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      A proof-of-concept study of extracting patient histories for rare/intractable diseases from social media

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          Abstract

          The amount of content on social media platforms such as Twitter is expanding rapidly. Simultaneously, the lack of patient information seriously hinders the diagnosis and treatment of rare/intractable diseases. However, these patient communities are especially active on social media. Data from social media could serve as a source of patient-centric knowledge for these diseases complementary to the information collected in clinical settings and patient registries, and may also have potential for research use. To explore this question, we attempted to extract patient-centric knowledge from social media as a task for the 3-day Biomedical Linked Annotation Hackathon 6 (BLAH6). We selected amyotrophic lateral sclerosis and multiple sclerosis as use cases of rare and intractable diseases, respectively, and we extracted patient histories related to these health conditions from Twitter. Four diagnosed patients for each disease were selected. From the user timelines of these eight patients, we extracted tweets that might be related to health conditions. Based on our experiment, we show that our approach has considerable potential, although we identified problems that should be addressed in future attempts to mine information about rare/intractable diseases from Twitter.

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          Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

          Abstract The Human Phenotype Ontology (HPO)—a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases—is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.
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            From scientific discovery to treatments for rare diseases – the view from the National Center for Advancing Translational Sciences – Office of Rare Diseases Research

            We now live in a time of unprecedented opportunities to turn scientific discoveries into better treatments for the estimated 30 million people in the US living with rare diseases. Despite these scientific advances, more than 90% of rare diseases still lack an effective treatment. New data and genetics technologies have resulted in the first transformational new treatments for a handful of rare diseases. This challenges us as a society to accelerate progress so that no disease and no patient is, ultimately, left behind in getting access to safe and effective therapeutics. This article reviews initiatives of the National Center for Advancing Translational Sciences (NCATS) Office of Rare Diseases Research (ORDR) that are aimed at catalyzing rare diseases research. These initiatives fall into two groups: Promoting information sharing; and building multi-disciplinary multi-stakeholder collaborations. Among ORDR’s information sharing initiatives are GARD (The Genetics and Rare Diseases Information Center), RaDaR (The Rare Diseases Registries Program) and the NCATS Toolkit for Patient-Focused Therapy Development (Toolkit). Among the collaboration initiatives are the RDCRN (Rare Diseases Clinical Research Network), and the NCATS ORDR support for conferences and workshops. Despite the success of these programs, there remains substantial work to be done to build enhanced collaborations, clinical harmonization and interoperability, and stakeholder engagement so that the recent scientific advances can benefit all patients on the long list of rare diseases waiting for help.
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              Social media methods for studying rare diseases.

              For pediatric rare diseases, the number of patients available to support traditional research methods is often inadequate. However, patients who have similar diseases cluster "virtually" online via social media. This study aimed to (1) determine whether patients who have the rare diseases Fontan-associated protein losing enteropathy (PLE) and plastic bronchitis (PB) would participate in online research, and (2) explore response patterns to examine social media's role in participation compared with other referral modalities. A novel, internet-based survey querying details of potential pathogenesis, course, and treatment of PLE and PB was created. The study was available online via web and Facebook portals for 1 year. Apart from 2 study-initiated posts on patient-run Facebook pages at the study initiation, all recruitment was driven by study respondents only. Response patterns and referral sources were tracked. A total of 671 respondents with a Fontan palliation completed a valid survey, including 76 who had PLE and 46 who had PB. Responses over time demonstrated periodic, marked increases as new online populations of Fontan patients were reached. Of the responses, 574 (86%) were from the United States and 97 (14%) were international. The leading referral sources were Facebook, internet forums, and traditional websites. Overall, social media outlets referred 84% of all responses, making it the dominant modality for recruiting the largest reported contemporary cohort of Fontan patients and patients who have PLE and PB. The methodology and response patterns from this study can be used to design research applications for other rare diseases. Copyright © 2014 by the American Academy of Pediatrics.
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                Author and article information

                Journal
                Genomics Inform
                Genomics Inform
                GNI
                Genomics & Informatics
                Korea Genome Organization
                1598-866X
                2234-0742
                June 2020
                18 June 2020
                : 18
                : 2
                : e17
                Affiliations
                [1 ]Tokyo City University, Setagaya, Tokyo 157-0087, Japan
                [2 ]Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
                Author notes
                [* ]Corresponding author: E-mail: atsuko@ 123456tcu.ac.jp
                Author information
                http://orcid.org/0000-0001-7538-5337
                http://orcid.org/0000-0003-0169-8159
                Article
                gi-2020-18-2-e17
                10.5808/GI.2020.18.2.e17
                7362943
                32634871
                53311931-9af3-4727-9cba-f4b081940ab6
                (c) 2020, Korea Genome Organization

                (CC) This is an open-access article distributed under the terms of the Creative Commons Attribution license( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 March 2020
                : 18 June 2020
                Categories
                Application Note

                Genetics
                intractable diseases,rare diseases,social media mining
                Genetics
                intractable diseases, rare diseases, social media mining

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