title: A custom 148 gene-based resequencing chip and the SNP explorer software: new tools to study antibody deficiency.
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.
authors.affiliation: Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Hong-Ying
authors.initials: HY
authors.lastname: Wang
authors.forename: Vivek
authors.initials: V
authors.lastname: Gopalan
authors.forename: Ivona
authors.initials: I
authors.lastname: Aksentijevich
authors.forename: Meredith
authors.initials: M
authors.lastname: Yeager
authors.forename: Chi Adrian
authors.initials: CA
authors.lastname: Ma
authors.forename: Yasmin Ali
authors.initials: YA
authors.lastname: Mohamoud
authors.forename: Mariam
authors.initials: M
authors.lastname: Quinones
authors.forename: Casey
authors.initials: C
authors.lastname: Matthews
authors.forename: Joseph
authors.initials: J
authors.lastname: Boland
authors.forename: Julie E
authors.initials: JE
authors.lastname: Niemela
authors.forename: Troy R
authors.initials: TR
authors.lastname: Torgerson
authors.forename: Silvia
authors.initials: S
authors.lastname: Giliani
authors.forename: Gulbu
authors.initials: G
authors.lastname: Uzel
authors.forename: Jordan S
authors.initials: JS
authors.lastname: Orange
authors.forename: Ralph
authors.initials: R
authors.lastname: Shapiro
authors.forename: Luigi
authors.initials: L
authors.lastname: Notarangelo
authors.forename: Hans D
authors.initials: HD
authors.lastname: Ochs
authors.forename: Thomas
authors.initials: T
authors.lastname: Fleisher
authors.forename: Daniel
authors.initials: D
authors.lastname: Kastner
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Chanock
authors.forename: Ashish
authors.initials: A
authors.lastname: Jain
mesh_terms: D005787:Gene Frequency / Q000235:genetics; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000175:diagnosis* / Q000235:genetics*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software