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

Hamoud Al-Mousa; Mohamed Abouelhoda; Dorota M. Monies; Nada Al-Tassan; Abdulaziz Al-Ghonaium; Bandar Al-Saud; Hasan Al-Dhekri; Rand Arnaout; Saleh Al-Muhsen; Nazema Ades; Sahar Elshorbagi; Sulaiman Al Gazlan; Farrukh Sheikh; Majed Dasouki; Lina El-Baik; Tanzeil Elamin; Amal Jaber; Omnia Kheir; Mohamed El-Kalioby; Shazia Subhani; Eman Al Idrissi; Mofareh Al-Zahrani; Maryam Alhelale; Noukha Alnader; Afaf Al-Otaibi; Rana Kattan; Khalid Al Abdelrahman; Muna M. Al Breacan; Faisal S. Bin Humaid; Salma Majid Wakil; Fadi Alzayer; Haya Al-Dusery; Tariq Faquih; Safa Al-Hissi; Brian F Meyer; Abbas Hawwari

doi:10.1016/j.jaci.2015.12.1310

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

Hamoud Al-Mousa^*
, Mohamed Abouelhoda
, Dorota M. Monies
, Nada Al-Tassan
, Abdulaziz Al-Ghonaium
, Bandar Al-Saud
, Hasan Al-Dhekri
, Rand Arnaout
, Saleh Al-Muhsen
, Nazema Ades
, Sahar Elshorbagi
, Sulaiman Al Gazlan
, Farrukh Sheikh
, Majed Dasouki
, Lina El-Baik
, Tanzeil Elamin
, Amal Jaber
, Omnia Kheir
, Mohamed El-Kalioby
, Shazia Subhani

Eman Al Idrissi, Mofareh Al-Zahrani, Maryam Alhelale, Noukha Alnader, Afaf Al-Otaibi, Rana Kattan, Khalid Al Abdelrahman, Muna M. Al Breacan, Faisal S. Bin Humaid, Salma Majid Wakil, Fadi Alzayer, Haya Al-Dusery, Tariq Faquih, Safa Al-Hissi, Brian F Meyer, Abbas Hawwari^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1780-1787
Number of pages	8
Journal	Journal of Allergy and Clinical Immunology
Volume	137
Issue number	6
Early online date	23 Feb 2016
DOIs	https://doi.org/10.1016/j.jaci.2015.12.1310
Publication status	Published - Jun 2016
Externally published	Yes

Bibliographical note

Keywords

Computational Biology
DNA Copy Number Variations
DNA Mutational Analysis
Genetic Markers
Genetic Predisposition to Disease
Genetic Testing
Genome-Wide Association Study
High-Throughput Nucleotide Sequencing
Humans
Immunologic Deficiency Syndromes/diagnosis
Mutation
Polymorphism, Single Nucleotide
Workflow

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10.1016/j.jaci.2015.12.1310

Cite this

Al-Mousa, H., Abouelhoda, M., Monies, D. M., Al-Tassan, N., Al-Ghonaium, A., Al-Saud, B., Al-Dhekri, H., Arnaout, R., Al-Muhsen, S., Ades, N., Elshorbagi, S., Al Gazlan, S., Sheikh, F., Dasouki, M., El-Baik, L., Elamin, T., Jaber, A., Kheir, O., El-Kalioby, M., ... Hawwari, A. (2016). Unbiased targeted next-generation sequencing molecular approach for primary immunodeficiency diseases. Journal of Allergy and Clinical Immunology, 137(6), 1780-1787. https://doi.org/10.1016/j.jaci.2015.12.1310

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title = "Unbiased targeted next-generation sequencing molecular approach for primary immunodeficiency diseases",

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.",

keywords = "Computational Biology, DNA Copy Number Variations, DNA Mutational Analysis, Genetic Markers, Genetic Predisposition to Disease, Genetic Testing, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing, Humans, Immunologic Deficiency Syndromes/diagnosis, Mutation, Polymorphism, Single Nucleotide, Workflow",

