Rare Disease Research Roadmap: Navigating the bioinformatics and translational challenges for improved patient health outcomes

Rare disease registries have now been recognized as a global priority for progress both in monitoring and documenting the natural course, and preventing and treating rare diseases. However, a disease registry is only one element of rare disease translational research. Here, we outline what we believe are ten key components in comprehensive rare disease translational research and describe critical relationships between them. These components are: (i) client–practitioner partnerships; (ii) disease registries; (iii) biobanks; (iv) genomics and other -omics platforms; (v) community-based and population-wide studies; (vi) bioinformatics and high performance computing; (vii) interactions with pharma to facilitate drug discovery; (viii) personalized treatments based on genotype-phenotype correlations; (ix) eHealth and a whole of life record; and (x) regulatory frameworks, particularly with regard to specimen and data sharing, and the return of results. Each component has its own inherent complexity, but if effectively integrated they will provide a comprehensive approach to the future management of rare diseases, and aid health care providers in delivering services to individuals affected with rare diseases. We demonstrate that navigation through the roadmap can provide relevant health stakeholders with a blueprint to understand the challenges and barriers which need to be overcome within and across the constituent components. The rare disease roadmap will assist decision-making at all health stakeholder levels and enable the seamless integration of new knowledge, standard operating procedures and the implementation of best practice.

[1]  Peter Saffrey,et al.  Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units , 2012, Science Translational Medicine.

[2]  Youwen Zhou,et al.  The US Orphan Drug Act: rare disease research stimulator or commercial opportunity? , 2010, Health policy.

[3]  H. Hakonarson,et al.  Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing , 2013, Genome Medicine.

[4]  K. Getz,et al.  Open innovation: the new face of pharmaceutical research and development , 2012, Expert review of clinical pharmacology.

[5]  Damian Smedley,et al.  The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data , 2014, Nucleic Acids Res..

[6]  J. Bourke,et al.  Exon skipping and dystrophin restoration in patients with Duchenne muscular dystrophy after systemic phosphorodiamidate morpholino oligomer treatment: an open-label, phase 2, dose-escalation study , 2011, The Lancet.

[7]  Christopher B. Forrest,et al.  The case for a global rare-diseases registry , 2011, The Lancet.

[8]  P. Claes,et al.  Objective Monitoring of mTOR Inhibitor Therapy by Three-Dimensional Facial Analysis , 2013, Twin Research and Human Genetics.

[9]  Maria Lluch,et al.  Incentives for telehealthcare deployment that support integrated care: a comparative analysis across eight European countries , 2013, International journal of integrated care.

[10]  D. Falconer The Problem of Environment and Selection , 1952, The American Naturalist.

[11]  Caron Molster,et al.  Key outcomes from stakeholder workshops at a symposium to inform the development of an Australian national plan for rare diseases , 2012, Orphanet Journal of Rare Diseases.

[12]  Adam Hunter,et al.  Correction to Dispelling myths about rare disease registry system development [Source Code Biol Med, 8, (2013), 21] 10.1186/1751-0473-8-21, 24131574 , 2014 .

[13]  Helen M. Moore,et al.  An NCI perspective on creating sustainable biospecimen resources. , 2011, Journal of the National Cancer Institute. Monographs.

[14]  Joanne Odenkirchen,et al.  National Institute of Neurological Disorders and Stroke Common Data Element Project – approach and methods , 2012, Clinical trials.

[15]  Christian Gieger,et al.  Genetic variation in metabolic phenotypes: study designs and applications , 2012, Nature Reviews Genetics.

[16]  Helen M. Moore,et al.  Creating a global rare disease patient registry linked to a rare diseases biorepository database: Rare Disease-HUB (RD-HUB). , 2010, Contemporary clinical trials.

[17]  Christophe Béroud,et al.  Dispelling myths about rare disease registry system development , 2013, Source Code for Biology and Medicine.

[18]  Adam Hunter,et al.  Second generation registry framework , 2014, Source Code for Biology and Medicine.

[19]  Hugo Y. K. Lam,et al.  Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes , 2012, Cell.

[20]  Matthew I. Bellgard,et al.  A Bioinformatics Framework for plant pathologists to deliver global food security outcomes , 2011, Australasian Plant Pathology.

