Presentation for the 2018 University of North Texas Open Access Symposium. This presentation discusses the adoption (or lack thereof) of Open Access and Open Data trends at for profit healthcare organizations from a scientist’s point of vie

Eggington, Julie M.

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Healthy Families Campaign - 2017The Need for Open Access Publications inCommercial Clinical Genetic WorkflowsA 501(c)(3) nonprofit humanitarian organization7 June 2018Julie M. Eggington, M.S., Ph.D.Co-founder and CEOjeggington@genomicinterpretation.orgTwitter: @Dr_J_Eggington www.genomicinterpretation.orgROADMAP2© 2018 Center for Genomic Interpretation1. Commercial clinical genetics overview.2. Restricted access can hurt genetics patients.3. CGI is working towards encouraging open access data publishing FROM commercial labs by using commercial forces. Intro:Open vs restricted access impact:Publishing FROM commercial laboratories:#UNTOA18       @Dr_J_Eggington ROADMAP3© 2018 Center for Genomic Interpretation1. Commercial clinical genetics overview.2. Restricted access can hurt genetics patients.3. CGI is working towards encouraging open access data publishing FROM commercial labs by using commercial forces. Intro:Open vs restricted access impact:Publishing FROM commercial laboratories:#UNTOA18       @Dr_J_Eggington GENETICS - BLAME YOUR PARENTS!4© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington 52 in every 25 people have a genetic disease~7000 patients tested everyday in the USA© 2018 Center for Genomic InterpretationGENETIC DISEASE IS COMMON#UNTOA18       @Dr_J_Eggington May 27, 2013GENETIC TESTING IS NOW MAINSTREAMDecember 24, 2012BRCA1Cystic fibrosis© 2018 Center for Genomic Interpretation 6#UNTOA18       @Dr_J_Eggington CLINICAL GENETICS PROCESS FLOWPATIENTACTCGTAGCTAACTCGTTGCTAACTCGTAGCTAACTCGTTGCTA7© 2018 Center for Genomic Interpretation...PATIENT#UNTOA18       @Dr_J_Eggington (Case level data is siloed)ROADMAP8© 2018 Center for Genomic Interpretation1. Commercial clinical genetics overview.2. Restricted access can hurt genetics patients.3. CGI is working towards encouraging open access data publishing FROM commercial labs by using commercial forces. Intro:Open vs restricted access impact:Publishing FROM commercial laboratories:#UNTOA18       @Dr_J_Eggington 9Five Classifications:❏ Pathogenic❏ Likely Pathogenic❏ Variant of Uncertain Significance❏ Likely Benign❏ BenignJUDGEMENTCLINICAL GENETICS: WHERE RESEARCH IS STILL TRANSLATED DIRECTLY INTO MEDICAL PRACTICE© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington RESEARCH LITERATURE IS RIDDLED WITH ERROR10“The literature is riddled with false claims of pathogenicities from researchers who have not done a good job of interpretation.” Heidi Rehm, PhD FACMG, Harvard Medical School17 August 2016, Wall Street Journal“As many as 30 percent of mutations associated with disease aren’t. We’re going to have to do a lot of cleanup work.”Michael Ackerman, MD PhD, Mayo Clinic31 Oct 2016, STAT© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington CLINICAL GENETIC ERRORS IMPACT THOUSANDS OF FAMILIES EACH YEAR11FALSE POSITIVE genetic tests erroneously send>100,000● Pregnancy termination● Organ and tissue removal● Traumatic therapiesindividuals into the US medical system EACH YEAR (1 every 5 minutes) for unnecessary:© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington CLINICAL GENETIC ERRORS IMPACT THOUSANDS OF FAMILIES EACH YEAR12Genetic diagnostic ERRORS cost at leastONE BILLION DOLLARSdirectly to the US medical system EACH YEAR as a result of unnecessary:● Pregnancy termination● Organ and tissue removal● Traumatic therapies© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington CLEAN UP REQUIRED13“As many as 30 percent of mutations associated with disease aren’t. We’re going to have to do a lot of cleanup work.”Michael Ackerman, MD PhD, Mayo Clinic31 Oct 2016, STATGoogle Scholar searchPublication rate for 3 of 8000 known clinically relevant genes© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington 14Majority of research conclusions are insufficientfor clinical application Is the experimental design correct? Is the organism relevant?Are the statistics sufficient?Are the relations strong enough?vsCLEAN UP: ASKING THE HARD QUESTIONS© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington 15COMMERCIAL LAB SCIENTISTS IN “PRODUCTION”Test BabyLaboratory turn-around-time and profitability requirements cap literature review efforts.