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Pérez EM, Torbay AG, López MS, de la Cámara RCM, Jiménez CR, Álvarez MÁM, Blanco JN, Gianelli C, Hijón CC, Granados EL, Pena RR, Del Pozo Mate Á, García-Morato MB. Genetics of inborn errors of immunity: Diagnostic strategies and new approaches to CNV detection. Eur J Clin Invest 2024; 54:e14191. [PMID: 38440843 DOI: 10.1111/eci.14191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Genetic diagnosis of inborn errors of immunity (IEI) is complex due to the large number of genes involved and their molecular features. Missense variants have been reported as the most common cause of IEI. However, the frequency of copy number variants (CNVs) may be underestimated since their detection requires specific quantitative techniques. At this point, the use of Next Generation Sequencing (NGS) is acquiring relevance. METHODS In this article, we present our experience in the genetic diagnosis of IEI based on three diagnostic algorithms that allowed the detection of single nucleotide variants (SNVs) and CNVs. Following this approximation, 703 index cases were evaluated between 2014 and 2021. Sanger sequencing, MLPA, CGH array, breakpoint spanning PCR or a customized NGS-based multigene-targeted panel were performed. RESULTS A genetic diagnosis was reached in 142 of the 703 index cases (20%), 19 of them presented deletions as causal variants. Deletions were also detected in 5 affected relatives and 16 healthy carriers during the family studies. Additionally, we compile, characterize and present all the CNVs detected by our diagnostic algorithms, representing the largest cohort of deletions related to IEI to date. Furthermore, three bioinformatic tools (LACONv, XHMM, VarSeq™) based on NGS data were evaluated. VarSeq™ was the most sensitive and specific bioinformatic tool; detecting 21/23 (91%) deletions located in captured regions. CONCLUSION Based on our results, we propose a strategy to guide the molecular diagnosis that can be followed by expert and non-expert centres in the field of IEI.
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Affiliation(s)
| | | | - Mario Solis López
- Bioinformatics Section, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, La Paz University Hospital, UAM, Madrid, Spain
| | | | - Carmen Rodríguez Jiménez
- Metabolic Disease Section, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, La Paz University Hospital, Madrid, Spain
- Group of Dislipemias of genetic origin and metabolic diseases, IdiPAZ, La Paz University Hospital, Madrid, Spain
| | - Mari Ángeles Mori Álvarez
- Functional and Structural Genomics Section, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, La Paz University Hospital, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Julián Nevado Blanco
- Functional and Structural Genomics Section, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, La Paz University Hospital, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Carla Gianelli
- Immunology Department, La Paz University Hospital, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain
- La Paz Institute of Biomedical Research, Madrid, Spain
| | | | - Eduardo López Granados
- Immunology Department, La Paz University Hospital, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain
- La Paz Institute of Biomedical Research, Madrid, Spain
| | - Rebeca Rodríguez Pena
- Immunology Department, La Paz University Hospital, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain
- La Paz Institute of Biomedical Research, Madrid, Spain
| | - Ángela Del Pozo Mate
- Bioinformatics Section, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, La Paz University Hospital, UAM, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Madrid, Spain
- ERN-ITHACA, La Paz University Hospital, Madrid, Spain
| | - María Bravo García-Morato
- Immunology Department, La Paz University Hospital, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain
- La Paz Institute of Biomedical Research, Madrid, Spain
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Chen M, Tan MH, Liu J, Yang YM, Yu JL, He LJ, Huang YZ, Sun YX, Qian YQ, Yan K, Dong MY. An efficient molecular genetic testing strategy for incontinentia pigmenti based on single-tube long fragment read sequencing. NPJ Genom Med 2024; 9:32. [PMID: 38811629 PMCID: PMC11137062 DOI: 10.1038/s41525-024-00421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/18/2024] [Indexed: 05/31/2024] Open
Abstract
Incontinentia pigmenti (IP) is a rare X-linked dominant neuroectodermal dysplasia that primarily affects females. The only known causative gene is IKBKG, and the most common genetic cause is the recurrent IKBKG△4-10 deletion resulting from recombination between two MER67B repeats. Detection of variants in IKBKG is challenging due to the presence of a highly homologous non-pathogenic pseudogene IKBKGP1. In this study, we successfully identified four pathogenic variants in four IP patients using a strategy based on single-tube long fragment read (stLFR) sequencing with a specialized analysis pipeline. Three frameshift variants (c.519-3_519dupCAGG, c.1167dupC, and c.700dupT) were identified and subsequently validated by Sanger sequencing. Notably, c.519-3_519dupCAGG was found in both IKBKG and IKBKGP1, whereas the other two variants were only detected in the functional gene. The IKBKG△4-10 deletion was identified and confirmed in one patient. These results demonstrate that the proposed strategy can identify potential pathogenic variants and distinguish whether they are derived from IKBKG or its pseudogene. Thus, this strategy can be an efficient genetic testing method for IKBKG. By providing a comprehensive understanding of the whole genome, it may also enable the exploration of other genes potentially associated with IP. Furthermore, the strategy may also provide insights into other diseases with detection challenges due to pseudogenes.
