEN Editions per Volume
  • Series C – two volumes times TEN Editions per Volume
  • Series D – three volume times TEN Editions per Volume
  • Series B – four volumes times TEN Editions per Volume

Thank you

Aviva Lev-Ari, PhD, RN

Editor-in-Chief, BioMed e-Series

http://PharmaceuticalIntelligence.com

Director & Founder

Leaders in Pharmaceutical Business Intelligence (LPBI) Group