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Dolled-Filhart M.P.,Rare Genomics Institute | Lee M.,Rare Genomics Institute | Ou-Yang C.-W.,Rare Genomics Institute | Haraksingh R.R.,Rare Genomics Institute | Lin J.C.-H.,Rare Genomics Institute
The Scientific World Journal | Year: 2013

It has become increasingly apparent that one of the major hurdles in the genomic age will be the bioinformatics challenges of next-generation sequencing. We provide an overview of a general framework of bioinformatics analysis. For each of the three stages of (1) alignment, (2) variant calling, and (3) filtering and annotation, we describe the analysis required and survey the different software packages that are used. Furthermore, we discuss possible future developments as data sources grow and highlight opportunities for new bioinformatics tools to be developed. © 2013 Marisa P. Dolled-Filhart et al.


Ong F.S.,Illumina | Lin J.C.,Rare Genomics Institute | Grosu D.S.,Illumina | Fan J.-B.,Illumina
Genomics | Year: 2013

The development of next-generation sequencing (NGS) technology has made DNA sequencing not only rapid and cost-effective, but also highly accurate and reproducible. The translational utility of genomic sequencing is clear, from understanding of human genetic variation and its association with disease risk and individual response to treatment, to the interpretation and translation of the data for clinical decision making. It will be a critical technology for disease characterization and monitoring in molecular pathology and is expected to become a central piece of routine healthcare management which will result in accurate and reliable reporting, a prerequisite for physicians to practice genomic medicine. © 2013 Elsevier Inc.


Fumagalli D.C.,Rare Genomics Institute | Gouw A.M.,Rare Genomics Institute | Gouw A.M.,Stanford University
Yale Journal of Biology and Medicine | Year: 2015

Given the current funding situation of the National Institutes of Health, getting funding for rare disease research is extremely difficult. In light of the enormous potential for research in the rare diseases and the scarcity of research funding, we provide a case study of a novel successful crowdfunding approach at a non-profit organization called Rare Genomics Institute. We partner with biotechnology companies willing to donate their products, such as mouse models, gene editing software, and sequencing services, for which researchers can apply. First, we find that personal stories can be powerful tools to seek funding from sympathetic donors who do not have the same rational considerations of impact and profit. Second, for foundations facing funding restrictions, company donations can be a valuable tool in addition to crowdfunding. Third, rare disease research is particularly rewarding for scientists as they proceed to be pioneers in the field during their academic careers. Overall, by connecting donors, foundations, researchers, and patients, crowdfunding has become a powerful alternative funding mechanism for personalized medicine. © 2015.


Danielsson K.,Rare Genomics Institute | Mun L.J.,Rare Genomics Institute | Lordemann A.,Rare Genomics Institute | Mao J.,Rare Genomics Institute | Lin C.-H.J.,Rare Genomics Institute
Expert Review of Molecular Diagnostics | Year: 2014

Genomics has revolutionized the study of rare diseases. In this review, we overview the latest technological development, rare disease discoveries, implementation obstacles and bioethical challenges. First, we discuss the technology of genome and exome sequencing, including the different next-generation platforms and exome enrichment technologies. Second, we survey the pioneering centers and discoveries for rare diseases, including few of the research institutions that have contributed to the field, as well as an overview survey of different types of rare diseases that have had new discoveries due to next-generation sequencing. Third, we discuss the obstacles and challenges that allow for clinical implementation, including returning of results, informed consent and privacy. Last, we discuss possible outlook as clinical genomics receives wider adoption, as third-generation sequencing is coming onto the horizon, and some needs in informatics and software to further advance the field. © Informa UK, Ltd.


Shen T.,Rare Genomics Institute | Shen T.,Washington University | Pajaro-Van de Stadt S.H.,Rare Genomics Institute | Yeat N.C.,Rare Genomics Institute | And 2 more authors.
Frontiers in Genetics | Year: 2015

This article will review recent impact of massively parallel next-generation sequencing (NGS) in our understanding and treatment of cancer. While whole exome sequencing (WES) remains popular and effective as a method of genetically profiling different cancers, advances in sequencing technology has enabled an increasing number of whole-genome based studies. Clinically, NGS has been used or is being developed for genetic screening, diagnostics, and clinical assessment. Though challenges remain, clinicians are in the early stages of using genetic data to make treatment decisions for cancer patients. As the integration of NGS in the study and treatment of cancer continues to mature, we believe that the field of cancer genomics will need to move toward more complete 100% genome sequencing. Current technologies and methods are largely limited to coding regions of the genome. A number of recent studies have demonstrated that mutations in non-coding regions may have direct tumorigenic effects or lead to genetic instability. Non-coding regions represent an important frontier in cancer genomics. © 2015 Shen, Pajaro-Van de Stadt, Yeat and Lin.


