Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Whole-genome sequencing of a sporadic primary immunodeficiency cohort.

Primary immunodeficiency (PID) is characterized by recurrent and often life-threatening infections, autoimmunity and cancer, and it poses major diagnostic and therapeutic challenges. Although the most severe forms of PID are identified in early childhood, most patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent and up to 10% develop lymphoid malignancies1-3. Consequently, in sporadic (or non-familial) PID genetic diagnosis is difficult and the role of genetics is not well defined. Here we address these challenges by performing whole-genome sequencing in a large PID cohort of 1,318 participants. An analysis of the coding regions of the genome in 886 index cases of PID found that disease-causing mutations in known genes that are implicated in monogenic PID occurred in 10.3% of these patients, and a Bayesian approach (BeviMed4) identified multiple new candidate PID-associated genes, including IVNS1ABP. We also examined the noncoding genome, and found deletions in regulatory regions that contribute to disease causation. In addition, we used a genome-wide association study to identify loci that are associated with PID, and found evidence for the colocalization of-and interplay between-novel high-penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to the variable penetrance and phenotypic complexity that are observed in PID. Thus, using a cohort-based whole-genome-sequencing approach in the diagnosis of PID can increase diagnostic yield and further our understanding of the key pathways that influence immune responsiveness in humans.

Systematic classification of primary immunodeficiencies based on clinical, pathological, and laboratory parameters.

The classification of diseases has several important applications ranging from diagnosis and choice of treatment to demographics. To date, classifications have been successfully created manually, often within international consortia. Some groups of diseases, such as primary immunodeficiencies (PIDs), are especially hard to nosologically cluster due, on one hand, to the presence of a wide variety of disorders and, in contrast, because of overlapping characteristics. More than 200 PIDs affecting components of the innate and adaptive immune systems have been described. Clinical, pathological, and laboratory characteristics were collected and used to group PIDs. A consensus of at least five independent methods provided a novel classification of 11 groups, which revealed previously unknown features and relationships of PIDs. Comparison of the classification to independent features, including the severity and therapy of the diseases, functional classification of proteins, and network vulnerability, indicated a strong statistical support. The method can be applied to any group of diseases.

Bioinformatics services related to diagnosis of primary immunodeficiencies.

PURPOSE OF REVIEW: Most primary immunodeficiencies (PIDs) have overlapping signs and symptoms - presenting a challenge for diagnosis. The information available from the Internet for over 200 PIDs is scattered between numerous services and databases. Patient information has been collected in different patient registries. Several software tools have been developed in order to build the databases, expert systems and other information systems useful in diagnosis or prediction. RECENT FINDINGS: Previously released services have been significantly improved and some new bioinformatics tools have been developed to help in diagnosis, prediction, mutation analysis and classification of PIDs. Several national initiatives have been launched for centralized PID information services. The very latest additions are tools and approaches for PID candidate gene prioritization, systematic classification and a medical expert system to help in diagnosis. SUMMARY: Many bioinformatics tools for PIDs are already freely available over the Internet. We expect bioinformatics tools to further help healthcare professionals in diagnosis, analysis and prediction. Currently, most of the resources are stand-alone and thus their integration will be a challenge for the future. Another challenge is to develop terminologies, ontologies and standards to achieve semantic interoperability.

IDR knowledge base for primary immunodeficiencies.

BACKGROUND: The ImmunoDeficiency Resource (IDR) is a knowledge base for the integration of the clinical, biochemical, genetic, genomic, proteomic, structural, and computational data of primary immunodeficiencies. The need for the IDR arises from the lack of structured and systematic information about primary immunodeficiencies on the Internet, and from the lack of a common platform which enables doctors, researchers, students, nurses and patients to find out validated information about these diseases. DESCRIPTION: The IDR knowledge base, first released in 1999, has grown substantially. It contains information for 158 diseases, both from a clinical as well as molecular point of view. The database and the user interface have been reformatted. This new IDR release has a richer and more complete breadth, depth and scope. The service provides the most complete and up-to-date dataset. The IDR has been integrated with several internal and external databases and services. The contents of the IDR are validated and selected for different types of users (doctors, nurses, researchers and students, as well as patients and their families). The search engine has been improved and allows either a detailed or a broad search from a simple user interface. CONCLUSION: The IDR is the first knowledge base specifically designed to capture in a systematic and validated way both clinical and molecular information for primary immunodeficiencies. The service is freely available at http://bioinf.uta.fi/idr and is regularly updated. The IDR facilitates primary immunodeficiencies informatics and helps to parameterise in silico modelling of these diseases. The IDR is useful also as an advanced education tool for medical students, and physicians.

Online registry of genetic and clinical immunodeficiency diagnostic laboratories, IDdiagnostics.

Primary immunodeficiencies (IDs) are caused by inherited genetic defects leading to intrinsic defects in cells of the immune systems. Most IDs are rare diseases and can be difficult to diagnose because similar symptoms characterize several disorders. Mutation detection is the most reliable method in such cases. These tests are not available at most centers and physicians can have difficulties in finding laboratories that could analyze the genetic defects because certain genes are possibly analyzed by just one laboratory. The IDdiagnostics registry has been established to provide information for physicians and other health care professionals. The database at http://bioinf.uta.fi/IDdiagnostics contains currently information for the analysis of defects in 30 ID-related genes. Another part of IDdiagnostics is a database of clinical tests. Laboratories performing these analyses, either gene or clinical tests, are asked to submit their information to the database by using a printed form or electronic submission at http://bioinf.uta.fi/cgi-bin/submit/IDClini.cgi. The clinical test database contains information about tests for clinical data, immune status, and studies of function, antibody response, cell function, enzyme assays, clinical function, and apoptosis assays. Both the services are freely available and regularly updated. The services aim at increasing the awareness of IDs and helping to obtain exact and early diagnosis.