Original article (Clinical research)

Gene diagnostic method for primary immunodeficiency disease based on targeted panel sequencing

  • YANG Li-jun ,
  • Li Niu ,
  • LIU Yi ,
  • WANG Jian
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  • 1. College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China; 2. Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China

Online published: 2017-03-30

Abstract

Objective · To design and build a high-throughput sequencing approach based on targeted panel sequencing (TPS) using for the primary immunodeficiency disease (PID) diagnosis. Methods · By reviewing the literature and querying the relevant databases to determine the known disease-causing genes of PID, capture probes using for the TPS were designed and customized for all exons and flanking sequences of these genes. A child suspected with PID was diagnosed by the customized TPS. Results · The PID sequencing panel contains a total of 100 known pathogenic genes. The sequencing data of the patient has 16 414 298 reads. The average coverage depth is 157 X, 98.35% of the target region sequencing depth is greater than 20 X, and 99.97% of the target region sequencing depth is greater than 1 X. Finally, a heterozygous nonsense mutation was found in the exon 2 of the CXCR4 gene (c.1000C>T, p.Arg334*) in the child. The results of Sanger sequencing confirmed the variation in the child and showed that his parents were wild-type at the corresponding sites, indicating the mutation is de novo. Conclusion · This study established a high-throughput sequencing diagnostic approach for PID, with which a case of WHIM syndrome was successfully diagnosed.

Cite this article

YANG Li-jun , Li Niu , LIU Yi , WANG Jian . Gene diagnostic method for primary immunodeficiency disease based on targeted panel sequencing[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2017 , 37(3) : 390 . DOI: 10.3969/j.issn.1674-8115.2017.03.022

Outlines

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