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Affiliation(s)
- Min Chen
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Mei-Hua Tan
- BGI Genomics, Shenzhen, Guangdong, 518083, P. R. China
| | - Jiao Liu
- Lishui Maternity and Child Health Care Hospital, Lishui, Zhejiang, 323000, P. R. China
| | - Yan-Mei Yang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Jia-Ling Yu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Li-Juan He
- BGI Genomics, Shenzhen, Guangdong, 518083, P. R. China
| | - Ying-Zhi Huang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Yi-Xi Sun
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Ye-Qing Qian
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Kai Yan
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Min-Yue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China.
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China.
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China.
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Herlin LK, Sørensen SB, Graakjaer JA, Andersen S, Schmidt SAJ, Sommerlund M, Mogensen TH. NF-κB Activation and X-Inactivation in Females with Incontinentia Pigmenti and Recurrent Infections. J Clin Immunol 2024; 44:136. [PMID: 38795145 DOI: 10.1007/s10875-024-01737-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/16/2024] [Indexed: 05/27/2024]
Affiliation(s)
- Laura Krogh Herlin
- Department of Dermatology, Aarhus University Hospital, Palle Juul Jensens Boulevard 67, Aarhus N, 8200, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | | | | | - Sisse Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Sigrun Alba Johannesdottir Schmidt
- Department of Dermatology, Aarhus University Hospital, Palle Juul Jensens Boulevard 67, Aarhus N, 8200, Denmark
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Mette Sommerlund
- Department of Dermatology, Aarhus University Hospital, Palle Juul Jensens Boulevard 67, Aarhus N, 8200, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
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How KN, Leong HJY, Pramono ZAD, Leong KF, Lai ZW, Yap WH. Uncovering incontinentia pigmenti: From DNA sequence to pathophysiology. Front Pediatr 2022; 10:900606. [PMID: 36147820 PMCID: PMC9485571 DOI: 10.3389/fped.2022.900606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Incontinentia pigmenti (IP) is an X-linked dominant genodermatosis. The disease is known to be caused by recurrent deletion of exons 4-10 of the Inhibitor Of Nuclear Factor Kappa B Kinase Regulatory Subunit Gamma (IKBKG) gene located at the Xq28 chromosomal region, which encodes for NEMO/IKKgamma, a regulatory protein involved in the nuclear factor kappa B (NF-κB) signaling pathway. NF-κB plays a prominent role in the modulation of cellular proliferation, apoptosis, and inflammation. IKBKG mutation that results in a loss-of-function or dysregulated NF-κB pathway contributes to the pathophysiology of IP. Aside from typical skin characteristics such as blistering rash and wart-like skin growth presented in IP patients, other clinical manifestations like central nervous system (CNS) and ocular anomalies have also been detected. To date, the clinical genotype-phenotype correlation remains unclear due to its highly variable phenotypic expressivity. Thus, genetic findings remain an essential tool in diagnosing IP, and understanding its genetic profile allows a greater possibility for personalized treatment. IP is slowly and gradually gaining attention in research, but there is much that remains to be understood. This review highlights the progress that has been made in IP including the different types of mutations detected in various populations, current diagnostic strategies, IKBKG pathophysiology, genotype-phenotype correlation, and treatment strategies, which provide insights into understanding this rare mendelian disorder.
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Affiliation(s)
- Kang Nien How
- Dermatology Unit, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Dermatology Unit, Hospital Pengajar Universiti Putra Malaysia, Serdang, Malaysia
| | | | | | - Kin Fon Leong
- Paediatric Dermatology Unit, Department of Paediatrics, Women and Children Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Zee Wei Lai
- School of Biosciences, Taylor's University, Subang Jaya, Malaysia
- Centre for Drug Discovery and Molecular Pharmacology, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Malaysia
| | - Wei Hsum Yap
- School of Biosciences, Taylor's University, Subang Jaya, Malaysia
- Centre for Drug Discovery and Molecular Pharmacology, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Malaysia
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5
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Jiang J, Zeng J, He Q, Yang J, Wang S, Zhang Z. NEMO Gene Mutations in Two Chinese Females with Incontinentia Pigmenti. Clin Cosmet Investig Dermatol 2022; 15:815-821. [PMID: 35547601 PMCID: PMC9084220 DOI: 10.2147/ccid.s363683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022]
Abstract
Purpose To identify the mutations of the NEMO gene in two Chinese females with incontinentia pigmenti. Patients and Methods Patients were both from Nanchong, Sichuan Province. Genomic DNA was extracted from the peripheral blood of patients and patient 1ʹs father. The mutations of the NEMO gene in patient 1 by GAP polymerase chain reaction and Sanger sequencing and her father were detected. NEMO-specific polymerase chain reaction and Sanger sequencing were used to identify the NEMO gene mutation in patient 2. Results DNA analysis identified a rare frameshift mutation, c.723_c.724insCAGG(p.A242QfsX15) in exon 5 of the NEMO gene in patient 1 with a family history but not in her healthy father. The common deletion of exons 4–10 of the NEMO gene was found in sporadic patient 2. Conclusion Our data revealed that the rare frameshift mutation, c.723_c.724insCAGG(p.A242QfsX15) in exon 5 of the NEMO gene in patient 1 and the deletion of exons 4–10 of the NEMO gene in patient 2 could cause the occurrence of IP. Genetic testing is helpful for early diagnosis and genetic counseling for families.
