LymphoSign Journal

Volume 3 • Number 4 • December 2016

Review

Whole exome and genome sequencing for Mendelian immune disorders: from molecular diagnostics to new disease variant and gene discovery

Daniele Merico

Vol. 3No. 4pp. 135–158

Whole exome and whole genome sequencing are next generation sequencing (NGS) applications that enable investigation of all coding variants (around 20 000) or all variants (around 4 million) in the human genome. They provide an extremely powerful tool for detecting variants with an established implication in Mendelian disorders as well as for discovering new disease variants and genes. The large number of variants generated requires elaborate databases, prediction models, and integrated workflows to identify which variants are more likely to contribute to disease. We discuss the whole exome and whole genome options, review the sequencing platforms and variant calling pipelines available for different variant types, and devote most of the review to how genetic variants can be annotated and prioritized to identify the ones likely contributing to disorder. The application focus will be Mendelian disorders; disorders caused by rare or common variants with a more complex genetic architecture will only be discussed briefly. For variant annotation and interpretation, we will concentrate on smaller variants (substitutions, insertions, and deletions), only briefly reviewing structural and copy number variation.

Original Article

A novel mutation in Roifman syndrome redefines the boundaries of the Sm protein-binding site

Vol. 3No. 4pp. 159–163

Roifman syndrome is an association of humoral immunodeficiency, growth retardation, spondyloepiphyseal dysplasia, developmental delay, retinal dystrophy, and unique dysmorphism. Compound heterozygote mutations in the RNU4ATAC gene, an essential component of the minor spliceosome, were found to be the culprit for this disorder. Here we report a novel mutation in the RNU4ATAC gene, involving position 116. This mutation redefines the Sm protein binding site of this gene.Statement of novelty: We report here a patient with a novel mutation in the Sm protein-binding site that redefined its boundaries to include position 116.

A database for immunodeficiency due to mutations in nuclear factor kappa B pathway genes

Arnon Broides

Vol. 3No. 4pp. 165–178

Nuclear factor kappa B (NFκB) pathway defects are associated with immunodeficiency; however, multiple phenotypes for mutations in genes encoding for NFκB proteins have been reported. We sought to create a database of published mutations in the genes encoding for IKKα and IKKβ and the regulatory subunit IKKγ, also referred to as NFκB essential modulator (NEMO). All published mutations were reviewed. The clinical and laboratory phenotypes were recorded and yearly updates of new mutations and phenotypes will be performed. Multiple immunodeficiency and infectious phenotypes were recorded particularly for patients with NEMO gene mutations. Even patients with the same NEMO mutation tended to have somewhat different phenotypes. In patients with primary immunodeficiency, the clinical phenotype may not direct the clinician to the genetic cause of the disease. Therefore, a comprehensive database will expand our knowledge and enhance the clinician’s ability to predict which gene mutation is the cause of the immunodeficiency. This database can assist clinicians in the diagnoses of patients with specific features of immunodeficiency.Statement of novelty: A comprehensive database of published mutations in the genes encoding for IKKα, IKKβ, and IKKγ was created. This database may aid the clinician in recognizing specific immunodeficiency phenotypes.