Bioinformatics services related to diagnosis of primary immunodeficiencies

The use of databases in primary immunodeficiencies

PURPOSE OF REVIEW

We provide an overview on the latest developments in primary immunodeficiency registries worldwide, on the basis of the recent literature amended by some older references to achieve completeness.

RECENT FINDINGS

New primary immunodeficiency registries are emerging worldwide, although existing databases continue to thrive and provide valuable insights for clinicians and researchers.

SUMMARY

In the area of rare disease research, data on a meaningful number of patients can only be achieved via collaboration. Registries for primary immunodeficiency are organized on different geographic levels and appear in various technical forms. Some registries are operated within single departments or hospitals, whereas others collect data from a country in the form of a national registry. With modern information technology and networks, it has become feasible to easily extend documentation to the transnational level. Most patient registries cover similar but not identical sets of data, whereas some have a special focus on, for example, genetics or incorporate only data from patients who have undergone a specific form of treatment. This review shows the usefulness and power of international immunodeficiency registries, as well as possible hurdles and limitations.

Newborn screening for SCID: three years of experience

Over the past three years, newborn blood screening (NBS) for severe T cell lymphopenia/severe combined immunodeficiency (sTCL/SCID) using the T cell receptor excision circle (TREC) assay has revolutionized the early detection of infants with primary immunodeficiencies (PIDs) associated with T cell lymphopenia. Nonetheless, despite the comprehensive NBS protocols developed by each state, additional issues unique to screening for sTCL/SCID have surfaced, including variability in the performance of the TREC assay, diagnostic and treatment algorithms, definition of sTCL/SCID, and approach to the discovery of new genetic variants. Although NBS using the TREC assay has been highly successful, new and difficult challenges have emerged that need to be addressed to enhance our knowledge of the causes of sTCL/SCID and to optimize the detection and outcomes of affected infants.

Patient-centred screening for primary immunodeficiency, a multi-stage diagnostic protocol designed for non-immunologists: 2011 update

Members of the European Society for Immunodeficiencies (ESID) and other colleagues have updated the multi-stage expert-opinion-based diagnostic protocol for non-immunologists incorporating newly defined primary immunodeficiency diseases (PIDs). The protocol presented here aims to increase the awareness of PIDs among doctors working in different fields. Prompt identification of PID is important for prognosis, but this may not be an easy task. The protocol therefore starts from the clinical presentation of the patient. Because PIDs may present at all ages, this protocol is aimed at both adult and paediatric physicians. The multi-stage design allows cost-effective screening for PID of the large number of potential cases in the early phases, with more expensive tests reserved for definitive classification in collaboration with a specialist in the field of immunodeficiency at a later stage.

Relevance of laboratory testing for the diagnosis of primary immunodeficiencies: a review of case-based examples of selected immunodeficiencies

The field of primary immunodeficiencies (PIDs) is one of several in the area of clinical immunology that has not been static, but rather has shown exponential growth due to enhanced physician, scientist and patient education and awareness, leading to identification of new diseases, new molecular diagnoses of existing clinical phenotypes, broadening of the spectrum of clinical and phenotypic presentations associated with a single or related gene defects, increased bioinformatics resources, and utilization of advanced diagnostic technology and methodology for disease diagnosis and management resulting in improved outcomes and survival. There are currently over 200 PIDs with at least 170 associated genetic defects identified, with several of these being reported in recent years. The enormous clinical and immunological heterogeneity in the PIDs makes diagnosis challenging, but there is no doubt that early and accurate diagnosis facilitates prompt intervention leading to decreased morbidity and mortality. Diagnosis of PIDs often requires correlation of data obtained from clinical and radiological findings with laboratory immunological analyses and genetic testing. The field of laboratory diagnostic immunology is also rapidly burgeoning, both in terms of novel technologies and applications, and knowledge of human immunology. Over the years, the classification of PIDs has been primarily based on the immunological defect(s) ("immunophenotype") with the relatively recent addition of genotype, though there are clinical classifications as well. There can be substantial overlap in terms of the broad immunophenotype and clinical features between PIDs, and therefore, it is relevant to refine, at a cellular and molecular level, unique immunological defects that allow for a specific and accurate diagnosis. The diagnostic testing armamentarium for PID includes flow cytometry - phenotyping and functional, cellular and molecular assays, protein analysis, and mutation identification by gene sequencing. The complexity and diversity of the laboratory diagnosis of PIDs necessitates many of the above-mentioned tests being performed in highly specialized reference laboratories. Despite these restrictions, there remains an urgent need for improved standardization and optimization of phenotypic and functional flow cytometry and protein-specific assays. A key component in the interpretation of immunological assays is the comparison of patient data to that obtained in a statistically-robust manner from age and gender-matched healthy donors. This review highlights a few of the laboratory assays available for the diagnostic work-up of broad categories of PIDs, based on immunophenotyping, followed by examples of disease-specific testing.

Clinical data mining and research in the allergy office

PURPOSE OF REVIEW

More data are anticipated from the expected increase in use of electronic health records (EHRs). Upcoming initiatives require reporting of quality measures, meaningful use of clinical decision support, alert systems, and pharmacovigilance - knowledge resulting through use of EHRs. Data mining is a new tool that will help us manage information and derive knowledge from these data, and is a part of evolving new disciplines of informatics and knowledge management.

RECENT FINDINGS

Studies are reported from smaller clinic data marts to larger repositories and warehouses in various health systems, biomedical registries, and the medical literature on the Internet. Data mining technologies show promise and challenges. Outcome measures as structured data and narrative text can be mined with human assistance and newer automated natural language processing software. Despite advances, the growing diversity of clinic EHRs lack integration and interoperability with Internet-based biomedical databases.

SUMMARY

Allergists have the capability to mine clinic EHRs to discover new information, which may be hidden in charts. A central allergy computer can serve not just as a registry but also allows functionalities to enable EHRs' meaningful use. Harmonization of technological and organizational standards will allow seamless use of new natural language processing (NLP) tools and ontologies through a semantic web.