Homozygous duplication identified by whole genome sequencing causes LRBA deficiency

In more than one-third of primary immunodeficiency (PID) patients, extensive genetic analysis including whole-exome sequencing (WES) fails to identify the genetic defect. Whole-genome sequencing (WGS) is able to detect variants missed by other genomics platforms, enabling the molecular diagnosis of otherwise unresolved cases. Here, we report two siblings, offspring of consanguineous parents, who experienced similar severe events encompassing early onset of colitis, lymphoproliferation, and hypogammaglobulinemia, typical of lipopolysaccharide-responsive and beige-like anchor (LRBA) or cytotoxic T lymphocyte antigen 4 (CTLA4) deficiencies. Gene-panel sequencing, comparative genomic hybridization (CGH) array, and WES failed to reveal a genetic aberration in relevant genes. WGS of these patients detected a 12.3 kb homozygous tandem duplication that was absent in control cohorts and is predicted to disrupt the reading frame of the LRBA gene. The variant was validated by PCR and Sanger sequencing, demonstrating the presence of the junction between the reference and the tandem-duplicated sequence. Droplet digital PCR (ddPCR) further confirmed the copy number in the unaffected parents (CN = 3, heterozygous) and affected siblings (CN = 4, homozygous), confirming the expected segregation pattern. In cases of suspected inherited immunodeficiency, WGS may reveal a mutation when other methods such as microarray and WES analysis failed to detect an aberration.

X-Linked Agammaglobulinemia Presenting as Neutropenia: Case Report and an Overview of Literature

X-linked agammaglobulinemia (XLA) is an inherited immunodeficiency caused by mutations in the Bruton Tyrosine Kinase (BTK) gene. Marked neutropenia can be the initial abnormal laboratory finding in patients with XLA who are presenting with their first illness. The two cases presented herein support early consideration of evaluation for primary humoral immune deficiency in previously healthy male patients under the age of 12 months who present with neutropenia in the setting of infection shortly after passively acquired maternal antibody has sufficiently waned. Initial consideration of XLA (or other humoral immune deficiencies) in this particular population of young male neutropenic patients may afford the opportunity to avoid bone marrow biopsy in otherwise stable cases with similar presentations.

Late-Onset of Chronic Granulomatous Disease Revealed By Paecilomyces Lilacinus Cutaneous Infection

Chronic granulomatous disease (CGD) is an inherited immunodeficiency due to defective leukocyte NADPH responsible for recurrent infections and aberrant inflammation. Mutations in the CYBB gene are responsible for the X-linked CGD and account for approximately 70% of the cases. CGD is diagnosed during childhood in males. Female carriers may have biased X inactivation and may present with clinical manifestations depending on the level of residual NADPH oxidase activity. We report the case of a previously asymptomatic female carrier who was diagnosed at age 67 with a skin infection with the rare fungus, Paecylomyces lilacinus as the first manifestation of CGD. Dihydrorhodamin 123 (DHR) activity was below 10%. Next-generation sequencing (NGS) revealed mutations in DNMT3A, ASXL1, and STAG2 suggesting that clonal hematopoiesis of undetermined potential (CHIP) could be responsible for a progressive loss of NADPH oxidase activity and the late onset of X-linked CGD in this patient. Long-term follow-up of asymptomatic carrier women seems to be essential after 50 years old.

Novel CD40LG Mutation in Two Cousins With Immunoglobulin Class Switch Recombinant Deficiency

The hyper-immunoglobulin M (HIGM) syndrome comprises a group of rare inherited immunodeficiency disorders characterized by normal or elevated levels of serum IgM with low or absent levels of serum IgG, IgA, and IgE. Patients with this syndrome usually present with a history of recurrent infections or opportunistic infections. Here, we report two male cousins from homozygote twin mothers. The first cousin presented with no signs or symptoms other than neutropenia, which was accidentally found in a routine blood test. Immunological workup in this patient showed undetectable IgG and IgA levels and normal IgM levels. The second cousin had a history of recurrent infections, and at the time of admission, he was diagnosed with Pneumocystis jirovecii infection. The immunologic workup of this patient showed undetectable IgG, decreased IgA, and increased IgM level. Due to their interesting family relationship, genetic analysis was performed, which detected a novel mutation in exon 2 (c.266 del G) of the CD40 ligand gene (CD40LG).

Haemopoietic stem cell transplantation

Haemopoietic stem cells (HSCs) give rise to the blood cell lineages and the cells of the immune system, and their transplantation may be an appropriate part of the management of conditions including (1) malignant haematological disorders (e.g. leukaemia, lymphoma, myeloma); (2) bone marrow failure syndromes (e.g. aplastic anaemia); and (3) congenital disorders—(a) haematological (e.g. Fanconi’s anaemia); (b) immunological—inherited immunodeficiency syndromes; and (c) metabolic (e.g. lysosomal storage diseases). Transplantation of HSCs uses either autologous HSCs (patient’s own stem cells) or allogeneic HSCs (harvested from an appropriately matched sibling or unrelated healthy donor). Successful engraftment of allogeneic HSCs depends upon (1) overcoming immune rejection by the recipient; (2) preventing or suppressing graft-versus-host disease (GVHD), in which donor cells mount an immune attack against recipient tissues; and (3) supporting the patient through periods of profound cytopenias and immune deficiency with susceptibility to infection. Identification and sources of HSCs—HSCs are principally identified by expression of the surface antigen CD34. Sources include (1) bone marrow; (2) peripheral blood—following stimulation by cytokines (e.g. granulocyte colony-stimulating factor); and (3) umbilical cord blood.

Autoimmune Lymphoproliferative Syndrome: An Overview

Autoimmune lymphoproliferative syndrome (ALPS) is an inherited nonmalignant lymphoproliferative disorder characterized by heterozygous mutations within the first apoptosis signal receptor (FAS) signaling pathway. Defects in FAS-mediated apoptosis cause an expansion and accumulation of autoreactive CD4− and CD8− (double-negative) T cells, leading to cytopenias, splenomegaly, lymphadenopathy, autoimmune disorders, and a greatly increased lifetime risk of lymphoma. The differential diagnosis of ALPS includes infection, other inherited immunodeficiency disorders, primary and secondary autoimmune syndromes, and lymphoma. The most consistent pathologic feature is a florid paracortical expansion of double-negative T cells in lymph nodes. A presumptive clinical diagnosis can be made from symptoms and a constellation of laboratory test results. However, a definitive diagnosis requires ancillary testing and enables disease subclassification. Recognition of ALPS is critical, as treatment with immunosuppressive therapies can effectively reduce or ameliorate symptoms for most patients.

Preimplantation genetic testing for inherited immunodeficiency

Preimplantation genetic testing (PGT) has become a practical tool for at risk couples to avoid affected pregnancies and have a healthy progeny free from genetic and chromosomal disorders. PGT is also an option for stem cell transplantation treatment through combining PGT with preimplantation HLA typing for couples with children affected by congenital disorders, for whom no other alternative therapies are available, such as for congenital immunodeficiency. We present here our experience of 135 PGT cycles performed for 74 couples at risk for producing offspring with 18 different congenital immunodeficiencies, resulting in birth of 54 healthy children free from inherited immunodeficiency, which is one of the world’s largest PGT series for immunodeficiency.