Unbiased targeted next-generation sequencing molecular approach for primary immunodeficiency diseases

• Published in: Journal of allergy and clinical immunology Vol. 137; no. 6; pp. 1780 - 1787
• Main Authors: Al-Mousa, Hamoud, Abouelhoda, Mohamed, Monies, Dorota M., Al-Tassan, Nada, Al-Ghonaium, Abdulaziz, Al-Saud, Bandar, Al-Dhekri, Hasan, Arnaout, Rand, Al-Muhsen, Saleh, Ades, Nazema, Elshorbagi, Sahar, Al Gazlan, Sulaiman, Sheikh, Farrukh, Dasouki, Majed, El-Baik, Lina, Elamin, Tanzeil, Jaber, Amal, Kheir, Omnia, El-Kalioby, Mohamed, Subhani, Shazia, Al Idrissi, Eman, Al-Zahrani, Mofareh, Alhelale, Maryam, Alnader, Noukha, Al-Otaibi, Afaf, Kattan, Rana, Al Abdelrahman, Khalid, Al Breacan, Muna M., Bin Humaid, Faisal S., Wakil, Salma Majid, Alzayer, Fadi, Al-Dusery, Haya, Faquih, Tariq, Al-Hissi, Safa, Meyer, Brian F., Hawwari, Abbas
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2016; Elsevier Limited
• Subjects: Allergy and Immunology; Ataxia; Computational Biology; Defects; diagnosis; Disease; DNA Copy Number Variations; DNA Mutational Analysis; Genes; genetic; Genetic counseling; Genetic Markers; Genetic Predisposition to Disease; Genetic Testing; Genome-Wide Association Study; Genomes; High-Throughput Nucleotide Sequencing; Humans; Immunodeficiency; Immunologic Deficiency Syndromes - diagnosis; Immunologic Deficiency Syndromes - genetics; Immunologic Deficiency Syndromes - immunology; Laboratories; Mutation; next-generation sequencing; Patients; Polymorphism, Single Nucleotide; primary immunodeficiency; Saudi; Studies; targeted; variants; Workflow; genetic; WGS; WES; next-generation sequencing; Immunodeficiency; diagnosis; CNV; PID; variants; SCID; mutation; Saudi; SNP; ePCR; HGMD; targeted; primary immunodeficiency; SNV; NGS; indel; CID; Copy number variation; Combined immunodeficiency; Primary immunodeficiency disease; Insertion/deletion; Single nucleotide variant; Whole-exome sequencing; Human Gene Mutation Database; Whole-genome sequencing; Severe combined immunodeficiency disease; Single nucleotide polymorphism; Emulsion PCR
• ISSN: 0091-6749; 1097-6825; 1097-6825
• DOI: 10.1016/j.jaci.2015.12.1310

Molecular genetics techniques are an essential diagnostic tool for primary immunodeficiency diseases (PIDs). The use of next-generation sequencing (NGS) provides a comprehensive way of concurrently screening a large number of PID genes. However, its validity and cost-effectiveness require verification. We sought to identify and overcome complications associated with the use of NGS in a comprehensive gene panel incorporating 162 PID genes. We aimed to ascertain the specificity, sensitivity, and clinical sensitivity of the gene panel and its utility as a diagnostic tool for PIDs. A total of 162 PID genes were screened in 261 patients by using the Ion Torrent Proton NGS sequencing platform. Of the 261 patients, 122 had at least 1 known causal mutation at the onset of the study and were used to assess the specificity and sensitivity of the assay. The remaining samples were from unsolved cases that were biased toward more phenotypically and genotypically complicated cases. The assay was able to detect the mutation in 117 (96%) of 122 positive control subjects with known causal mutations. For the unsolved cases, our assay resulted in a molecular genetic diagnosis for 35 of 139 patients. Interestingly, most of these cases represented atypical clinical presentations of known PIDs. The targeted NGS PID gene panel is a sensitive and cost-effective diagnostic tool that can be used as a first-line molecular assay in patients with PIDs. The assay is an alternative choice to the complex and costly candidate gene approach, particularly for patients with atypical presentation of known PID genes.