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Moreover, because the patenting process is costly, institutions with limited resources may be forced to choose which discoveries they will seek to protect and which they will not. In these circumstances, the limited commercial prospects for many products for rare diseases may influence institutions to bypass future commercialization opportunities, and the lack of patent protection may discourage the sharing of data and materials with potential collaborators. One study of access to genetic data and materials reported that nearly 50 percent of genetic researchers have encountered negative responses to their requests for data or materials related to published research (Campbell et al. Reasons cited for denying access included not only desires to protect the commercial value of the intellectual property but also to maintain publication opportunities. Although barriers are significant, a range of infrastructure and information sharing innovations can be cited, including several that operate under the auspices of the National Center for Biotechnology. A significant incentive for such submissions is the requirement by scientific journals for deposition to GenBank or a similar database so that an accession number will be included in a published article. More examples of initiatives to increase access to information and other infrastructure resources are described below and in Chapter 5. Recently, in a case involving gene patents held by Myriad Genetics, the ruling of a federal district court would, if upheld on appeal, invalidate or restrict patents on individual genes (Pollack, 2010). Mouse models are common, but simpler, more rapidly reproducing models such as the zebrafish are also valuable where genetic mouse models do not fully recreate human disease. Technological advances have allowed the development of long-sought alternative animal models for Huntington disease (monkey) and cystic fibrosis (pig) (Wolfe, 2009), but satisfactory animal models still await many rare diseases, for example, Smith Lemli Opitz syndrome (Merkens et al. Mouse models, and occasionally other animal models, can be created using both forward and reverse genetic manipulation. Forward genetics involves the altering of specific genes to change their expression patterns and products. Although expensive and time-consuming, this approach is now a fundamental experimental strategy and has been an important contributor to research advances for an array of rare diseases. Reverse genetics is carried out by exposing animals to mutagenic agents and identifying genetic disorders by careful genotyping and phenotyping of the animals. The ability to carry out these studies requires animal (especially mouse) manipulation and maintenance facilities that are now available in most major academic research centers. Adequate funding for these studies is a challenge for fledgling research programs. Expanded development and access to genetically modified mice that are relevant to rare diseases will promote research progress and accelerate work aimed at identifying potential therapeutic agents for rare diseases. Other research approaches have used cultured cells from mouse models of rare disease. Interestingly, it was research on tyrosinemia, a rare disease that led to this model (Azuma et al. Progress at the preclinical stage will undoubtedly be aided by the creative use of human cells, both normal and those derived from patients with genetic defects. An emerging option may be the in vitro generation of normal or disorder-specific differentiated cells from human pluripotent cells. Mice with genetic disorders are collected, studied, and made available to researchers by various organizations, including the National Cancer Institute mouse. One initiative of the Friedreich Ataxia Research Alliance was to arrange with Jackson Laboratories to make mice available so that researchers no longer had to maintain their own research animals (Farmer, 2009). They can also serve as a recruitment tool for the launch of studies focused on disease etiology, pathogenesis, diagnosis, or therapy. When combined with genetic information, patient registries can inform the correlation of patient genotype with the distribution, onset, severity, or progression of clinical manifestations or response to treatment (phenotype-genotype correlations). In essence, for rare disorders it is necessary to collect as much information as possible on as many patients as possible to discriminate predictive patterns from chance correlations, to validate these patterns using statistical methods, and to apply them productively in individual patient diagnosis, prognostication, counseling, and management. Decisions about whether a registry should attempt to capture a comprehensive or representative sample are often influenced by disease prevalence. This approach can serve as a model for certain other rare disorders, although it will be limited to patient advocacy groups or other coordinating entities that have substantial sophistication, organization, and resources to exert as leverage.

