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Rawat A, Sharma M, Vignesh P, Jindal AK, Suri D, Das J, Joshi V, Tyagi R, Sharma J, Kaur G, Lau YL, Imai K, Nonoyama S, Lenardo M, Singh S. Utility of targeted next generation sequencing for inborn errors of immunity at a tertiary care centre in North India. Sci Rep 2022; 12:10416. [PMID: 35729272 PMCID: PMC9213413 DOI: 10.1038/s41598-022-14522-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022] Open
Abstract
Inborn errors of immunity (IEI) are a heterogeneous group of monogenic disorders that include primary immunodeficiency's and other disorders affecting different aspects of the immune system. Next-Generation Sequencing (NGS) is an essential tool to diagnose IEI. We report our 3-year experience in setting up facilities for NGS for diagnosis of IEI in Chandigarh, North India. We used a targeted, customized gene panel of 44 genes known to result in IEI. Variant analysis was done using Ion Reporter software. The in-house NGS has enabled us to offer genetic diagnoses to patients with IEI at minimal costs. Of 121 patients who were included pathogenic variants were identified in 77 patients. These included patients with Chronic Granulomatous Disease, Severe Combined Immune Deficiency, leukocyte adhesion defect, X-linked agammaglobulinemia, Ataxia Telangiectasia, Hyper-IgE syndrome, Wiskott Aldrich syndrome, Mendelian susceptibility to mycobacterial diseases, Hyper-IgM syndrome, autoimmune lymphoproliferative syndrome, and GATA-2 deficiency. This manuscript discusses the challenges encountered while setting up and running targeted NGS for IEI in our unit. Genetic diagnosis has helped our patients with IEI in genetic counselling, prenatal diagnosis, and accessing appropriate therapeutic options.
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Affiliation(s)
- Amit Rawat
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India.
| | - Madhubala Sharma
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Pandiarajan Vignesh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Ankur Kumar Jindal
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Deepti Suri
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Jhumki Das
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Vibhu Joshi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Rahul Tyagi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Jyoti Sharma
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Gurjit Kaur
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kohsuke Imai
- Department of Pediatric, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, National Defence Medical College, Tokyo, 113-8519, Japan
| | - Shigeaki Nonoyama
- Department of Pediatric, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, National Defence Medical College, Tokyo, 113-8519, Japan
| | - Michael Lenardo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA
| | - Surjit Singh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
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Bukowska-Olech E, Sowińska-Seidler A, Larysz D, Gawliński P, Koczyk G, Popiel D, Gurba-Bryśkiewicz L, Materna-Kiryluk A, Adamek Z, Szczepankiewicz A, Dominiak P, Glista F, Matuszewska K, Jamsheer A. Results from Genetic Studies in Patients Affected with Craniosynostosis: Clinical and Molecular Aspects. Front Mol Biosci 2022; 9:865494. [PMID: 35591945 PMCID: PMC9112228 DOI: 10.3389/fmolb.2022.865494] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Craniosynostosis (CS) represents a highly heterogeneous genetic condition whose genetic background has not been yet revealed. The abnormality occurs either in isolated form or syndromic, as an element of hundreds of different inborn syndromes. Consequently, CS may often represent a challenging diagnostic issue. Methods: We investigated a three-tiered approach (karyotyping, Sanger sequencing, followed by custom gene panel/chromosomal microarray analysis, and exome sequencing), coupled with prioritization of variants based on dysmorphological assessment and description in terms of human phenotype ontology. In addition, we have also performed a statistical analysis of the obtained clinical data using the nonparametric test χ2. Results: We achieved a 43% diagnostic success rate and have demonstrated the complexity of mutations’ type harbored by the patients, which were either chromosomal aberrations, copy number variations, or point mutations. The majority of pathogenic variants were found in the well-known CS genes, however, variants found in genes associated with chromatinopathies or RASopathies are of particular interest. Conclusion: We have critically summarized and then optimised a cost-effective diagnostic algorithm, which may be helpful in a daily diagnostic routine and future clinical research of various CS types. Moreover, we have pinpointed the possible underestimated co-occurrence of CS and intellectual disability, suggesting it may be overlooked when intellectual disability constitutes a primary clinical complaint. On the other hand, in any case of already detected syndromic CS and intellectual disability, the possible occurrence of clinical features suggestive for chromatinopathies or RASopathies should also be considered.
