title: Unbiased targeted next-generation sequencing molecular approach for primary immunodeficiency diseases.
abstract: 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.
authors.affiliation: Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia. Electronic address: hamoudalmousa@kfshrc.edu.sa.
authors.forename: Hamoud
authors.initials: H
authors.lastname: Al-Mousa
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Abouelhoda
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
authors.forename: Dorota M
authors.initials: DM
authors.lastname: Monies
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
authors.forename: Nada
authors.initials: N
authors.lastname: Al-Tassan
authors.affiliation: Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Abdulaziz
authors.initials: A
authors.lastname: Al-Ghonaium
authors.affiliation: Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
authors.forename: Bandar
authors.initials: B
authors.lastname: Al-Saud
authors.affiliation: Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Hasan
authors.initials: H
authors.lastname: Al-Dhekri
authors.affiliation: Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Rand
authors.initials: R
authors.lastname: Arnaout
authors.affiliation: Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Department of Pediatrics, King Saud University, Riyadh, Saudi Arabia.
authors.forename: Saleh
authors.initials: S
authors.lastname: Al-Muhsen
authors.affiliation: Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Nazema
authors.initials: N
authors.lastname: Ades
authors.affiliation: Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Sahar
authors.initials: S
authors.lastname: Elshorbagi
authors.affiliation: Department of Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Sulaiman
authors.initials: S
authors.lastname: Al Gazlan
authors.affiliation: Department of Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Farrukh
authors.initials: F
authors.lastname: Sheikh
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Majed
authors.initials: M
authors.lastname: Dasouki
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Lina
authors.initials: L
authors.lastname: El-Baik
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Tanzeil
authors.initials: T
authors.lastname: Elamin
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Amal
authors.initials: A
authors.lastname: Jaber
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Omnia
authors.initials: O
authors.lastname: Kheir
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Mohamed
authors.initials: M
authors.lastname: El-Kalioby
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
authors.forename: Shazia
authors.initials: S
authors.lastname: Subhani
authors.affiliation: Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia.
authors.forename: Eman
authors.initials: E
authors.lastname: Al Idrissi
authors.affiliation: Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia.
authors.forename: Mofareh
authors.initials: M
authors.lastname: Al-Zahrani
authors.affiliation: Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
authors.forename: Maryam
authors.initials: M
authors.lastname: Alhelale
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Noukha
authors.initials: N
authors.lastname: Alnader
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Afaf
authors.initials: A
authors.lastname: Al-Otaibi
authors.affiliation: Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
authors.forename: Rana
authors.initials: R
authors.lastname: Kattan
authors.affiliation: Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
authors.forename: Khalid
authors.initials: K
authors.lastname: Al Abdelrahman
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Muna M
authors.initials: MM
authors.lastname: Al Breacan
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Faisal S
authors.initials: FS
authors.lastname: Bin Humaid
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Salma Majid
authors.initials: SM
authors.lastname: Wakil
authors.affiliation: Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Fadi
authors.initials: F
authors.lastname: Alzayer
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Haya
authors.initials: H
authors.lastname: Al-Dusery
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Tariq
authors.initials: T
authors.lastname: Faquih
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
authors.forename: Safa
authors.initials: S
authors.lastname: Al-Hissi
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
authors.forename: Brian F
authors.initials: BF
authors.lastname: Meyer
authors.affiliation: Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia. Electronic address: ahawwari@kfshrc.edu.sa.
authors.forename: Abbas
authors.initials: A
authors.lastname: Hawwari
mesh_terms: D019295:Computational Biology; D056915:DNA Copy Number Variations; D004252:DNA Mutational Analysis; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000175:diagnosis* / Q000235:genetics* / Q000276:immunology; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D057188:Workflow
chemical_list: D005819:Genetic Markers
keywords: Immunodeficiency; Saudi; diagnosis; genetic; mutation; next-generation sequencing; primary immunodeficiency; targeted; variants