INTRODUCTION — The goal of newborn screening (NBS) is to detect treatable disorders that are threatening to life or long-term health before they become symptomatic [1]. Early treatment of these rare disorders may significantly reduce mortality and morbidity in affected patients, making screening programs using a high-throughput, low-cost screening test with high sensitivity and specificity an important and cost-effective public health measure. Severe combined immunodeficiency (SCID) meets these criteria for inclusion in NBS due to the availability of an effective assay for T cell receptor excision circles (TRECs), a biomarker for normal T cell development. Other primary immunodeficiencies (PIDs) in addition to SCID are potential targets for NBS if suitable biomarkers can be identified and put to use in screening assays [1,2].
The rationale and tests available for NBS for PIDs are reviewed here. The general principles of NBS, screening policies, testing, and follow-up are discussed in detail separately. (See "Newborn screening".)
WHY SCREEN FOR PRIMARY IMMUNODEFICIENCY DISORDERS? — PIDs, also called inborn errors of immunity (IEI), are a group of disorders of the immune system that result in recurrent infections, or, in some instances, predominantly dysregulated immunity, that can significantly impact long-term health and life expectancy [3]. They are estimated to occur in as many as 1 in 1200 live births [4]. Over 450 PIDs have been described, encompassing a wide range of clinical presentations and disease severity [3].
PIDs are classified according to the immunologic mechanisms and clinical presentations that result from the underlying defects, as well as the functional consequences of variants upon their gene products [3]. Adaptive immune defects predominantly affect antigen-driven processes. These defects include humoral immunodeficiencies (due to impaired production of antibody by B cells) and combined immunodeficiencies (with impairments in both T and B cells). Innate immune disorders arise from impaired antigen-independent pathways and include defects in natural killer (NK) cell cytotoxicity, toll-like receptor (TLR) activation, phagocytosis, macrophage activation, and complement defects. More and more PIDs are associated with single gene defects. (See "Inborn errors of immunity (primary immunodeficiencies): Classification".)
Treatment for PIDs depends upon the part(s) of the immune system affected and can include allogeneic hematopoietic cell transplantation (HCT), gene therapy (for X-linked severe combined immunodeficiency [SCID], adenosine deaminase [ADA] deficient SCID, and Artemis-deficient SCID), enzyme replacement therapy (for ADA-deficient SCID), immune globulin replacement therapy, and antimicrobial therapy to prevent or limit infections. Delay in diagnosis and treatment of PIDs leads to significant morbidity and sometimes early death from infections, and affected infants may die of infections without recognition that they have an immune system defect. Thus, early identification via NBS prior to the onset of infections should improve detection and decrease the morbidity and mortality associated with these disorders. (See "Hematopoietic cell transplantation for severe combined immunodeficiencies" and "Hematopoietic cell transplantation for non-SCID inborn errors of immunity" and "Primary immunodeficiency: Overview of management" and "Immune globulin therapy in primary immunodeficiency" and "Overview of gene therapy for primary immunodeficiency".)
A retrospective study from the Primary Immune Deficiency Treatment Consortium (PIDTC) of 240 infants diagnosed with SCID and transplanted between 2000 and 2009 showed that the best overall survival (OS) at five years after transplant was seen amongst infants who received HCT at age <3.5 months (94 percent OS, 95% CI 85-98) [5]. Similar survival was noted in SCID infants transplanted at age >3.5 months who were continuously infection free (90 percent OS, 95% CI 67-98) and even at age >3.5 months, provided all infections had been treated and resolved prior to HCT (82 percent OS, 95% CI 70-90). In contrast, infants who were >3.5 months with active infection at time of transplant had only 50 percent OS (95% CI 39-61), despite modern supportive care and antimicrobials [5].
SCREENING FOR SCID AND OTHER T CELL DEFECTS — The first group of immune disorders targeted for NBS was severe combined immunodeficiency (SCID). The term "severe combined immunodeficiency" encompasses a genetically heterogenous group of disorders characterized by profound impairment in T cell development and function with either primary or secondary defects in B cells (table 1). Infants with SCID are generally healthy at birth, protected by transplacentally acquired maternal immunoglobulin G (IgG) antibodies in the first one to three months of life. As this protection wanes, these infants develop severe and recurrent infections (including infections caused by live vaccines given early in life, such as Bacillus Calmette-Guérin (BCG) against tuberculosis and live-attenuated rotavirus vaccine). Allogeneic hematopoietic cell transplantation (HCT) is an effective treatment for SCID, particularly if performed early in infancy, before the development of recurrent and increasingly severe infections. Infants with SCID without reconstitution of a functioning immune system usually die of overwhelming infection by one year of age. Only 20 percent or fewer of infants with SCID have a family history that prompts early testing [6,7]. (See "Severe combined immunodeficiency (SCID): An overview", section on 'Clinical manifestations' and "Hematopoietic cell transplantation for severe combined immunodeficiencies" and "Hematopoietic cell transplantation for non-SCID inborn errors of immunity".)
