A single-center pilot study in Malaysia on the clinical utility of whole-exome sequencing for inborn errors of immunity

Ripen, Adiratna Mat; Chear, Chai Teng; Baharin, Mohd Farid; Nallusamy, Revathy; Chan, Kwai Cheng; Kassim, Asiah; Choo, Chong Ming; Wong, Ke Juin; Fong, Siew Moy; Tan, Kah Kee; Nachiappan, Jeyaseelan P.; Teo, Kai Ru; Chiow, Mei Yee; Hishamshah, Munirah; Ghani, Hamidah; Muralitharan, Rikeish R.; Mohamad, Saharuddin Bin

doi:10.1111/cei.13626

Cited by 9 publications

(9 citation statements)

References 28 publications

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“…The genetic heterogeneity of the IEI as well as the delay in the diagnosis in atypical cases leads to significant morbidity and mortality. Establishing definitive genetic diagnosis is very important for patients’ management [ 8 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic Testing in Egyptian Patients with Inborn Errors of Immunity: a Single-Center Experience

et al. 2022

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Background Inborn errors of immunity (IEI) are a group of heterogeneous disorders with geographic and ethnic diversities. Although IEI are common in Egypt, genetic diagnosis is limited due to financial restrictions. This study aims to characterize the genetic spectrum of IEI patients in Egypt and highlights the adaptation of the molecular diagnostic methods to a resource-limited setting. Methods Genetic material from 504 patients was studied, and proper diagnosis was achieved in 282 patients from 246 families. Mutational analysis was done by Sanger sequencing, next-generation sequencing (NGS) targeting customized genes panels, and whole-exome sequencing (WES) according to the patients’ phenotypes and availability of genetic testing. Results A total of 194 variants involving 72 different genes were detected with RAG1/2 genes being the most encountered followed by DOCK8, CYBA, LRBA, NCF1, and JAK3. Autosomal recessive (AR) inheritance was detected in 233/282 patients (82.6%), X-linked (XL) recessive inheritance in 32/282 patients (11.3%), and autosomal dominant (AD) inheritance in 18/282 patients (6.4%), reflecting the impact of consanguineous marriages on the prevalence of different modes of inheritance and the distribution of the various IEI disorders. Conclusion The study showed that a combination of Sanger sequencing in selected patients associated with targeted NGS or WES in other patients is an effective diagnostic strategy for IEI diagnosis in countries with limited diagnostic resources. Molecular testing can be used to validate other nonexpensive laboratory techniques that help to reach definitive diagnosis and help in genetic counseling and taking proper therapeutic decisions including stem cell transplantation or gene therapy.

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Section: Discussionmentioning

confidence: 99%

Genetic Testing in Egyptian Patients with Inborn Errors of Immunity: a Single-Center Experience

et al. 2022

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“…According to the International Union of Immunological Societies (IUIS), a total of 485 IEIs have been reported arising from defects in more than 490 genes [ 2 ]. The use of next-generation sequencing (NGS), particularly whole-exome sequencing (WES), has improved clinical diagnosis and unraveled novel genes and variants underlying IEIs [ 3 , 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

A Novel De Novo NFKBIA Missense Mutation Associated to Ectodermal Dysplasia with Dysgammaglobulinemia

Chear

Farran

Sham

et al. 2022

Genes

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Background: Inborn errors of immunity (IEIs) are comprised of heterogeneous groups of genetic disorders affecting immune function. In this report, a 17-month-old Malay patient suspected of having Hyper IgM syndrome, a type of IEIs, was described. However, the diagnosis of Hyper IgM syndrome was excluded by the normal functional studies and the mild features of ectodermal dysplasia observed from a further clinical phenotype inspection. Methods: Whole-exome sequencing (WES) was performed to unravel the causative mutation in this patient. Results: The variant analysis demonstrated a novel missense mutation in NFKBIA (NM_020529:c.94A > T,NP_065390:p.Ser32Cys) and was predicted as damaging by in silico prediction tools. The NFKBIA gene encodes for IκBα, a member of nuclear factor kappa B (NF-κB) inhibitors, playing an important role in regulating NF-κB activity. The mutation occurred at the six degrons (Asp31-Ser36) in IκBα which were evolutionarily conserved across several species. Prediction analysis suggested that the substitution of Ser32Cys may cause a loss of the phosphorylation site at residue 32 and a gain of the sumoylation site at residue 38, resulting in the alteration of post-translational modifications of IκBα required for NF-κB activation. Conclusion: Our analysis hints that the post-translational modification in the NFKBIA Ser32Cys mutant would alter the signaling pathway of NF-κB. Our findings support the usefulness of WES in diagnosing IEIs and suggest the role of post-translational modification of IκBα.

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“…Our previous studies reported successful use of WES to identify genetic mutations for several types of monogenic disease that belong to the group of inborn errors of immunity ( 17 , 18 ). In the present study, the application of WES to ADPKD was evaluated.…”

Section: Introductionmentioning

confidence: 99%

Visual inspection reveals a novel pathogenic mutation inPKD1missed by the variant caller in whole‑exome sequencing

et al. 2022

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autosomal dominant polycystic kidney disease (adPKd) is the most common type of inherited cystic kidney disease. The feasibility of whole-exome sequencing (WeS) to obtain molecular diagnosis of adPKd is still in question as previous studies showed conflicting results. Utilizing WeS on a patient with adPKd, standard bioinformatics pipeline demonstrated no pathogenic variant in the genes of interest. By visualizing read alignments using the Integrative Genomics Viewer, a region with atypical alignment of numerous soft-clipped reads at exon 45 of polycystin 1, transient receptor potential channel interacting (PKD1) gene was demonstrated. a total of four visual inspection steps were outlined to assess the origin of these soft-clipped reads as strand bias during capture, poor mapping, sequencing error or dna template contamination. Following assessment, the atypical alignment at PKD1 was hypothesized to be caused by an insertion/deletion mutation. Sanger sequencing confirmed the presence of a novel 20-bp insertion in PKD1 (nM_001009944.3; c.12143_12144insTcc ccG caG TcT Tcc ccG ca; p.Val4048leufsTer157), which introduced a premature stop codon and was predicted to be pathogenic. The present study demonstrated that WES could be utilized as a molecular diagnostic tool for adPKd. Furthermore, visual inspection of read alignments was key in identifying the pathogenic variant. The proposed visual inspection steps may be incorporated into a typical WES data analysis workflow to improve the diagnostic yield.

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A single-center pilot study in Malaysia on the clinical utility of whole-exome sequencing for inborn errors of immunity

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 9 publications

References 28 publications

Genetic Testing in Egyptian Patients with Inborn Errors of Immunity: a Single-Center Experience

Genetic Testing in Egyptian Patients with Inborn Errors of Immunity: a Single-Center Experience

A Novel De Novo NFKBIA Missense Mutation Associated to Ectodermal Dysplasia with Dysgammaglobulinemia

Visual inspection reveals a novel pathogenic mutation inPKD1missed by the variant caller in whole‑exome sequencing

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