[21]  S. Peltz,et al.  Ataluren as an agent for therapeutic nonsense suppression. , 2013, Annual review of medicine.

[22]  Matthew Bellgard,et al.  The New Zealand Neuromuscular Disease Registry , 2012, Journal of Clinical Neuroscience.

[23]  M. Field,et al.  Rare Diseases and Orphan Products: Accelerating Research and Development , 2010 .

[24]  S. Wilton,et al.  RNA splicing manipulation: strategies to modify gene expression for a variety of therapeutic outcomes. , 2005, Current gene therapy.

[25]  A. Bittles,et al.  A Community-Based Study of Mucopolysaccharidosis Type VI in Brazil: The Influence of Founder Effect, Endogamy and Consanguinity , 2014, Human Heredity.

[26]  David Cox,et al.  Toward a roadmap in global biobanking for health , 2012, European Journal of Human Genetics.

[27]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[28]  S. Groft Rare diseases research: expanding collaborative translational research opportunities. , 2013, Chest.

[29]  O. Drummer,et al.  Review: Pharmacogenetic aspects of the effect of cytochrome P450 polymorphisms on serotonergic drug metabolism, response, interactions, and adverse effects , 2011, Forensic science, medicine, and pathology.

[30]  Monya Baker,et al.  Biorepositories: Building better biobanks , 2012, Nature.

[31]  Gideon Koren,et al.  The Canadian Pharmacogenomics Network for Drug Safety: a model for safety pharmacology. , 2010, Thyroid : official journal of the American Thyroid Association.

[32]  M. Goldman,et al.  The Innovative Medicines Initiative: A European Response to the Innovation Challenge , 2012, Clinical pharmacology and therapeutics.

[33]  Michael Brudno,et al.  PhenoTips: Patient Phenotyping Software for Clinical and Research Use , 2013, Human mutation.

[34]  A. Bittles Consanguinity in Context , 2012 .

[35]  Sean Ekins,et al.  A generalizable pre-clinical research approach for orphan disease therapy , 2012, Orphanet Journal of Rare Diseases.

[36]  Claudia Hemmelmann,et al.  Statistical analysis of rare sequence variants: an overview of collapsing methods , 2011, Genetic epidemiology.

[37]  A. Vanderver,et al.  Identification of a novel de novo p.Phe932Ile KCNT1 mutation in a patient with leukoencephalopathy and severe epilepsy. , 2014, Pediatric neurology.

[38]  D. Goldstein Common genetic variation and human traits. , 2009, The New England journal of medicine.

[39]  A. Bittles,et al.  Consanguinity, human evolution, and complex diseases , 2010, Proceedings of the National Academy of Sciences.

[40]  Adam Hunter,et al.  A modular approach to disease registry design: Successful adoption of an internet‐based rare disease registry , 2012, Human mutation.

[41]  M. Daly,et al.  Searching for missing heritability: Designing rare variant association studies , 2014, Proceedings of the National Academy of Sciences.

[42]  J. Mendell,et al.  Gentamicin‐induced readthrough of stop codons in duchenne muscular dystrophy , 2010, Annals of neurology.

[43]  M. Field,et al.  Rare Diseases and Orphan Products , 2010 .

[44]  Stuart P. McElroy,et al.  A Lack of Premature Termination Codon Read-Through Efficacy of PTC124 (Ataluren) in a Diverse Array of Reporter Assays , 2013, PLoS biology.

[45]  J. Mendell,et al.  Eteplirsen for the treatment of Duchenne muscular dystrophy , 2013, Annals of neurology.

[46]  T. LaFramboise,et al.  Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances , 2009, Nucleic acids research.

[47]  B. Knoppers,et al.  Current trends in biobanking for rare diseases: a review , 2014 .

[48]  Luigi Ferrucci,et al.  Imputation of Variants from the 1000 Genomes Project Modestly Improves Known Associations and Can Identify Low-frequency Variant - Phenotype Associations Undetected by HapMap Based Imputation , 2013, PloS one.

[49]  Ilona Miko Epistasis: Gene Interactions and Phenotypic Effects , 2008 .

[50]  Adam Hunter,et al.  Yabi: An online research environment for grid, high performance and cloud computing , 2012, Source Code for Biology and Medicine.