Initial attempts at screening for one type of SCID, adenosine deaminase (ADA) deficiency, using a colorimetric ADA enzyme assay in the 1970s were unsuccessful [8-10]. A quantitative real-time polymerase chain reaction (PCR) test was subsequently devised that used dried blood spots (DBS) already being collected for NBS for other conditions to measure T cell receptor excision circles (TRECs) as a biomarker of naïve T cells. The TREC screening test proved a sensitive and specific, as well as cost effective, method for SCID NBS [11-15]. Next-generation sequencing and proteomic technologies are also under investigation for NBS [16-18]; however, sequencing is probably insufficiently sensitive as a sole method for NBS [19].
Any genetic defect that disrupts T cell development, induces T cell apoptosis, or blocks T cell maturation in the thymus will result in T cell lymphopenia (TCL) and low TRECs in peripheral blood [20]. Thus, infants with SCID caused by genetic defects that adversely affect T cell development prior to the formation of TRECs are expected to be identified by the TREC assay performed on DNA isolated from heel-stick DBS, as well as infants with other non-SCID immunodeficiencies in which there is a profound decrease in circulating naïve T cells. However, not all functional T cell disorders are detected with this screen, and very rare hypomorphic variants leading to delayed or late-onset leaky SCID may be missed since these patients have some T cells present at birth. This was demonstrated in the California TREC NBS program, in which two infants out of 3.25 million screened over 6.5 years escaped detection by screening during the newborn period but came to medical attention later and were diagnosed with atypical SCID with hypomorphic variants [21].
Long-term follow-up data on treatment outcomes and complications will help fully assess the impact of NBS for SCID patients [22]. While survival has improved in infants with and without newborn identification by screening, those who received an early diagnosis through screening in California have shown not only a broader genotype distribution (figure 1), reflecting better unbiased ascertainment with universal screening, but also a high proportion of infants fully reconstituted and able to discontinue immune globulin infusions [21]. (See 'Diseases identified by TREC testing' below and "Newborn screening" and 'Formation of TRECs' below.)
Overview of TREC screening test — T cell receptor excision circle (TREC) screening identifies infants who have low numbers of circulating T cells. All infants with typical SCID have absent or very low production of T cells from their thymus, affecting both T cell number and diversity. Other diseases that have TCL as a feature, such as other genetic multisystem syndromes (eg, DiGeorge syndrome [DGS]) or conditions with increased removal of T cells from the circulation (eg, hydrops or congenital heart disease), also lead to reduced circulating T cells. Thus, while the primary target of the TREC screening test is to identify infants with SCID, other diseases with TCL are secondary targets of this screening test. (See 'Diseases identified by TREC testing' below.)
Formation of TRECs — T cell development occurs in the thymus, where T cell antigen receptor (TCR) gene rearrangements involve cutting and splicing of the DNA encoding the alternate variable, diversity, and joining (VDJ) segments to generate a wide repertoire of unique T cells with diverse specificities. Formation of T cell receptor excision circles (TRECs) from excised DNA occurs during the programmed gene rearrangements in the thymus. One particular rearrangement, excision of the TCR delta gene locus in precursors of alpha/beta TCR expressing T cells, gives rise to the delta-Rec and psi-Joining segment-alpha TREC. This circular DNA molecule is produced late in the T cell maturation sequence and is found in 70 percent of all thymocytes that express alpha/beta TCRs [13]. TRECs are stable but not replicated during mitosis. They therefore become diluted as mature T cells proliferate. Thus, the number of TREC copies per T cell reflects primarily the production of naïve T cells by the thymus, and a normal TREC number is a biomarker for adequate autologous T cell production [23]. Conversely, low or absent TREC numbers indicate either poor T cell production or increased T cell loss, provided that the DNA quality is adequate for PCR. (See "Normal B and T lymphocyte development", section on 'T cell development' and "Normal B and T lymphocyte development", section on 'The mature phase'.)
