CNV plot showing detected copy number alterations in <i>RAG1</i> (patient 534, panel A) and <i>XIAP</i> (patient 523, panel B).

<p>CNV plot showing detected copy number alterations in <i>RAG1</i> (patient 534, panel A) and <i>XIAP</i> (patient 523, panel B).</p

Mutations detected in patients with unknown disease causing variant.

<p>A clinical phenotype was reported as follows: EGS538 and 550 have symptoms and signs compatible with STAT3 mutations, including increased IgE-levels and <i>S. aureus</i> infections. Prior to the analysis EGS539 and 540 had 6% and <1% B-lymphocytes in peripheral blood and an increased susceptibility to bacterial infections. EGS542 has been prone to bacterial infections since childhood. EGS543, 546–548, 554, 555, 557 and 559 have reduced levels of B-lymphocytes and of immunoglobulins. EGS560 has a clinical phenotype related to common variable immunodeficiency, but also has congenital defects affecting non-lymphoid organs.</p>a<p>(Potentially) causal mutations are listed in bold.</p>b<p>Patient diagnosed with asplenia. Candidate genes not included in this assay.</p>c<p>No potential causing variants were found for these individuals in the NGS data</p>d<p>Manuscript in preparation.</p><p>Mutations detected in patients with unknown disease causing variant.</p

Number of reads, average read depth, coverage and specificity values per. patient.

a<p>Av. Read depth is the average number of reads obtained per position in the targeted region.</p>b<p>F_1x =  fraction of targeted region covered by at least 1 read.</p>c<p>Fc_20x  =  fraction of captured fragments covered by at least 20 reads.</p><p>Number of reads, average read depth, coverage and specificity values per. patient.</p

SNV, indel and CNV detection in patients with known causal mutation(s).

<p>Abbreviations: NGS: Next Generation Sequencing; CNV: Copy Number Variant</p><p>SNV, indel and CNV detection in patients with known causal mutation(s).</p

Cumulative survival of AR patients compared to XL patients.

<p><i>*Log rank statistics for difference in survival between X-linked and AR: 7.01 (p = 0.0081)</i>.</p

Distribution of different subtypes of CGD according to sex.

*<p>Female X-linked patients are extremely lyonized heterozygous carrriers.</p

Gastrointestinal manifestations of CGD.

<p>Gastrointestinal manifestations of CGD.</p

Different subtypes of autosomal recessive CGD.

<p>Different subtypes of autosomal recessive CGD.</p

Pulmonary involvement and cultured microorganisms.

<p>Pulmonary involvement and cultured microorganisms (in total 634 episodes in 284 patients). Percentages are the number of episodes with a positive culture of a certain pathogen divided by the total number of reported episodes.</p

Average Age at Establishment of Diagnosis “CGD”.

<p>Average Age at Establishment of Diagnosis “CGD”.</p