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Nomakuchi TT, Teferedegn EY, Li D, Muirhead KJ, Dubbs H, Leonard J, Muraresku C, Sergio E, Arnold K, Pizzino A, Skraban CM, Zackai EH, Wang K, Ganetzky RD, Vanderver AL, Ahrens-Nicklas RC, Bhoj EJK. Utility of genome sequencing in exome-negative pediatric patients with neurodevelopmental phenotypes. Am J Med Genet A 2024:e63817. [PMID: 39031459 DOI: 10.1002/ajmg.a.63817] [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: 06/25/2024] [Revised: 07/03/2024] [Accepted: 07/07/2024] [Indexed: 07/22/2024]
Abstract
Exome sequencing (ES) has emerged as an essential tool in the evaluation of neurodevelopmental disorders (NDD) of unknown etiology. Genome sequencing (GS) offers advantages over ES due to improved detection of structural, copy number, repeat number and non-coding variants. However, GS is less commonly utilized due to higher cost and more intense analysis. Here, we present nine cases of pediatric NDD that were molecularly diagnosed with GS between 2017 and 2022, following non-diagnostic ES. All individuals presented with global developmental delay or regression. Other features present in our cohort included epilepsy, white matter abnormalities, brain malformation and dysmorphic features. Two cases were diagnosed on GS due to newly described gene-disease relationship or variant reclassification (MAPK8IP3, CHD3). Additional features missed on ES that were later detected on GS were: intermediate-size deletions in three cases who underwent ES that were not validated for CNV detection, pathogenic variants within the non-protein coding genes SNORD118 and RNU7-1, pathogenic variant within the promoter region of GJB1, and a coding pathogenic variant within BCAP31 which was not sufficiently covered on ES. GS following non-diagnostic ES led to the identification of pathogenic variants in this cohort of nine cases, four of which would not have been identified by reanalysis alone.
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Affiliation(s)
- Tomoki T Nomakuchi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Eden Y Teferedegn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dong Li
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kayla J Muirhead
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Holly Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jacqueline Leonard
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Colleen Muraresku
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Emily Sergio
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kaley Arnold
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Amy Pizzino
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cara M Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kai Wang
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebecca D Ganetzky
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adeline L Vanderver
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth J K Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Sánchez-Gaya V, Rada-Iglesias A. POSTRE: a tool to predict the pathological effects of human structural variants. Nucleic Acids Res 2023; 51:e54. [PMID: 36999617 PMCID: PMC10201441 DOI: 10.1093/nar/gkad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Understanding the pathological impact of non-coding genetic variation is a major challenge in medical genetics. Accumulating evidences indicate that a significant fraction of genetic alterations, including structural variants (SVs), can cause human disease by altering the function of non-coding regulatory elements, such as enhancers. In the case of SVs, described pathomechanisms include changes in enhancer dosage and long-range enhancer-gene communication. However, there is still a clear gap between the need to predict and interpret the medical impact of non-coding variants, and the existence of tools to properly perform these tasks. To reduce this gap, we have developed POSTRE (Prediction Of STRuctural variant Effects), a computational tool to predict the pathogenicity of SVs implicated in a broad range of human congenital disorders. By considering disease-relevant cellular contexts, POSTRE identifies SVs with either coding or long-range pathological consequences with high specificity and sensitivity. Furthermore, POSTRE not only identifies pathogenic SVs, but also predicts the disease-causative genes and the underlying pathological mechanism (e.g, gene deletion, enhancer disconnection, enhancer adoption, etc.). POSTRE is available at https://github.com/vicsanga/Postre.
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Affiliation(s)
- Víctor Sánchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011 Santander, Spain
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011 Santander, Spain
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Kircher M, Ludwig KU. Systematic assays and resources for the functional annotation of non-coding variants. MED GENET-BERLIN 2022; 34:275-286. [PMID: 37034418 PMCID: PMC10081529 DOI: 10.1515/medgen-2022-2161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abstract
Identification of genetic variation in individual genomes is now a routine procedure in human genetic research and diagnostics. For many variants, however, insufficient evidence is available to establish a pathogenic effect, particularly for variants in non-coding regions. Furthermore, the sheer number of candidate variants renders testing in individual assays virtually impossible. While scalable approaches are being developed, the selection of methods and resources and the application of a given framework to a particular disease or trait remain major challenges. This limits the translation of results from both genome-wide association studies and genome sequencing. Here, we discuss computational and experimental approaches available for functional annotation of non-coding variation.
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Affiliation(s)
- Martin Kircher
- Institute of Human Genetics , University of Lübeck , Lübeck , Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin , Berlin , Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University Hospital Bonn , University of Bonn , Venusberg-Campus 1, Building 76 , Bonn , Germany
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