Normal newborns have approximately 1 TREC per 10 T cells, reflecting high numbers of naïve T cells that have not yet proliferated extensively, whereas older children and adults have approximately 1 per 100 and 1 per 1000 T cells, respectively, reflecting peripheral T cell expansion by mitosis [24]. Infants with SCID have very low or undetectable TRECs [11]. Even maternal T cells that can be present in an infant with SCID do not falsely raise the TREC count, because maternal cells have few TRECs.
Adaptation and implementation for newborn screening — TRECs present in peripheral blood can be measured using quantitative PCR (qPCR) specific for the delta-Rec and psi-Joining segment-alpha signal joint, and this measurement reflects the number of recently formed T cells in the circulation [11]. Newborn DBS can be used for screening for TRECs to detect SCID because TREC DNA circles are stable in DBS collected by screening programs. TRECs are quantified by extracting genomic DNA from DBS specimens and performing the above qPCR reaction. A control qPCR reaction amplifying a genomic segment from the actin or RNAseP gene is used to distinguish samples with inadequate DNA from those specifically lacking TRECs.
All states in the United States perform universal SCID NBS [15,25-29]. Israel [30], Norway, New Zealand, Taiwan, Germany, Switzerland, Iceland, and an increasing number of other countries are performing universal SCID NBS, as are several Canadian provinces and parts of Australia, Italy, Spain, and many others. Several pilot programs are ongoing in Europe, South America, the Middle East, and Asia [15,31,32]. Some locales such as the Middle East, where consanguinity is associated with autosomal-recessive conditions due to founder variants, have adapted the TREC assay to include PCR determination of other frequent founder variants causing immune disorders [31]. Screening for known frequent founder variants is also performed in Manitoba, Canada, where First Nations infants are at risk for inhibitor of nuclear factor kappa B kinase subunit beta (IKBKB) and Mennonites for zeta chain of T cell receptor-associated protein kinase 70 (ZAP70) gene defects [33]. Sequencing a panel of frequently mutated loci may also become an add-on to the TREC test [34]. (See 'Diseases not identified by TREC testing' below.)
A retrospective study in 2014 analyzed SCID screening results in over three million infants from 11 programs in the United States that had implemented population-based NBS with the TREC assay. Fifty-two cases of SCID and leaky SCID/Omenn syndrome were detected, an incidence of 1 in 58,000 births (95% CI, 1 in 46,000 to 1 in 80,000) [26]. This incidence is nearly double that of previous estimates of 1 in 100,000, indicating that SCID was previously underdiagnosed in the absence of unbiased population screening. Although individual programs had different normal cutoffs for TRECs and different criteria to define TCL, cases of SCID and TCL were appropriately detected by screening, and infants were referred for early evaluation and treatment in all programs. In a report of 6.5 years of SCID NBS in California in which over 3.25 million infants had TREC testing and follow-up [21], 50 cases of SCID, or 1/65,000 births (CI 1/51,000 to 90,000), were found. Only two of these cases were anticipated because of a positive family history, although, in retrospect, probable or confirmed family history of SCID was elicited in eight others after NBS had brought the infant to medical attention. Prompt treatment led to 94 percent survival.
For the first time, this California study reported two infants with delayed-onset SCID who were missed by TREC screening at birth. Both had newborn DBS with TREC numbers well above the cutoff in the normal range, although, at ages 7 and 23 months, there were very low T cell numbers and TRECs, and hypomorphic variants in the X-linked interleukin 2 receptor subunit gamma (IL2RG) gene and ADA gene, respectively, were found [21]. These two cases in over three million infants screened were examples of known delayed and late-onset leaky SCID. (See "Severe combined immunodeficiency (SCID): An overview", section on 'Epidemiology'.)
Diseases identified by TREC testing — Disorders identified by T cell receptor excision circle (TREC) testing include the following [21,26]:
●Typical SCID – These forms of SCID are characterized by <300 autologous T cells/microL of blood and <10 percent of normal proliferation to mitogens (eg, phytohemagglutinin [PHA]). Patients frequently also had maternally engrafted T cells. Deleterious variants in known SCID genes were often identified (table 1). (See "Severe combined immunodeficiency (SCID): Specific defects".)