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The proper handling of biospecimens creates opportunities for pathologists to improve their diagnoses while assessing prognosis and treatment. In addition, the growing need for high-quality biorepositories represents an opportunity for community pathologists to strengthen their role within the health care team, ensuring that clinical care is not compromised while facilitating research. Section 2 community pathologists learning how to create high-quality biorepositories and participating in emerging opportunities in the biorepository field. While a variety of topics are covered to provide breadth of information, the intent is to facilitate a level of understanding that permits community pathologists to make more informed choices in identifying how best their skills and practice may be augmented to address developments in this field. Preservation of Nucleic Acids and Tissue Morphology in Paraffin-embedded Clinical Samples: Comparison of Five Molecular Fixatives. Summary: Formalin fixation preserves tissue morphology at the expense of macromolecule integrity. Factors Influencing the Degradation of Archival Formalin-Fixed Paraffin-Embedded Tissue Sections. To test their hypothesis, they examined fixation time, processing time, and humidity of storage environment on protein integrity and antigenicity by immunohistochemistry, Western blotting, and protein extraction. This study revealed that inadequate tissue processing, resulting in retention of endogenous water in tissue sections, results in antigen degradation. Exposure to high humidity during storage results in significant protein degradation and reduced immunoreactivity, and the effects of storage humidity are temperature dependent. Slides stored under vacuum with desiccant do not protect against the effects of residual water from inadequate tissue processing. These results support that the presence of water, both endogenously and exogenously, plays a central role in antigenicity loss. The parameters of optimal storage of unstained slides remain to be defined, as they are directly affected by preanalytic variables. Objective-To review current molecular biomarkers and tumorspecific assays most useful in solid tumor testing, specifically of breast, colon, lung, thyroid, and soft tissue tumors, malignant melanoma, and tumors of unknown origin. A few upcoming molecular diagnostic assays that may become standard of care in the near future will also be discussed. Conclusions-Molecular testing in anatomic pathology is firmly established and will continue to gain ground as the need for more specific diagnoses and new targeted therapies evolve. Knowledge of the more common and clinically relevant molecular tests available for solid tumor diagnosis and management, and their indications and limitations, is necessary if anatomic pathologists are to optimally use these tests and act as consultants for fellow clinicians directly involved in patient care. Summary: Molecular methods have been suggested as a way to enhance or replace current morphology-based staging methods. Lung cancer with epidermal growth factor receptor exon 20 mutations is associated with poor gefitinib treatment response. Molecular genetic testing for lung adenocarcinomas: a practical approach to clinically relevant mutations and translocations. Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. Jovanovic P, Mihajlovic M, Djordjevic-Jocic J, Vlajkovic S, Cekic S, Stefanovic V. Summary: Cancers arise owing to the accumulation of mutations in critical genes that alter normal programmes of cell proliferation, differentiation and death. As the first stage of a systematic genomewide screen for these genes, we have prioritized for analysis signalling pathways in which at least one gene is mutated in human cancer. All mutations are within the kinase domain, with a single substitution (V599E) accounting for 80%. The pathologist plays a key role in this process because assessment of morphological features of the tumor is important prior to molecular analysis. This article provides a summary of the performance characteristics of various molecular testing methods and addresses other key aspects of testing necessary to provide relevant information to help determine appropriate therapy choices. Summary: Molecular testing in pathology emerged shortly after polymerase chain reaction became a standard molecular biology assay. Testing efforts began in the clinical laboratories primarily with assays for genetically inherited diseases and assays for clonality in hematologic malignancies. Today, the field has evolved into "molecular diagnostics," which encompasses testing in almost every area of anatomic pathology.

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There is low-quality evidence that plasmapheresis provides additional benefit for diffuse pulmonary hemorrhage. There is evidence that rituximab is not inferior to cyclophosphamide in induction therapy. All patients with extrarenal manifestations of disease should receive immunosuppressive therapy, regardless of the degree of kidney dysfunction. The rare possible exception relates to patients with severe kidney-limited disease, in the absence of extrarenal manifestations of small-vessel vasculitis. Cyclophosphamide the addition of cyclophosphamide to corticosteroids in induction therapy improved the remission rate from about 55% to about 85%, and decreased the relapse rate three-fold. There was no significant difference between the two treatment groups in rates of complete remission at 6 months, adverse events, or relapse rates. Rituximab shows equivalent efficacy to cyclophosphamide in initial therapy and the evidence does not suggest a difference in rates of adverse effects. In addition, the very high cost of rituximab compared to cyclophosphamide limits its application from a global perspective. Plasmapheresis the value of pulse methylprednisolone induction therapy has not been tested directly. The rationale for pulse methylprednisolone is related to its rapid anti-inflammatory effect. There are no data that 1000 mg daily for 3 days is better than 500 mg; this lower dose is widely used in clinical practice, and the higher dose may be associated with increased short- and long-term risks of infection and other complications of steroids. Both groups received standard therapy with oral cyclophosphamide and oral prednisone followed by azathioprine for maintenance therapy. Plasmapheresis was associated with a significantly higher rate of kidney recovery at 3 months (69% of patients with plasmapheresis vs. Plasmapheresis for Patients with Diffuse Alveolar Hemorrhage the impact of plasmapheresis in patients with diffuse, severe alveolar hemorrhage is the reduction of mortality, based on retrospective case series. When patients lost to follow-up were excluded from the analysis, the rates of remission were similar in the two groups. Therefore, the likely benefit of maintenance therapy depends on the assessment of the risk of relapse, which differs among various subgroups of patients. For example, the risk of low-dose maintenance immunosuppression in a frail, elderly patient has to be weighed against the very high risk for such a patient of severe relapse. Maintenance immunosuppressive therapy is justified in patients at high risk of relapse, but the potential benefit of maintenance therapy may be low in patients who have a low likelihood of relapse. There is low-quality evidence that the duration of maintenance therapy should be at least 18 months. There is moderate-quality evidence that trimethoprimsulfamethoxazole as an adjunct to maintenance therapy reduces the risk of relapse, but only in those with upper respiratory disease due to vasculitis. The goal of maintenance therapy is to decrease the incidence and severity of relapsing vasculitis. It is unknown whether patients with none of the risk factors for relapse need maintenance immunosuppression. The risk-benefit ratio of maintenance therapy has not been evaluated in such patients. The tailoring of maintenance therapy, based on the risk factors of relapse, has not been tested in clinical trials. In a placebo-controlled trial, the use of trimethoprimsulfamethoxazole was associated with a decreased rate of upper airway-relapse.

