Diagnostic Challenges in the Era of Genomic Sequencing and Newborn Screening

Early diagnosis of rare immune disorders is important for clinical care and of great interest for the study of immune pathways. Severe combined immunodeficiency (SCID) is a collective term for the most profound inherited defects of T cell development combined with B cell defects or dysfunction. While fatal without treatment, SCID is treatable by allogeneic hematopoietic cell transplantation, or in certain genotypes by enzyme or gene therapy. Avoidance of life-threatening infections to provide optimal treatment and outcomes for affected infants has led to population-based SCID newborn screening (NBS). Infants with SCID fail to generate a diverse repertoire of functional T cells, and consequently have very low numbers of T cells and T cell receptor excision circles (TRECs), DNA byproducts of T cell receptor gene rearrangement. TRECs are readily measured in DNA isolated from newborn dried blood spots (DBS) collected for population based screening. Thus newborn screening for insufficient TRECs identifies SCID before infections occur. As SCID NBS has become widespread, new disease definitions are required for healthy-appearing affected infants without failure to thrive or opportunistic infections. Typical SCID cases have <300 autologous T cells/uL, <10% of the lower range of normal proliferation to the mitogen phytohemmaglutinin A, and/or detectable maternal T cell engraftment, most often with deleterious mutations in recognized SCID genes. One fourth of all SCID cases are "leaky" due to hypomorphic SCID gene mutations; these cases are also detected by TREC testing; they may have >300 T cells/uL, but have impaired T cell function and lack naïve CD4 T cells expressing CD45RA. A subset of infants with leaky SCID have Omenn syndrome, with expansion of oligoclonal, dysregulated T cells leading to adenopathy, erythroderma, hepatosplenomegaly, eosinophilia, and elevated IgE. In addition to these primary target disorders of population screening for SCID, the TREC test identifies infants with additional conditions due to either impaired production or increased loss of T cells. Non-SCID congenital syndromes with variable degrees of T cell lymphopenia (TCL) include DiGeorge syndrome/22q11.2 deletion, CHARGE syndrome, trisomy 21, and ataxia telangiectasia, among others. TREC NBS also finds infants with secondary TCL, in which T cell generating capacity is intrinsically normal, but circulating T cells are diminished as a consequence of other factors, including hydrops, congenital heart disease, chylothorax, neonatal leukemia, maternal immunosuppressive medications taken during pregnancy, or extreme preterm birth. The T cells of these infants normalize once their primary problems resolve. A particularly challenging group of infants are those with abnormal TREC screen results and non-SCID TCL, but no immediate diagnosis. About half of these have syndromes, such as DiGeorge/22q deletion, but with mild or initially unapparent features; others experience resolution of TCL over time, while still others prove to have previously unknown immune disorders that may be diagnosed after deep sequencing and research functional studies. It is important to remember that many serious disorders of T cells are not identified by TREC screening if the block in T cell development or function occurs at a later stage than T cell receptor rearrangement; combined immunodeficiencies (CIDs) with TRECs that are often normal include Zap-70 deficiency and MHC class I and II non-expression. Thus, while virtually completely sensitive and highly specific for the intended target, SCID, population based TREC screening leaves us with both diagnostic dilemmas presented by non-symptomatic infants with low T cells and inability to capture individuals with the >300 non-SCID primary immunodeficiency disorders that would also benefit from early intervention. Deep sequencing is not yet clinically useful, not only due to cost, turnaround time and technical limitations, but primarily due to problems of interpretation, given the extraordinary number of genomic variants of uncertain significance.