●Leaky SCID or Omenn syndrome – These types of SCID are caused by incomplete or hypomorphic defects in known SCID genes, with 300 to 1500 or even greater autologous T cells/microL and no evidence of maternal engraftment. Patients with Omenn syndrome may have normal or elevated CD3 T cell counts, but they have restricted TCR diversity (oligoclonality) of T cells. Very rarely, such patients may have TRECs at birth and therefore fail to be detected by NBS. (See "T-B-NK+ SCID: Pathogenesis, clinical manifestations, and diagnosis", section on 'T-B-NK+ SCID without radiation sensitivity due to RAG defects (includes most cases of Omenn syndrome)' and "T-B-NK+ SCID: Pathogenesis, clinical manifestations, and diagnosis", section on 'Omenn syndrome phenotype' and "Combined immunodeficiencies".)
●Idiopathic T cell lymphopenia (TCL) or variant SCID – This category is comprised of infants identified on NBS as having low TRECs who have 300 to 1500 autologous T cells/microL but do not have a recognized PID or variants detected in known SCID genes.
●Syndromes with TCL – Some syndromes have a variable spectrum of immune involvement that can include TCL (CD3 T cells ≤1500/microL) or T cell impairment. Examples include DGS and CHARGE (coloboma, heart defects, atresia choanae [also known as choanal atresia], retarded growth and central nervous system development, genital abnormalities, and ear abnormalities) syndromes, trisomy 21 (Down syndrome), Rac2 and dedicator of cytokinesis 8 (DOCK8) deficiencies, and ataxia-telangiectasia [14,21,26,35,36]. Not all infants with these syndromes will be identified by TREC screening, but the TREC test will flag infants affected with these syndromes who have T cells sufficiently low to be of clinical concern [15]. (See "DiGeorge (22q11.2 deletion) syndrome: Clinical features and diagnosis", section on 'Complete DGS' and "DiGeorge (22q11.2 deletion) syndrome: Clinical features and diagnosis", section on 'CHARGE syndrome' and "Leukocyte-adhesion deficiency", section on 'Rac2 deficiency' and "Ataxia-telangiectasia" and "Combined immunodeficiencies", section on 'Dedicator of cytokinesis 8 deficiency'.)
As an example, typical patients with DGS have impaired T cell production in the first months of life, but some have normal or near-normal T cell production, and a minority have almost no detectable T cell production. In general, the T cell deficit improves during the first two years of life. The TREC NBS test identifies DGS patients with the lowest TRECs. Patients with clinically significant TCL of ≤1500 CD3 T cells/microL confirmed by immunophenotyping have increased susceptibility to infection. However, patients with DGS who have >1500 CD3 T cells/microL are presumed to have enough immunity to combat infections. There have been no reports of patients with DGS who have low TRECs identified through NBS and >1500 CD3 T cells/microL who have succumbed to opportunistic infections, but further experience with screening is needed to establish the predictive value of screening for these patients. (See "DiGeorge (22q11.2 deletion) syndrome: Clinical features and diagnosis", section on 'Complete DGS'.)
●Secondary TCL – Secondary TCL (CD3 T cells ≤1500/microL) is diagnosed in a subset of infants with recognized congenital conditions, such as intestinal lymphangiectasia, hydrops, gastroschisis, a congenital heart defect, chylothorax, or neonatal leukemia [15]. It can also occur due to transfer to the fetus of an immunosuppressant medication prescribed for maternal autoimmune diseases (eg, prenatal administration of glucocorticoids). Severe infant stress or inflammatory conditions (eg, sepsis) may cause acquired TCL. A small proportion of preterm infants, often those of very low birth weight, also have TCL with no other congenital abnormalities or recognizable disorder. While TCL of prematurity was not appreciated before the advent of NBS, these infants may be at increased risk for infections. The T cell numbers in these infants generally increase as they mature. Reference ranges are available for lymphocyte subsets in low-birthweight and preterm infants born as early as 22 weeks' gestation [37].
Diseases not identified by TREC testing — A low T cell number is a common feature of many PID disorders. However, there are also a number of circumstances in which the T cell receptor excision circle (TREC) test is not able to identify disorders characterized by impairment of T cell function. As an example, some incomplete and hypomorphic defects in SCID genes are sufficiently mild to allow for sufficient T cell function that results in TRECs within the normal range. As another example, some infants with SCID caused by a defect in ADA have maternal detoxification of purine intermediates in utero that rescues fetal T cells, resulting in normal TREC levels at birth. This protection wanes with time, TRECs and T cell numbers drop, and these children manifest delayed- or late-onset ADA-SCID [21].
