The Matchmaker Exchange: a platform for rare disease gene discovery

There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.

Realizing Our Potential in Biobanking: Disease Advocacy Organizations Enliven Translational Research

Biobanks are increasingly powerful tools used in translational research, and disease advocacy organizations (DAOs) are making their presence known as research drivers and partners. We examined DAO approaches to biobanking to inform how the enterprise of biobanking can grow and become even more impactful in human health. In this commentary, we outline overarching approaches from successful DAO biobanks. These lessons learned suggest principles that can create a more participant-centric approach and illustrate the key roles DAOs can play as partners in research initiatives. DAO approaches to biobanking for translational research include the following: be outcome driven; forge alliances that are unexpected-build bridges to enhance translation; come ready for success; be nimble, flexible, and adaptable; and remember that people matter. Each of these principles led to particular practices that have increased the translational impact of biobank collections. The research practices discussed can inform partnerships in all sectors going forward.

Governance Through Privacy, Fairness, and Respect for Individuals

INTRODUCTION

Individuals have a moral claim to be involved in the governance of their personal data. Individuals' rights include privacy, autonomy, and the ability to choose for themselves how they want to manage risk, consistent with their own personal values and life situations. The Fair Information Practices principles (FIPPs) offer a framework for governance. Privacy-enhancing technology that complies with applicable law and FIPPs offers a dynamic governance tool for enabling the fair and open use of individual's personal data.

PERCEPTIONS OF RISK

Any governance model must protect against the risks posed by data misuse. Individual perceptions of risks are a subjective function involving individuals' values toward self, family, and society, their perceptions of trust, and their cognitive decision-making skills.

THE HIPAA PRIVACY RULE PUTS SOME GOVERNANCE IN THE HANDS OF INDIVIDUALS

Individual privacy protections and individuals' right to choose are codified in the HIPAA Privacy Rule, which attempts to strike a balance between the dual goals of information flow and privacy protection. The choices most commonly given individuals regarding the use of their health information are binary ("yes" or "no") and immutable. Recent federal recommendations and law recognize the need for granular, dynamic choices.

BUILDING A GOVERNANCE FRAMEWORK BASED IN TRUST AVOIDING SURPRISES

Individuals expect that they will govern the use of their own health and genomic data. Failure to build and maintain individuals' trust increases the likelihood that they will refuse to grant permission to access or use their data. The "no surprises principle" asserts that an individual's personal information should never be collected, used, transmitted, or disclosed in a way that would surprise the individual were she to learn about it.

FAIR INFORMATION PRACTICES PRINCIPLES

The FIPPs provide a powerful framework for enabling data sharing and use, while maintaining trust. We introduce the eight FIPPs adopted by the Department of Health and Human Services, and provide examples of their interpretation and implementation.

REDUCING RISK THROUGH CONSUMER ENGAGEMENT

Privacy risk and health risk can be reduced by giving consumers control, autonomy, and transparency, and by engaging them in managing their own health. Explicit "consent" may not always be necessary - the FIPPs offer multiple ways to engender trust and avoid surprises.

Research Progress in Pseudoxanthoma Elasticum and Related Ectopic Mineralization Disorders

Heritable ectopic mineralization disorders represent a phenotypically diverse group of conditions characterized by deposition of calcium phosphate complexes in soft connective tissues. The prototype of such conditions is pseudoxanthoma elasticum, and related conditions with overlapping clinical features include generalized arterial calcification of infancy and arterial calcification due to CD73 deficiency. Molecular genetic investigations have revealed mutations in the genes physiologically involved in generation of inorganic pyrophosphate and inorganic phosphate, and the findings suggest a unifying pathomechanism relating to reduced inorganic pyrophosphate/inorganic phosphate ratio. This hypothesis is based on the notion that inorganic pyrophosphate serves as a powerful inhibitor of mineralization, whereas inorganic phosphate is a promineralization factor, and an appropriate inorganic pyrophosphate/inorganic phosphate ratio is critical for prevention of ectopic mineralization under homeostatic conditions.

Toward clinical genomics in everyday medicine: perspectives and recommendations

Precision or personalized medicine through clinical genome and exome sequencing has been described by some as a revolution that could transform healthcare delivery, yet it is currently used in only a small fraction of patients, principally for the diagnosis of suspected Mendelian conditions and for targeting cancer treatments. Given the burden of illness in our society, it is of interest to ask how clinical genome and exome sequencing can be constructively integrated more broadly into the routine practice of medicine for the betterment of public health. In November 2014, 46 experts from academia, industry, policy and patient advocacy gathered in a conference sponsored by Illumina, Inc. to discuss this question, share viewpoints and propose recommendations. This perspective summarizes that work and identifies some of the obstacles and opportunities that must be considered in translating advances in genomics more widely into the practice of medicine.

The effects of bisphosphonates on ectopic soft tissue mineralization caused by mutations in the ABCC6 gene

Pseudoxanthoma elasticum (PXE) and generalized arterial calcification of infancy (GACI) are heritable ectopic mineralization disorders. Most cases of PXE and many cases of GACI harbor mutations in the ABCC6 gene. There is no effective treatment for these disorders. We explored the potential efficacy of bisphosphonates to prevent ectopic calcification caused by ABCC6 mutations by feeding Abcc6(-/-) mice with diet containing etidronate disodium (ETD) or alendronate sodium trihydrate (AST) in quantities corresponding to 1x, 5x, or 12x of the doses used to treat osteoporosis in humans. The mice were placed on diet at 4 weeks of age, and the degree of mineralization was assessed at 12 weeks by quantitation of the calcium deposits in the dermal sheath of vibrissae, a progressive biomarker of the mineralization, by computerized morphometry of histopathologic sections and by direct chemical assay of calcium. We found that ETD, but not AST, at the 12x dosage, significantly reduced mineralization, suggesting that selected bisphosphonates may be helpful for prevention of mineral deposits in PXE and GACI caused by mutations in the ABCC6 gene, when combined with careful monitoring of efficacy and potential side-effects.