© 2018 Center for Genomic Interpretation90% of scientists cannot easily access the literature they need.(Source: Reprints Desk, http://info.reprintsdesk.com)#UNTOA18       @Dr_J_Eggington 16DesiredpublicationsCreative AccessRestricted AccessOpen AccessMANY CLINICAL VARIANT SCIENTISTS RELY ON ABSTRACTS ONLY FOR RESTRICTED ACCESS ARTICLES60%20%20%✔✔❌❌$$ © 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington 17TITLES & ABSTRACTS VS. FULL CONTENTAUTHOR LIST:Respected scientists at top institutionsTITLE:“XYZ is the most deadly genetic variant in human history”ABSTRACT:We did a lot of awesome science and PROVED that XYZ is really, really bad and is going to kill any person that carries it, like, tomorrow.CRITICAL READING OF FULL ARTICLE:-Single case report (N=1)-Scientific conclusions were made using approaches that have not been clinically validated, with some algorithms that have already been debunked repeatedly in numerous well powered studies.Generic example of a genetic variant report publication:Title & Abstract: Full Content:© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington 18DesiredpublicationsCreative AccessOpen Access 60%20%20%✔✔❌❌$$ © 2018 Center for Genomic InterpretationRestricted Access#UNTOA18       @Dr_J_Eggington MANY CLINICAL VARIANT SCIENTISTS RELY ON ABSTRACTS ONLY FOR RESTRICTED ACCESS ARTICLESRESTRICTED ACCESS ARTICLES CONTRIBUTES TO ERROR19FALSE POSITIVE genetic tests erroneously send>100,000● Pregnancy termination● Organ and tissue removal● Traumatic therapiesindividuals into the US medical system EACH YEAR (1 every 5 minutes) for unnecessary:© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington ROADMAP20© 2018 Center for Genomic Interpretation1. Commercial clinical genetics overview.2. Restricted access can hurt genetics patients.3. CGI is working towards encouraging open access data publishing FROM commercial labs by using commercial forces. Intro:Open vs restricted access impact:Publishing FROM commercial laboratories:#UNTOA18       @Dr_J_Eggington 21OPEN ACCESS ARTICLES SAVES & IMPROVESTHE LIVES OF CLINICAL GENETICS PATIENTSHIGH VOLUME COMMERCIAL CLINICAL GENETIC DISCOVERIESOpen Access Articles ~100%A CGI GOAL:© 2018 Center for Genomic Interpretation #UNTOA18       @Dr_J_Eggington (ClinVar) 22PUBLIC GOOD IS RARELY A MOTIVATING FACTOR© 2018 Center for Genomic Interpretation● When working with companies to encourage open access publishing of their data, we must demonstrate that data sharing will ultimately increase their profits.○ If this isn’t true, can it be made true?For profit companies answer to investors. #UNTOA18       @Dr_J_Eggington 23CGI’S PLANS FOR HIGH THROUGHPUT OPEN ACCESS PUBLISHING FROM COMMERCIAL DATA4. Impact3. Services2. Aggregating and analyzing data1. “Un-siloing” and curating dataData PublishingVUSolveTMFiNDitALLTMVariant ClassificationVariant FactCheckerTMVariant Reclassification© 2018 Center for Genomic InterpretationCGI: BETTER, FASTER, CHEAPER VARIANT CLASSIFICATION AS A SERVICE#UNTOA18       @Dr_J_Eggington QUESTIONS?24© 2018 Center for Genomic InterpretationCenter for Genomic InterpretationJulie M. Eggington, M.S., Ph.D.Co-founder and CEOwww.genomicinterpretation.orgjeggington@genomicinterpretation.orgTwitter: @Dr_J_Eggington#UNTOA18       @Dr_J_Eggington 

The Need for Open Access Publications in Commercial Clinical Genetic Workflows

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The Need for Open Access Publications in Commercial Clinical Genetic Workflows

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