In addition, TRECs and T cells may be present in normal or near-normal numbers, but T cells are functionally compromised, in genetic defects that affect T cell development after VDJ recombination in the thymus (eg, ZAP-70 deficiency [38], major histocompatibility complex [MHC] class II deficiency [39], and CD40 ligand deficiency). Furthermore, PIDs limited to B cells and affecting humoral immunity, or to neutrophils, will not be detected by TREC screening. Thus, a negative (normal) TREC test does not rule out the possibility of a PID. It is important for clinicians to maintain awareness of the clinical presentations of immunodeficient infants and to be vigilant for risk factors including family history of early childhood deaths, poor growth, recurrent or severe infections, and physical features and to investigate accordingly. (See "ZAP-70 deficiency" and "CD3/T cell receptor complex disorders causing immunodeficiency", section on 'MHC (HLA) class II deficiency' and "Hyperimmunoglobulin M syndromes" and "Approach to the child with recurrent infections" and "Recognition of immunodeficiency in the first three months of life".)
Interpreting TREC results — The SCID NBS is considered abnormal if the T cell receptor excision circle (TREC) assay has a value below the designated cutoff determined by the laboratory (the cutoff values vary from laboratory to laboratory). The variability in newborn DBS specimen collection adds to the challenge of distinguishing abnormal samples.
Results can be artifactually low due to [13]:
●An inadequate blood sample
●Failure to elute sufficient DNA from the DBS
●The presence of PCR inhibitors, such as heparin, which may be present in samples from infants in neonatal intensive care with percutaneous catheters
To determine whether a low TREC result is due to an artifact, SCID NBS employs amplification of a reference DNA segment, such as a sequence within the ribonuclease P (RNase P) or beta-actin genes. The following approach is typical (algorithm 1) [13]:
●DBS samples with an abnormal TREC result are retested for TREC number plus copy number of the control DNA sequence.
●If the initial low TREC result is due to insufficient DNA or an inhibitor, both the repeat TREC and control qPCR will be low. These cases of DNA amplification failure are considered incomplete or indeterminate. The infant is recalled to give a further DBS sample obtained via heelstick to avoid contamination with heparin or other PCR inhibitors. If the second DBS specimen also results in low TRECs, the infant is recalled for venous blood sampling to measure T cells by flow cytometry and other confirmatory testing as indicated. (See 'Follow-up testing' below.)
●In a true-positive screen, TREC copy number is undetectable or very low, but the reference DNA copy number is normal. A true-positive screen will trigger the infant being recalled for immediate venous blood sampling for flow cytometric determination of lymphocyte subset numbers (algorithm 1). (See 'Follow-up testing' below.)
A normal TREC assay has a copy number value of above the designated cutoff determined by the laboratory. No further testing is recommended if the SCID NBS is normal, unless the infant begins to show signs of a PID. (See 'Diseases not identified by TREC testing' above and "Approach to the child with recurrent infections".)
Follow-up testing — Immunophenotyping is performed in California (with varying rules in other screening programs) after a positive screening TREC test or two incomplete tests [21,25,32]. This follow-up testing is integrated within the NBS program to facilitate rapid, consistent evaluation of the significance of the TREC screen result. The state-mandated flow panel consists of a complete blood count with differential white blood count and lymphocyte subsets: CD3, CD4, and CD8 T cells with CD45RA versus CD45RO CD4 and CD8 subsets to indicate naïve versus memory cells, CD19 B cells, and CD16/CD56 NK cells. Few or undetectable CD45RA naïve T cells with predominance of CD45RO memory cells suggest insufficient diverse T cell production, even if overall T cell number may appear normal due to expansion of oligoclonal T cells in the periphery or presence of maternally engrafted T cells. (See "Laboratory evaluation of the immune system".)
A CD3 T cell count of ≤1500 cells/microL is considered clinically significant, identifying infants at risk for life-threatening and/or opportunistic infections [13]. The lymphocyte subsets permit determination of the T/B/NK cell phenotype, giving clues to probable gene defects as indicated in the table (table 1). The absence of naïve T cells is also significant, with <2 percent of the CD4 T cells having the naïve marker CD45RA, suggesting oligoclonal expansion rather than a properly diverse T cell repertoire.
