1.Gene-targeted testing         Gene-targeted testing requires clinicians to determine a priori which are the likely genes involved in an individual’s presentation, and include “off the shelf” gene panels (including those commonly associated with broad phenotypes or recognisable clinical syndromes with heterogeneous genetic aetiologies) and custom-designed panels (the clinician selects genes for analysis) [172]. Multigene panels vary by laboratory in terms of gene coverage and technique, and assays may include sequence and CNV analysis, as well as ancillary tests to cover regions that are problematic for conventional NGS (e.g., highly homologous pseudogenes, deep intronic pathogenic variants, and expanded nucleotide repeats) [172].         Gene panels have certain advantages over comprehensive testing. Included genes have usually been specifically targeted and validated by the laboratory, allowing greater confidence in complete sequencing of the genes of interest, and often include relevant targeted noncoding regions, which may be missed by exome sequencing [172]. Choosing a narrow phenotype-focussed panel also has the advantages of streamlined analysis, reduced costs, quicker turnaround time, and limited identification of VUS and incidental variants in genes unrelated to the disease phenotype, which may cause further clinical uncertainty or be clinically unactionable [172]. 2.Comprehensive genomic testing         Comprehensive genomic testing does not require the clinician to determine which are the likely genes involved in the individual’s presentation. Comprehensive testing is most likely to be useful where the clinical features are not suggestive of a known genetic condition decipherable from the phenotype alone, or are suggestive of several genetic conditions at once, which are not included within one multigene panel [172]. Comprehensive testing may also be appropriate where the phenotype is poorly defined (e.g., at earlier stages in the diagnostic evaluation of an acutely and severely unwell child), or where a rare disorder is suspected, which would not routinely be tested for within available multigene panels [172]. Mitochondrial DNA sequencing can also be requested as a separate test where mitochondrial disorder is suspected.         Whole exome sequencing (WES) and whole genome sequencing (WGS) can reliably detect missense or nonsense variants, and small indels (<50 bp) within nonrepetitive coding DNA that are rare in the population and previously reported as pathogenic [172]. WES examines the approximate 180,000 protein-coding segments of the genome (exons), which comprise 1–2% of the genome and account for the majority of recognised pathogenic variants [172]. About 95% of the exome can be sequenced with current NGS methodologies [176,177]. WGS examines the entirety of the approximate 20,000 genes, noncoding RNAs, intronic and intergenic regions of DNA [172]. WGS has the advantages of (1) being able to detect intronic or intergenic variants not covered by WES, (2) simpler sample preparation methods (e.g., no need for sequence enrichment for coding regions), and (3) being able to identify structural variants and chromosomal breakpoints in noncoding regions [172].         Certain regions still remain elusive to standard NGS technologies, and the specific methodology used to target these will vary by laboratory. WGS is slower and more expensive than WES, and yet the majority of pathogenic variants identified by WGS are located within exons [172]. Rapid evolution of WES/WGS sequencing and analysis methods in recent years precludes precise estimation of their diagnostic accuracy for inborn errors of immunity (IEI), but reported estimates of sensitivity range from 83 to 100%, and of specificity range from 45 to 88% [178]. Of note, where more genes are tested at once, there is greater likelihood of finding VUS and incidental pathogenic variants, which may pose difficulties for clinical interpretation and management [179]. 3.Copy number variant analysis and ancillary methods         Chromosomal microarrays (CMAs) detect copy number variants (CNVs), which may range in size from 1 kilobase to multiple megabases or even whole chromosomes, and therefore contain 0, 1 or many genes or parts thereof [179]. Microarrays include oligonucleotide comparative genomic hybridisation (CGH) arrays, single nucleotide variant (SNV) arrays, or combinations of these technologies, and can be designed to test at genome-wide scale or in targeted regions with appropriate resolution [172]. CMAs are more sensitive than traditional karyotyping for CNV detection, and can even be designed at exon-level resolution for specific genes [180,181].         Ancillary methods may be used to supplement genetic or genomic results obtained by conventional means. For example, the impact of predicted pathogenic intronic variants (especially those outside of the core or essential splice site) may be confirmed by RNA analysis, as missplicing may lead to complete or partial exon skipping or inclusion of intronic sequence in mature mRNA, with deleterious consequences [170].