Novel genetic discoveries in rare primary immunodeficiencies

Introduction
Rare genetic diseases provide an insight into otherwise obscure mechanisms of human health. Single-case and cohort studies of rare disease can reveal precise and fundamental features of biology that are not as readily apparent in the study of common disease genomics. Furthermore, cases of rare disease also provide a jump start to the incremental scientific method. Statistically robust associations between genetic variation and disease are the most reliable sources of this information. However, since the number of cases in rare disease cohorts is generally low alternative methods must be used to functionally validate genomic findings. Herein, we use best practices in genomic analysis followed by functional validation studies and where possible demonstrate methods for statistically driven analysis of cohorts.

Methods
A combination of genomic sequencing methods were used to uncover the genetic deter- minants of primary immunodeficiencies (PID). Tailored analysis in single case studies and statistical methods in cohort analysis were used to find candidate causes of disease. Best practices were used for routine analysis of genomic data, complemented by novel bioinformatic approaches. We performed functional investigations using in vitro and in vivo assays to model disease and protein mechanisms and thereby confirm the mode of disease for some patients.

Results
Our results are separated on the basis of patient disorder. First, patients with RAG deficiency may survive into adulthood and the presented findings suggest that prevalence of such cases varies between 1% to 1.9% in adult PID cohorts. Second, we predict a list of amino acid residues for RAG1 and RAG2 that have not been reported to date but are most likely to present clinically as RAG deficiency. Third, our findings in TET2 deficiency expand the understanding of its critical role within the human hematopoietic system and define a new inborn error of immunity. Fourth, we provide validated methods for the investigation of rare genetic disease.

Conclusion
Genetic investigation in rare PIDs not only provides critical information for clinical care but can provide answers to fundamental questions in basic science.