Establishing the diagnosis of SCID requires the further demonstration of abnormal T cell function, as measured by proliferation of lymphocytes after stimulation with the mitogen PHA. Another indicator of SCID is presence of maternal cells, transmitted through the placenta and not eliminated due to the infant's immune incompetence. Deleterious variants in known SCID-associated genes also confirm the diagnosis of SCID (see "Severe combined immunodeficiency (SCID): An overview", section on 'Diagnosis'). Note that TREC screening and very low T cells are not sufficient to distinguish between SCID due to intrinsic defects in the development of T cells from hematopoietic progenitors and SCID due to thymic defects, in which pathogenic variants in genes such as forkhead box N1 (FOXN1), paired box 1 (PAX1), T-box transcription factor 1 (TBX1), T-box transcription factor 2 (TBX2), as well as complete DGS and CHARGE syndrome prevent terminal differentiation of thymocytes. Thus, while allogeneic HCT will establish T cell immunity for SCID, only implantation of thymus tissue may rescue immunity in patients with thymic insufficiency [21].
Syndromes that are not SCID, but that have insufficient T cells, and also secondary depletion of circulating T cells, constitute risks for infection in infancy. Infants with these findings from NBS require follow-up by pediatric immunology specialists to perform appropriate evaluations and institute protective measures that may include antibiotics, immune globulin replacement therapy, and avoidance of live vaccines until T cells have normalized. For an individual patient who might have SCID or a related T lymphopenic disorder, any immunologic abnormalities should be followed up by further testing, such as lymphocyte proliferation, determination of serum immunoglobulin concentrations, measurement of specific titers after administration of killed vaccines, and molecular diagnosis by gene sequencing. (See "Severe combined immunodeficiency (SCID): An overview", section on 'Protective measures' and "Primary immunodeficiency: Overview of management" and "Laboratory evaluation of the immune system".)
SCREENING FOR B CELL DEFECTS — Generation of diverse B cell receptor (BCR) light chains results in kappa-deleting recombination excision circles (KRECs). Coding joint (cj) recombined sequences reside within the chromosome, whereas signal joint (sj) KRECs are excised and joined at their ends to form an extrachromosomal excision product similar to T cell receptor excision circles (TRECs). As with TRECs, the sjKRECs cannot replicate in the cell, are stable, and are found in peripheral blood. After hematopoietic cell transplantation (HCT), a rise in KRECs reflects newly derived bone marrow B cells [40,41]. (See "Normal B and T lymphocyte development", section on 'Immature B cells'.)
KREC levels in blood and in DNA isolated from dried blood spots (DBS) are undetectable in PIDs in which B cells are absent or dysfunctional, such as X-linked agammaglobulinemia (XLA) caused by pathogenic variants in Bruton tyrosine kinase (BTK) or B cell-negative severe combined immunodeficiency (SCID), whereas samples from unaffected infants have detectable KRECs. Thus, KREC testing of newborn blood spots is potentially useful in identifying neonates with defects of early B cell maturation [42,43]. KREC testing does not, however, predict which individuals may develop antibody deficiencies later in life such as common variable immunodeficiency (CVID), the most common type of antibody deficiency.
TRECs and KRECs can be measured simultaneously using a multiplex polymerase chain reaction (PCR) reaction. When used in combination, TREC/KREC screening may identify certain PIDs including dedicator of cytokinesis 8 (DOCK8) deficiency, hyperimmunoglobulin E syndrome, ataxia-telangiectasia, and Comel-Netherton syndrome [43]. It is not yet established whether the number of KRECs is sufficiently high in all unaffected infants (including preterm and ill infants) to achieve acceptably low rates of false-positive tests for a successful NBS approach [44].
SCREENING IN SUBPOPULATIONS WITH KNOWN GENETIC RISK — DNA screening, as employed in the T cell receptor excision circle (TREC) assay, opens the door to additional high-throughput screening for DNA variants. Certain populations derived from a restricted pool of ancestors may harbor recessive founder variants for PIDs that raise the risk well above that of the general population and, as such, represent attractive targets for NBS [16,17,31,34]. It is technically possible to screen newborns in such populations for the carrier state and homozygous variant state for specific DNA pathogenic variants, as is now widely done as a second-tier test to screen for sickle cell disease in many programs. In addition, X-linked genetic variants cause disease almost exclusively in males, suggesting that efficient NBS could be selective.