PubMed | Rare Genomics Institute
Type: | Journal: Genetics research | Year: 2015

There are an estimated 6000-8000 rare Mendelian diseases that collectively affect 30 million individuals in the United States. The low incidence and prevalence of these diseases present significant challenges to improving diagnostics and treatments. Next-generation sequencing (NGS) technologies have revolutionized research of rare diseases. This article will first comment on the effectiveness of NGS through the lens of long-tailed economics. We then provide an overview of recent developments and challenges of NGS-based research on rare diseases. As the quality of NGS studies improve and the cost of sequencing decreases, NGS will continue to make a significant impact on the study of rare diseases moving forward.


PubMed | Rare Genomics Institute
Type: Review | Journal: Orphanet journal of rare diseases | Year: 2017

While regulatory policy is well defined for orphan drug development in the United States and Europe, rare disease policy in China is still evolving. Many Chinese patients currently pay out of pocket for international treatments that are not yet approved in China. The lack of a clear definition and therefore regulatory approval process for rare diseases has, until now, de-incentivized pharmaceutical companies to pursue rare disease drug development in China. In turn, many grassroots movements have begun to support rare disease patients and facilitate drug discovery through research. Recently, the Chinese FDA set new regulatory guidelines for drugs being developed in China, including an expedited review process for life-saving treatments. In this review, we discuss the effects of these new policy changes on and suggest potential solutions to innovate orphan drug development in China.


PubMed | Stanford University and Rare Genomics Institute
Type: Journal Article | Journal: The Yale journal of biology and medicine | Year: 2015

Given the current funding situation of the National Institutes of Health, getting funding for rare disease research is extremely difficult. In light of the enormous potential for research in the rare diseases and the scarcity of research funding, we provide a case study of a novel successful crowdfunding approach at a non-profit organization called Rare Genomics Institute. We partner with biotechnology companies willing to donate their products, such as mouse models, gene editing software, and sequencing services, for which researchers can apply. First, we find that personal stories can be powerful tools to seek funding from sympathetic donors who do not have the same rational considerations of impact and profit. Second, for foundations facing funding restrictions, company donations can be a valuable tool in addition to crowdfunding. Third, rare disease research is particularly rewarding for scientists as they proceed to be pioneers in the field during their academic careers. Overall, by connecting donors, foundations, researchers, and patients, crowdfunding has become a powerful alternative funding mechanism for personalized medicine.


News Article | February 17, 2017
Site: www.marketwired.com

HUDSON, NY--(Marketwired - Feb 17, 2017) - Taconic Biosciences, a global leader in genetically engineered rodent models and associated services, announced it has generated a novel mouse model of Vici syndrome for use by two investigators studying this rare disease. As a corporate sponsor of the Rare Disease Science Challenge: BeHEARD, hosted by the Rare Genomics Institute, Taconic donated model development services. Using CRISPR/Cas9 gene editing, Taconic developed and validated a mouse model carrying the EPG5 mutation found in Vici syndrome patients in multiple families. A highly efficient way to generate custom mouse and rat models on a short timeline, CRISPR is one of many technologies Taconic employs to generate models of human disease and support investigator studies of gene function in vivo. Genetically engineered mice of the Vici syndrome model have been delivered to the investigators working on the BeHEARD project: Mathias Gautel, BHF Chair of Molecular Cardiology at King's College London BHF Research Excellence Centre, and Heinz Jungbluth, Reader in Paediatric Neurology at King's College, and Consultant at the Evelina Children's Hospital, Guy's & St Thomas' NHS Foundation Trust, London. "The precision of the genetic manipulation by Taconic and their speed of delivery were critical to our work," Prof. Gautel and Dr. Jungbluth said. The investigators are now using the mice to validate the model's replication of the human phenotype of the disease, in terms of neurological, musculoskeletal and other organ symptoms. "If the model replicates the human phenotype with significant fidelity, it could be applied quite rapidly to screening drug compounds for Vici syndrome," Prof. Gautel said. Rachel and Michael Harris, parents of 10-year-old Vici syndrome patient David, submitted the proposal for the BeHEARD project and are hopeful the model will facilitate development of effective therapies. "While the initial research is focused upon understanding the disease mechanisms, we hope to soon see translational research that will bring new therapies to David and other patients," Michael Harris said. "Taconic's core mission is to provide animal models that help accelerate drug discovery. Being able to support critical research on a rare disease like Vici syndrome through custom genetically engineered models is extremely rewarding," said Dr. Robert Rosenthal, chief executive officer of Taconic Biosciences. Taconic has over twenty years' experience designing custom transgenic models for leading pharmaceutical, biotech and academic clients. Taconic is fully licensed to utilize CRISPR/CAS9, homologous recombination and other technologies to develop custom mouse and rat models, including humanized, knockout, knock-in, inducible shRNA, or microRNA expressing models. Vici syndrome is a severe congenital multisystem disorder characterized by a failure to develop the corpus callosum region of the brain, along with a cardiomyopathy, cataracts, hypopigmentation of the skin, eyes and hair, and a combined immunodeficiency. To learn more about Taconic's custom model generation, please call 1-888-TACONIC (888-822-6642) in the US or +45 70 23 04 05 in Europe, or email info@taconic.com. To learn more about the BeHeard Project, visit http://www.raregenomics.org/beheard-competition/. About Taconic Biosciences, Inc. Taconic Biosciences is a fully-licensed, global leader in genetically engineered rodent models and services. Founded in 1952, Taconic helps biotechnology companies and institutions acquire, custom generate, breed, precondition, test, and distribute valuable research models worldwide. Specialists in genetically engineered mouse and rat models, precision research mouse models, and integrated model design and breeding services, Taconic operates three service laboratories and six breeding facilities in the U.S. and Europe, maintains distributor relationships in Asia and has global shipping capabilities to provide animal models almost anywhere in the world.