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Affiliation(s)
- Jingjing Jiang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
| | - Junjie Zeng
- Department of Dermatology, Taikang Sichuan Southwest Hospital Company Limited, Chengdu, Sichuan Province, People's Republic of China
| | - Qi He
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
| | - Jiao Yang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
| | - Shenglan Wang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
| | - Zhengzhong Zhang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
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6
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Human Genetic Diseases Linked to the Absence of NEMO: An Obligatory Somatic Mosaic Disorder in Male. Int J Mol Sci 2022; 23:ijms23031179. [PMID: 35163099 PMCID: PMC8835834 DOI: 10.3390/ijms23031179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/22/2023] Open
Abstract
De novo somatic mutations are well documented in diseases such as neoplasia but are rarely reported in rare diseases. Hovewer, severe genetic diseases that are not compatible with embryonic development are caused exclusively by deleterious mutations that could only be found as mosaic and not as inherited mutations. We will review here the paradigmatic case of Incontinentia Pigmenti, a rare X-linked dominant disease caused by deficiency of the NEMO (also called IKKgamma) protein, which plays a pivotal role in tissue homeostasis. The loss-of-function mutations of NEMO are embryonically lethal in males while females survive because of unbalanced X-inactivation due to NEMO wild type (WT) expressing cells survival despite of NEMO mutant expressing cells. The few surviving IP males are obligatory mosaic mutants with the typical clinical presentation of IP in female. Indeed, the IP pathogenesis in the female and most likely also in the male somatic mosaics is based on the cellular effects of an impaired NEMO activity, but in the context of the interaction of genetically different cells in the affected tissue, which might underline the inflammatory status.
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Shibata K, Kunisada M, Miyai S, Kawamori S, Kurahashi H, Nishigori C. Incontinentia pigmenti in a female infant with somatic mosaicism due to the IKBKG variant. J Dermatol 2021; 48:e577-e578. [PMID: 34480359 DOI: 10.1111/1346-8138.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/11/2021] [Accepted: 08/19/2021] [Indexed: 01/18/2023]
Affiliation(s)
- Keiko Shibata
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Makoto Kunisada
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Shunsuke Miyai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Shigeki Kawamori
- Division of Pediatrics, Hyogo Prefectural Nishinomiya Hospital, Nishinomiya, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, Kobe, Japan
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Samara A, Gusman M, Aker L, Parsons MS, Mian AY, Eldaya RW. The Forgotten Phacomatoses: A Neuroimaging Review of Rare Neurocutaneous Disorders. Curr Probl Diagn Radiol 2021; 51:747-758. [PMID: 34607749 DOI: 10.1067/j.cpradiol.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/07/2021] [Accepted: 07/18/2021] [Indexed: 01/05/2023]
Abstract
Phakomatoses, or neurocutaneous syndromes, are a heterogeneous group of rare genetic disorders that predominantly affect structures arising from the embryonic ectoderm, namely the skin, eye globe, retina, tooth enamel, and central nervous system. Other organs are also involved in some syndromes, mainly cardiovascular, pulmonary, renal, and musculoskeletal systems. Currently, more than sixty distinct entities belonging to this category have been described in the literature. Common phakomatoses include conditions like Neurofibromatosis and Tuberous sclerosis. Several review papers have focused on various aspects of these common conditions, including clinical presentation, genetic and molecular basis, and neuroimaging features. In this review, we focus on rare neurocutaneous syndromes: Melanophakomatoses (Ie, Neurocutaneous Melanosis, and Incontinentia Pigmenti), Vascular Phakomatoses (Ie, Ataxia Telangiectasia and PHACE Syndrome), and other conditions such as Cowden Syndrome, Basal Nevus Syndrome, Schwannomatosis, Progressive Facial Hemiatrophy, Gomez-Lopez-Hernandez Syndrome, Wyburn-Mason Syndrome, CHILD Syndrome, and Proteus Syndrome. We also review the neuroradiologic manifestations of these conditions as a guide for neurologists and neuroradiologists in their daily practice.
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Affiliation(s)
- Amjad Samara
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO..
| | - Mariya Gusman
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO
| | - Loai Aker
- Department of Radiology, Hamad General Hospital, Doha, Qatar
| | - Matthew S Parsons
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO
| | - Ali Y Mian
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO
| | - Rami W Eldaya
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO
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