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Affiliation(s)
- Ewelina Bukowska-Olech
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- *Correspondence: Ewelina Bukowska-Olech, ; Aleksander Jamsheer,
| | - Anna Sowińska-Seidler
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Dawid Larysz
- Department of Head and Neck Surgery for Children and Adolescents, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- Prof. St. Popowski Regional Specialized Children's Hospital, Olsztyn, Poland
| | - Paweł Gawliński
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Grzegorz Koczyk
- Centers for Medical Genetics GENESIS, Poznan, Poland
- Biometry and Bioinformatics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
| | | | - Aleksandra Szczepankiewicz
- Molecular and Cell Biology Unit, Department of Paediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Filip Glista
- Poznan University of Medical Sciences, Poznan, Poland
| | - Karolina Matuszewska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
- *Correspondence: Ewelina Bukowska-Olech, ; Aleksander Jamsheer,
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Bukowska-Olech E, Materna-Kiryluk A, Walczak-Sztulpa J, Popiel D, Badura-Stronka M, Koczyk G, Dawidziuk A, Jamsheer A. Targeted Next-Generation Sequencing in the Diagnosis of Facial Dysostoses. Front Genet 2020; 11:580477. [PMID: 33262786 PMCID: PMC7686794 DOI: 10.3389/fgene.2020.580477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
Background Defects in the development of the first and second pharyngeal arches and their derivatives result in abnormal formation of the craniofacial complex, consequently giving rise to facial dysostoses (FDs). FDs represent a group of rare and highly heterogeneous disease entities that encompass mandibulofacial dysostoses (MFDs) with normal extremities and acrofacial dysostoses (AFDs) with limb anomalies in addition to craniofacial defects. Methods We examined 11 families with variable clinical symptoms of FDs, in most of which only one member was affected. We applied two custom gene panels—first comprising 37 genes related to the genetic disorders of craniofacial development such as FDs (On-Demand AmpliSeq Thermo Fisher Scientific gene panel with two primer pools) and second composed of 61 genes and 11 single nucleotide variants (SNVs) known to be involved in the development of skull malformations, mainly in the form of craniosynostoses (SureSelect Agilent Technologies). Targeted next-generation sequencing (NGS) was performed using the Ion Torrent S5 platform. To confirm the presence of each detected variant, we have analyzed a genomic region of interest using Sanger sequencing. Results In this paper, we summarized the results of custom targeted gene panel sequencing in the cohort of sixteen patients from 11 consecutive families affected by distinct forms of FDs. We have found three novel pathogenic variants in the TCOF1 gene—c.2145_2148dupAAAG p.(Ser717Lysfs∗42), c.4370delA p.(Lys1457Argfs∗118), c.83G>C p.(Arg28Pro) causing Treacher Collins syndrome type 1, two novel missense variants in the EFTUD2 gene–c.491A>G p.(Asp164Gly) and c.779T>A p.(Ile260Asn) in two female patients affected by acrofacial dysostosis Guion-Almeida type, one previously reported–c.403C>T (p.Arg135Cys), as well as one novel missense variant–c.128C>T p.(Pro43Leu) in the DHODH gene in the male patient with Miller syndrome and finally one known pathogenic variant c.574G>T p.(Glu192∗) in the SF3B4 gene in the patient with Nager syndrome. Conclusion Our study confirms the efficiency and clinical utility of the targeted gene panel sequencing and shows that this strategy is suitable and efficient in the molecular screening of variable forms of FDs.
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Affiliation(s)
- Ewelina Bukowska-Olech
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland.,Centers for Medical Genetics GENESIS, Poznań, Poland
| | | | | | - Magdalena Badura-Stronka
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland.,Centers for Medical Genetics GENESIS, Poznań, Poland
| | - Grzegorz Koczyk
- Centers for Medical Genetics GENESIS, Poznań, Poland.,Department of Biometry and Bioinformatics, Institute of Plant Genetics Polish Academy of Sciences, Poznań, Poland
| | | | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznań, Poland.,Centers for Medical Genetics GENESIS, Poznań, Poland
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