author = "Hamoud Al-Mousa and Mohamed Abouelhoda and Monies, \{Dorota M.\} and Nada Al-Tassan and Abdulaziz Al-Ghonaium and Bandar Al-Saud and Hasan Al-Dhekri and Rand Arnaout and Saleh Al-Muhsen and Nazema Ades and Sahar Elshorbagi and \{Al Gazlan\}, Sulaiman and Farrukh Sheikh and Majed Dasouki and Lina El-Baik and Tanzeil Elamin and Amal Jaber and Omnia Kheir and Mohamed El-Kalioby and Shazia Subhani and \{Al Idrissi\}, Eman and Mofareh Al-Zahrani and Maryam Alhelale and Noukha Alnader and Afaf Al-Otaibi and Rana Kattan and \{Al Abdelrahman\}, Khalid and \{Al Breacan\}, \{Muna M.\} and \{Bin Humaid\}, \{Faisal S.\} and Wakil, \{Salma Majid\} and Fadi Alzayer and Haya Al-Dusery and Tariq Faquih and Safa Al-Hissi and Meyer, \{Brian F\} and Abbas Hawwari",

year = "2016",

month = jun,

doi = "10.1016/j.jaci.2015.12.1310",

language = "English",

volume = "137",

pages = "1780--1787",

journal = "Journal of Allergy and Clinical Immunology",

issn = "0091-6749",

publisher = "Elsevier",

number = "6",

}

Al-Mousa, H, Abouelhoda, M, Monies, DM, Al-Tassan, N, Al-Ghonaium, A, Al-Saud, B, Al-Dhekri, H, Arnaout, R, Al-Muhsen, S, Ades, N, Elshorbagi, S, Al Gazlan, S, Sheikh, F, Dasouki, M, El-Baik, L, Elamin, T, Jaber, A, Kheir, O, El-Kalioby, M, Subhani, S, Al Idrissi, E, Al-Zahrani, M, Alhelale, M, Alnader, N, Al-Otaibi, A, Kattan, R, Al Abdelrahman, K, Al Breacan, MM, Bin Humaid, FS, Wakil, SM, Alzayer, F, Al-Dusery, H, Faquih, T, Al-Hissi, S, Meyer, BF & Hawwari, A 2016, 'Unbiased targeted next-generation sequencing molecular approach for primary immunodeficiency diseases', Journal of Allergy and Clinical Immunology, vol. 137, no. 6, pp. 1780-1787. https://doi.org/10.1016/j.jaci.2015.12.1310

TY - JOUR

T1 - Unbiased targeted next-generation sequencing molecular approach for primary immunodeficiency diseases

AU - Al-Mousa, Hamoud

AU - Abouelhoda, Mohamed

AU - Monies, Dorota M.

AU - Al-Tassan, Nada

AU - Al-Ghonaium, Abdulaziz

AU - Al-Saud, Bandar

AU - Al-Dhekri, Hasan

AU - Arnaout, Rand

AU - Al-Muhsen, Saleh

AU - Ades, Nazema

AU - Elshorbagi, Sahar

AU - Al Gazlan, Sulaiman

AU - Sheikh, Farrukh

AU - Dasouki, Majed

AU - El-Baik, Lina

AU - Elamin, Tanzeil

AU - Jaber, Amal

AU - Kheir, Omnia

AU - El-Kalioby, Mohamed

AU - Subhani, Shazia

AU - Al Idrissi, Eman

AU - Al-Zahrani, Mofareh

AU - Alhelale, Maryam

AU - Alnader, Noukha

AU - Al-Otaibi, Afaf

AU - Kattan, Rana

AU - Al Abdelrahman, Khalid

AU - Al Breacan, Muna M.

AU - Bin Humaid, Faisal S.

AU - Wakil, Salma Majid

AU - Alzayer, Fadi

AU - Al-Dusery, Haya

AU - Faquih, Tariq

AU - Al-Hissi, Safa

AU - Meyer, Brian F

AU - Hawwari, Abbas

PY - 2016/6

Y1 - 2016/6

N2 - 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.

AB - 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.

KW - Computational Biology

KW - DNA Copy Number Variations

KW - DNA Mutational Analysis

KW - Genetic Markers

KW - Genetic Predisposition to Disease

KW - Genetic Testing

KW - Genome-Wide Association Study

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Immunologic Deficiency Syndromes/diagnosis

KW - Mutation

KW - Polymorphism, Single Nucleotide

KW - Workflow

U2 - 10.1016/j.jaci.2015.12.1310

DO - 10.1016/j.jaci.2015.12.1310

M3 - Article

C2 - 26915675

SN - 0091-6749

VL - 137

SP - 1780

EP - 1787

JO - Journal of Allergy and Clinical Immunology

JF - Journal of Allergy and Clinical Immunology

IS - 6

ER -

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

Abstract

Bibliographical note

Keywords

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