News Article | December 20, 2016
Site: www.businesswire.com

CAMBRIDGE, Mass.--(BUSINESS WIRE)--Sanofi Genzyme, the specialty care global business unit of Sanofi, today announced the recipients of the sixth annual Patient Advocacy Leadership (PAL) Awards. The global PAL Awards program supports projects by non-profit organizations that serve patients living with lysosomal storage disorders (LSDs), a group of rare, inherited disorders that can cause progressive and debilitating health problems. Recipients were chosen by a review committee, composed of Sanofi Genzyme and outside experts, from among 27 proposals submitted by organizations from 15 different countries. Collaboration is a key component of the program, and grants were awarded to initiatives that involve two or more organizations working together to support the LSD community. This year, application guides and proposal forms were made available in five different languages, English, Spanish, Portuguese, Chinese and French. “ It’s important that these awards are accessible to non-profits around the world,” said Sanofi Genzyme’s Head of Global Rare Diseases, Richard Peters, MD, Ph.D. “This year, organizations were encouraged to apply in their own language, and we were thrilled to see 16 organizations submit applications in their native language.” Since 2011, through the PAL Awards program, Sanofi Genzyme has recognized 46 organizations around the world supporting disease awareness, community mobilization, non-profit development and good governance activities. The PAL Awards program supplements Sanofi Genzyme’s charitable giving and does not replace the contributions made each year to support advocacy groups. The program is continuously reviewed and modified in an effort to best meet the needs of the global LSD community. More information on the PAL Awards program can be found at: www.PALAwards.com. Sanofi Genzyme is pleased to announce the following 2016 PAL Award recipients: Polish Association of Families Affected by Gaucher Disease, Polish Association of Families Affected by Fabry Disease, and Polish Pompe Association (Poland) The Polish Association of Families Affected by Gaucher Disease, the Polish Association of Families Affected by Fabry Disease and the Polish Pompe Association are joining forces to create an online platform called “Storage” that provides comprehensive education about lysosomal storage disorders and an interactive forum for patients to connect with one another. As the project progresses, the platform will be used to gather and assess the needs of the LSD community to further inform Poland’s patient organizations’ programs and initiatives. Croatian Alliance for Rare Diseases and National Organization for Rare Disease of Serbia (Croatia) A rare disease patient’s diagnostic journey is often long, complex and filled with misdiagnoses. Aimed at reducing the length of time to diagnosis, the Croatian Alliance for Rare Diseases and the National Organization for Rare Disease of Serbia are collaborating on a project called “Little Big Signs of Diagnosis,” an educational online platform for medical students. The platform will include videos of patients and their caregivers describing the first and most important symptoms of their disease, in an effort to raise awareness among medical students and better prepare them to correctly diagnosis LSDs in the future. Rare Genomics Institute and Organization for Rare Disease India (United States and India) The genes that cause many LSDs have been identified, often making genetic sequencing a useful diagnostic tool. However, in order for genetic sequencing to be performed, patient advocate associates, who help patients navigate the process, must be properly trained, and patients and their caregivers must be properly informed. In an effort to strengthen and optimize genetic sequencing support functions, the Rare Genomics Institute in the United States and the Organization for Rare Disease India are working together to create training modules and educational resources for patient advocate associates, patients, caregivers and physicians. Vietnam Rare Disease Network and the Vietnam National Hospital of Pediatrics (Vietnam) Increasing knowledge and reducing stigma around rare diseases are two big challenges for advocacy organizations. To address both issues, the Vietnam Rare Disease Network, in collaboration with the Vietnam National Hospital of Pediatrics, is publishing a book to provide disease information about specific LSDs, as well as share the stories of 22 rare disease patients and their families. It will be the first rare disease awareness book in Vietnam and can also serve as a reference manual for healthcare students. The Association for Glycogen Storage Disease and Royal College of General Practitioners (UK) For many rare disease patients, their diagnostic odysseys often begin with a general practitioner who does not recognize diagnostic symptoms or refer them to the appropriate specialist. The Association for Glycogen Storage Disease is working with the Royal College of General Practitioners to educate general practitioners in the UK on the early signs and symptoms of Pompe disease and other glycogen storage diseases. They are developing concise visual