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If researchers have not yet identified the genetic or other cause of a condition or delineated how the disease develops, a group may concentrate its grants and other activities on closing these gaps in knowledge. Policies of Other Countries and International Initiatives the policies of the United States on orphan drugs and pharmaceuticals do not exist in isolation. The United States was the earliest adopter of formal incentives for orphan drug development, but a number of other nations have followed with policies that are broadly similar, although differing in some details. The European Union has developed a common policy for its member states on some issues. Each agency still makes its own decisions, but the two regularly communicate about application reviews. Work to harmonize views on what constitutes acceptable clinical trial design and analytic strategies is particularly important when patient populations are small, multi-nation studies are essential, and confirmatory trials are difficult or impossible. As discussions progressed, the focus expanded from drugs and biologics to include medical devices. In developing its conclusions and recommendations, the committee reviewed the literature on rare diseases and orphan product development and also examined the broader literature on scientific and policy issues related to medical product discovery and development. The literature review was complicated by both the very large number of diseases categorized as rare and the limited base of knowledge about most of these conditions. The committee also solicited information and perspectives from a range of individuals and organizations, including voluntary organizations that promote research on specific conditions or rare conditions more generally, companies that develop drugs and medical devices, and researchers engaged in various aspects of basic, translational, and clinical research. Thus, this report does not examine in depth the various initiatives related to neglected tropical diseases such as Chagas disease, onchocerciasis (river blindness), and trypanosomiasis or sleeping sickness. Many products for rare diseases are approved with requirements for postmarket studies, but the committee did not examine the conduct, outcomes, or review of these studies. It also did not review health services research on the translation of research findings and achievements into clinical practice. Notwithstanding its focus on research and development, the committee recognized the crucial importance of applying preventive, diagnostic, and therapeutic advances in clinical care, public health practice, and personal behavior. Without this further effort, scientific advances will not benefit individual and public health. Also, it is often in clinical practice that the limitations of products are revealed when drugs or devices that were studied under highly controlled conditions with carefully selected populations are used in real-world conditions with broader populations. The term condition is useful in describing injuries and entities such as hemochromatosis and sickle cell trait that do not cause symptoms or distress in the majority of people who have them. Defining and Tabulating Rare Diseases this report follows the statutory definition of a rare disease or condition as one that affects fewer than 200,000 people in the United States. As is true of many qualitative descriptions or definitions of magnitude, any operational definition of a term such as "rare" is subjective. That subjectivity is reflected in the variations in definitions adopted by different national policymakers as shown in Table 1-4. Some definitions specify absolute numbers of affected people whereas others specify rates. Japan and, in particular, Australia define "rare" more conservatively than the United States or the European Union. In contrast to the policy of the European Union, the United States definition does not specify that a disease condition must be chronically debilitating or life-threatening. In general, however, the committee found that public programs and industry activities tended to concentrate on serious conditions. Census Bureau, 2001, 2009; Australian Bureau of Statistics, 2008; Statistics Bureau (Japan), 2008; Eurostat, 2010. If the legislative definition of rare disease had been expressed as the 1984 rate, a rare disease could have affected nearly 258,000 people in the United States as of 2008. Overall, the committee views the choice of a number rather than a rate to be reasonable. It is consistent with the rationale that conditions affecting small numbers of people may create particular problems for research and product development that may require special responses, including incentives of the kind adopted by Congress in 1983. Estimates of the number of rare diseases in the United States and Europe range from approximately 5,000 conditions to approximately 8,000 (see. The Office of Rare Diseases Research at the National Institutes of Health includes more than 6,800 conditions in its list of rare diseases, which is available online rarediseases. The preface to the list states that it is based on "either (1) terms for which information requests have been made to the Office of Rare Diseases Research, the Genetic and Rare Diseases Information Center, or the National Human Genome Research Institute; or (2) diseases that have been suggested as being rare.