There are several known PID risk alleles in Amish, Native American, Middle Eastern, and many other populations worldwide, and several PIDs are caused by X-linked gene variants. However, practical considerations regarding whom to test and how to implement subgroup testing in newborn nurseries, as well as ethical considerations, such as stigmatization of specific groups who may carry risk alleles, present major challenges, not the least of which would be failing to test and identify true cases.
DEEP SEQUENCING IN NEWBORNS FOR SCREENING OR DIAGNOSIS — The advent of massively parallel high-throughput sequencing has also presented the possibility of sequencing panels of genes or even whole exomes or whole genomes for "actionable" gene variants, recognizable pathogenic variants with a high probability of causing treatable diseases that would benefit from early recognition [16,17]. The DNA contained in dried blood spots (DBS) has proven adequate for whole-exome sequencing [45], though costs and turnaround time remain prohibitive for use of deep sequencing on a population-wide basis.
Further major problems exist [21]. First, there is insufficient predictive value for many gene variants to be sure that the variants cause disease given the wide variety of observed DNA changes in PID genes combined with the rarity of the PID diseases. Second, a large number of novel variants and variants of uncertain significance are uninterpretable without a prior reason to suspect PID in otherwise healthy newborns. Sharing such results with primary clinicians and parents/caregivers will cause anxiety and lead to expensive further testing that will not confirm disease in a great majority of cases. Finally, issues of parent/caregiver consent and patient autonomy are raised. Rather than implement deep sequencing for all newborns as part of screening programs, it may be preferable to undertake sequencing as follow-up testing after TREC screening indicates a potential abnormality. Optional sequencing of any infant with parent/caregiver consent may also be a more acceptable approach, even if this limits such testing to those with the means to pay for it [46].
SOCIETY GUIDELINE LINKS — Links to society and government-sponsored guidelines from selected countries and regions around the world are provided separately. (See "Society guideline links: Inborn errors of immunity (previously called primary immunodeficiencies)".)
SUMMARY AND RECOMMENDATIONS
●Primary immunodeficiencies (PIDs), such as severe combined immunodeficiency (SCID), are good candidates for newborn screening (NBS) because infants appear normal at birth, the natural history is understood, and treatment is more efficacious if initiated early. (See 'Why screen for primary immunodeficiency disorders?' above and 'Screening for SCID and other T cell defects' above.)
●T cell receptor excision circles (TRECs) are a biomarker of naïve T cells that can be detected in newborn dried blood spots (DBS). The TREC assay is expected to identify all infants with low T cells, including those with SCID and leaky SCID (primary target), as well as conditions that present with low T cells (secondary targets), such as congenital syndromes or other problems at birth that cause secondary loss of circulating naïve T cells. (See 'Overview of TREC screening test' above.)
●If the TREC level on NBS is abnormally low as determined by the performing laboratory, then the TREC test is repeated on another punch from the original DBS, and a reference gene segment is also amplified. If the initial low TREC result is due to insufficient DNA, both the repeat TREC and reference gene will be low, and the test is considered incomplete or indeterminate. The infant is then recalled, and the TREC assay is repeated on a second DBS sample. If this assay is also abnormal, or if the initial repeat TREC on the DBS is low but the reference gene is normal (positive test), then venous blood sampling is performed for flow cytometric determination of lymphocyte subset numbers (algorithm 1). (See 'Interpreting TREC results' above.)
●A CD3 T cell count of ≤1500 cells/microL on immunophenotyping is considered clinically significant, identifying infants at risk for life-threatening and/or opportunistic infections. The lymphocyte subsets permit determination of the T/B/natural killer (NK) cell phenotype, giving clues to likely gene defects as indicated in the table (table 1). Establishing the diagnosis of SCID requires the further demonstration of abnormal T cell function. (See 'Follow-up testing' above.)
●Kappa-deleting recombination excision circles (KRECs) are a biomarker of mature B cells. KREC testing of newborn blood spots is potentially useful in identifying neonates with defects of early B cell maturation. In addition, KRECs can be measured simultaneously with TRECs, giving a more comprehensive newborn screen for PID. (See 'Screening for B cell defects' above.)
ACKNOWLEDGMENT — The UpToDate editorial staff acknowledges Antonia Kwan, PhD, MRCPCH who contributed to earlier versions of this topic review.
The UpToDate editorial staff also acknowledges E Richard Stiehm, MD, who contributed as a Section Editor to earlier versions of this topic review.