e-learning modules to be featured on the website of the Royal College of General Practitioners, an organization with more than 52,000 general practitioner members. Associação Catarinense de Pacientes e Amigos de Gaucher and Associação Gaúcha de Fabry (Brazil) Many health professionals are not specifically trained on how to care for patients living with rare and chronic health issues. To address this knowledge gap in Brazil, the Associação Catarinense de Pacientes e Amigos de Gaucher and the Associação Gaúcha de Fabry are collaborating to provide informational materials and trainings at community health centers, targeting doctors, nurses, receptionists, psychologists, and social workers. The trainings aim to help healthcare professionals identify rare disease patients early in their visit to a health center, so they can offer personalized care that addresses the particular needs of their disease and reduces the risk of inappropriate procedures. About Lysosomal Storage Disorders Lysosomal storage disorders (LSDs) are a group of more than 40 diseases. Each is caused by a genetic mutation that results in the deficiency or malfunction of a particular enzyme needed to remove waste material from cells. These waste molecules then accumulate, or build up, in cell lysosomes (smaller compartments within cells), disrupting cell function and causing a variety of symptoms. LSDs can be progressive, life-threatening and severely debilitating. Because these disorders are extremely rare, it can be difficult to find information about them. In the case of the most common of these disorders, Gaucher disease, it is estimated that only 10,000 people have been diagnosed worldwide. It is thought that many more people are affected by rare diseases than have been diagnosed. This is why access to information about LSDs is so important. About Sanofi Sanofi, a global healthcare leader, discovers, develops and distributes therapeutic solutions focused on patients' needs. Sanofi is organized into five global business units: Diabetes and Cardiovascular, General Medicines and Emerging Markets, Sanofi Genzyme, Sanofi Pasteur and Merial. Sanofi Genzyme focuses on developing specialty treatments for debilitating diseases that are often difficult to diagnose and treat, providing hope to patients and their families. Genzyme® is a registered trademark of Genzyme Corporation. Sanofi® is a registered trademark of Sanofi. All rights reserved. Forward-Looking Statements This press release contains forward-looking statements as defined in the Private Securities Litigation Reform Act of 1995, as amended. Forward-looking statements are statements that are not historical facts. These statements include projections and estimates and their underlying assumptions, statements regarding plans, objectives, intentions and expectations with respect to future financial results, events, operations, services, product development and potential, and statements regarding future performance. Forward-looking statements are generally identified by the words "expects", "anticipates", "believes", "intends", "estimates", "plans" and similar expressions. Although Sanofi's management believes that the expectations reflected in such forward-looking statements are reasonable, investors are cautioned that forward-looking information and statements are subject to various risks and uncertainties, many of which are difficult to predict and generally beyond the control of Sanofi, that could cause actual results and developments to differ materially from those expressed in, or implied or projected by, the forward-looking information and statements. These risks and uncertainties include among other things, the uncertainties inherent in research and development, future clinical data and analysis, including post marketing, decisions by regulatory authorities, such as the FDA or the EMA, regarding whether and when to approve any drug, device or biological application that may be filed for any such product candidates as well as their decisions regarding labelling and other matters that could affect the availability or commercial potential of such product candidates, the absence of guarantee that the product candidates if approved will be commercially successful, the future approval and commercial success of therapeutic alternatives, Sanofi's ability to benefit from external growth opportunities and/or obtain regulatory clearances, risks associated with intellectual property and any related pending or future litigation and the ultimate outcome of such litigation, trends in exchange rates and prevailing interest rates, volatile economic conditions, the impact of cost containment initiatives and subsequent changes thereto, the average number of shares outstanding as well as those discussed or identified in the public filings with the SEC and the AMF made by Sanofi, including those listed under "Risk Factors" and "Cautionary Statement Regarding Forward-Looking Statements" in Sanofi's annual report on Form 20-F for the year ended December 31, 2015. Other than as required by applicable law, Sanofi does not undertake any obligation to update or revise any forward-looking information or statements.

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