Hamoud Al-Mousa1, Mohamed Abouelhoda2, Dorota M Monies2, Nada Al-Tassan2, Abdulaziz Al-Ghonaium3, Bandar Al-Saud4, Hasan Al-Dhekri3, Rand Arnaout3, Saleh Al-Muhsen5, Nazema Ades3, Sahar Elshorbagi3, Sulaiman Al Gazlan6, Farrukh Sheikh6, Majed Dasouki7, Lina El-Baik7, Tanzeil Elamin7, Amal Jaber7, Omnia Kheir7, Mohamed El-Kalioby7, Shazia Subhani2, Eman Al Idrissi8, Mofareh Al-Zahrani8, Maryam Alhelale9, Noukha Alnader7, Afaf Al-Otaibi7, Rana Kattan10, Khalid Al Abdelrahman10, Muna M Al Breacan7, Faisal S Bin Humaid7, Salma Majid Wakil7, Fadi Alzayer11, Haya Al-Dusery7, Tariq Faquih7, Safa Al-Hissi7, Brian F Meyer2, Abbas Hawwari12. 1. 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. 2. 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. 3. Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia. 4. Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia. 5. Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Department of Pediatrics, King Saud University, Riyadh, Saudi Arabia. 6. Department of Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia. 7. Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia. 8. Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia. 9. Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia. 10. Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. 11. Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia. 12. Department of Genetics (Research Center), King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia. Electronic address: ahawwari@kfshrc.edu.sa.
Abstract
BACKGROUND: 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. OBJECTIVES: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.
BACKGROUND: 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. OBJECTIVES: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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: Heather Minto; Kofi A Mensah; Paul R Reynolds; Eric Meffre; Kira Rubtsova; Erwin W Gelfand Journal: Clin Immunol Date: 2019-01-09 Impact factor: 3.969
Authors: Asbjørg Stray-Pedersen; Hanne Sørmo Sorte; Pubudu Samarakoon; Tomasz Gambin; Ivan K Chinn; Zeynep H Coban Akdemir; Hans Christian Erichsen; Lisa R Forbes; Shen Gu; Bo Yuan; Shalini N Jhangiani; Donna M Muzny; Olaug Kristin Rødningen; Ying Sheng; Sarah K Nicholas; Lenora M Noroski; Filiz O Seeborg; Carla M Davis; Debra L Canter; Emily M Mace; Timothy J Vece; Carl E Allen; Harshal A Abhyankar; Philip M Boone; Christine R Beck; Wojciech Wiszniewski; Børre Fevang; Pål Aukrust; Geir E Tjønnfjord; Tobias Gedde-Dahl; Henrik Hjorth-Hansen; Ingunn Dybedal; Ingvild Nordøy; Silje F Jørgensen; Tore G Abrahamsen; Torstein Øverland; Anne Grete Bechensteen; Vegard Skogen; Liv T N Osnes; Mari Ann Kulseth; Trine E Prescott; Cecilie F Rustad; Ketil R Heimdal; John W Belmont; Nicholas L Rider; Javier Chinen; Tram N Cao; Eric A Smith; Maria Soledad Caldirola; Liliana Bezrodnik; Saul Oswaldo Lugo Reyes; Francisco J Espinosa Rosales; Nina Denisse Guerrero-Cursaru; Luis Alberto Pedroza; Cecilia M Poli; Jose L Franco; Claudia M Trujillo Vargas; Juan Carlos Aldave Becerra; Nicola Wright; Thomas B Issekutz; Andrew C Issekutz; Jordan Abbott; Jason W Caldwell; Diana K Bayer; Alice Y Chan; Alessandro Aiuti; Caterina Cancrini; Eva Holmberg; Christina West; Magnus Burstedt; Ender Karaca; Gözde Yesil; Hasibe Artac; Yavuz Bayram; Mehmed Musa Atik; Mohammad K Eldomery; Mohammad S Ehlayel; Stephen Jolles; Berit Flatø; Alison A Bertuch; I Celine Hanson; Victor W Zhang; Lee-Jun Wong; Jianhong Hu; Magdalena Walkiewicz; Yaping Yang; Christine M Eng; Eric Boerwinkle; Richard A Gibbs; William T Shearer; Robert Lyle; Jordan S Orange; James R Lupski Journal: J Allergy Clin Immunol Date: 2016-07-16 Impact factor: 10.793
Authors: M Dasouki; A Jabr; G AlDakheel; F Elbadaoui; A M Alazami; B Al-Saud; R Arnaout; H Aldhekri; I Alotaibi; H Al-Mousa; A Hawwari Journal: Clin Exp Immunol Date: 2020-07-21 Impact factor: 4.330