A custom 148 gene-based resequencing chip and the SNP explorer software: new tools to study antibody deficiency
- 22 July 2010
- journal article
- research article
- Published by Hindawi Limited in Human Mutation
- Vol. 31 (9), 1080-1088
- https://doi.org/10.1002/humu.21322
Abstract
Hyper‐IgM syndrome and Common Variable Immunodeficiency are heterogeneous disorders characterized by a predisposition to serious infection and impaired or absent neutralizing antibody responses. Although a number of single gene defects have been associated with these immune deficiency disorders, the genetic basis of many cases is not known. To facilitate mutation screening in patients with these syndromes, we have developed a custom 300‐kb resequencing array, the Hyper‐IgM/CVID chip, which interrogates 1,576 coding exons and intron–exon junction regions from 148 genes implicated in B‐cell development and immunoglobulin isotype switching. Genomic DNAs extracted from patients were hybridized to the array using a high‐throughput protocol for target sequence amplification, pooling, and hybridization. A Web‐based application, SNP Explorer, was developed to directly analyze and visualize the single nucleotide polymorphism (SNP) annotation and for quality filtering. Several mutations in known disease‐susceptibility genes such as CD40LG, TNFRSF13B, IKBKG, AICDA , as well as rare nucleotide changes in other genes such as TRAF3IP2 , were identified in patient DNA samples and validated by direct sequencing. We conclude that the Hyper‐IgM/CVID chip combined with SNP Explorer may provide a cost‐effective tool for high‐throughput discovery of novel mutations among hundreds of disease‐relevant genes in patients with inherited antibody deficiency. Hum Mutat 31:1080–1088, 2010. Published 2010 Wiley‐Liss, Inc.Keywords
This publication has 33 references indexed in Scilit:
- High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarraysBMC Biotechnology, 2010
- Act1, a U-box E3 Ubiquitin Ligase for IL-17 SignalingScience Signaling, 2009
- B-cell activating factor receptor deficiency is associated with an adult-onset antibody deficiency syndrome in humansProceedings of the National Academy of Sciences of the United States of America, 2009
- Primary B Cell Immunodeficiencies: Comparisons and ContrastsAnnual Review of Immunology, 2009
- IKBKG (nuclear factor-κB essential modulator) mutation can be associated with opportunistic infection without impairing Toll-like receptor functionJournal of Allergy and Clinical Immunology, 2008
- Direct selection of human genomic loci by microarray hybridizationNature Methods, 2007
- Microarray-based genomic selection for high-throughput resequencingNature Methods, 2007
- Promiscuous Mutations Activate the Noncanonical NF-κB Pathway in Multiple MyelomaCancer Cell, 2007
- Molecular analysis of a large cohort of patients with the hyper immunoglobulin M (IgM) syndromeBlood, 2005
- The CD40 ligand, gp39, is defective in activated T cells from patients with X-linked hyper-IgM syndromeCell, 1993