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Stenton SL, O'Leary MC, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson MW, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A. Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project. Hum Genomics 2024; 18:44. [PMID: 38685113 PMCID: PMC11057178 DOI: 10.1186/s40246-024-00604-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting. METHODS We utilized genome sequencing (GS) data from families sequenced in the Rare Genomes Project (RGP), a direct-to-participant research study on the utility of GS for rare disease diagnosis and gene discovery. Challenge predictors were provided with a dataset of variant calls and phenotype terms from 175 RGP individuals (65 families), including 35 solved training set families with causal variants specified, and 30 unlabeled test set families (14 solved, 16 unsolved). We tasked teams to identify causal variants in as many families as possible. Predictors submitted variant predictions with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on the rank position of causal variants, and the maximum F-measure, based on precision and recall of causal variants across all EPCR values. RESULTS Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performers recalled causal variants in up to 13 of 14 solved families within the top 5 ranked variants. Newly discovered diagnostic variants were returned to two previously unsolved families following confirmatory RNA sequencing, and two novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant in an unsolved proband with phenotypes consistent with asparagine synthetase deficiency. CONCLUSIONS Model methodology and performance was highly variable. Models weighing call quality, allele frequency, predicted deleteriousness, segregation, and phenotype were effective in identifying causal variants, and models open to phenotype expansion and non-coding variants were able to capture more difficult diagnoses and discover new diagnoses. Overall, computational models can significantly aid variant prioritization. For use in diagnostics, detailed review and conservative assessment of prioritized variants against established criteria is needed.
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Affiliation(s)
- Sarah L Stenton
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Melanie C O'Leary
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace E VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie DiTroia
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay S Ganesh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily O'Heir
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Mangilog
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lynn S Pais
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jillian Serrano
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marwa Abdelhakim
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Azza Althagafi
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computer Science Department, College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Giulia Babbi
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Riccardo Bellazzi
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Maria Giulia Carta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Manavalan Gajapathy
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Thomas Joseph
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Yulan Lu
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Tarun Karthik Kumar Mamidi
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Mulargia
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanna Nicora
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | | | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yisu Peng
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Maurizio S Podda
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
- CTGLab, Institute of Informatics and Telematics (IIT), CNR, ViaMoruzzi 1, 56124, Pisa, Italy
| | - Aditya Rao
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | | | - Vangala G Saipradeep
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Peter Schols
- Invitae, San Francisco, CA, USA
- Codon One, Louvain, EU, Belgium
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA
| | - Naveen Sivadasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | | | - Rajgopal Srinivasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Uma Sunderam
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Naina Tiwari
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Xiao Wang
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth A Worthey
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rujie Yin
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Yuning You
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Daniel Zeiberg
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Constantina Bakolitsa
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
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Staklinski SJ, Scheben A, Siepel A, Kilberg MS. Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification. bioRxiv 2023:2023.10.30.564808. [PMID: 37961642 PMCID: PMC10634951 DOI: 10.1101/2023.10.30.564808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
AlphaMissense is a recently developed method that is designed to classify missense variants into pathogenic, benign, or ambiguous categories across the entire human proteome. Asparagine Synthetase Deficiency (ASNSD) is a developmental disorder associated with severe symptoms, including congenital microcephaly, seizures, and premature death. Diagnosing ASNSD relies on identifying mutations in the asparagine synthetase (ASNS) gene through DNA sequencing and determining whether these variants are pathogenic or benign. Pathogenic ASNS variants are predicted to disrupt the protein's structure and/or function, leading to asparagine depletion within cells and inhibition of cell growth. AlphaMissense offers a promising solution for the rapid classification of ASNS variants established by DNA sequencing and provides a community resource of pathogenicity scores and classifications for newly diagnosed ASNSD patients. Here, we assessed AlphaMissense's utility in ASNSD by benchmarking it against known critical residues in ASNS and evaluating its performance against a list of previously reported ASNSD-associated variants. We also present a pipeline to calculate AlphaMissense scores for any protein in the UniProt database. AlphaMissense accurately attributed a high average pathogenicity score to known critical residues within the two ASNS active sites and the connecting intramolecular tunnel. The program successfully categorized 78.9% of known ASNSD-associated missense variants as pathogenic. The remaining variants were primarily labeled as ambiguous, with a smaller proportion classified as benign. This study underscores the potential role of AlphaMissense in classifying ASNS variants in suspected cases of ASNSD, potentially providing clarity to patients and their families grappling with ongoing diagnostic uncertainty.
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Affiliation(s)
- Stephen J. Staklinski
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Box 100245, Gainesville, FL 326010-0245
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Zhu L, Sun Y, Xu Y, Jin P, Ding H, Dong M. Case report: A compound heterozygous mutations in ASNS broadens the spectrum of asparagine synthetase deficiency in the prenatal diagnosis. Front Pediatr 2023; 11:1273789. [PMID: 37900678 PMCID: PMC10611455 DOI: 10.3389/fped.2023.1273789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Asparagine synthetase deficiency (ASNSD) is a rare congenital disorder characterized by severe progressive microcephaly, global developmental delay, spastic quadriplegia, and refractory seizures. ASNSD is caused by variations of the ASNS gene. The present study showed a Chinese family with a fetus suffering microcephaly. Whole-exome sequencing and Sanger sequencing were used to identify the disease-associated genetic variants. Compound heterozygous variants c.97C>T p. (R33C) and c.1031-2_1033del were identified in the ASNS gene and the variants were inherited from the parents. The mutation site c.97C>T was highly conserved across a wide range of species and predicted to alter the local electrostatic potential. The variant c.1031-2_1033del was classified pathogenic. However, there is no case report of prenatal diagnosis of ASNSD. This is the first description of fetal compound mutations in the ASNS gene leading to ASNSD, which expanded the spectrum of ASNSD.
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Affiliation(s)
- Linyan Zhu
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yixi Sun
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yuqing Xu
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Pengzhen Jin
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Huiqing Ding
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Minyue Dong
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
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4
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Stenton SL, O’Leary M, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O’Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson M, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JO, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O’Donnell-Luria A. Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project. medRxiv 2023:2023.08.02.23293212. [PMID: 37577678 PMCID: PMC10418577 DOI: 10.1101/2023.08.02.23293212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Background A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years, and causal variants are identified in under 50%. The Rare Genomes Project (RGP) is a direct-to-participant research study on the utility of genome sequencing (GS) for diagnosis and gene discovery. Families are consented for sharing of sequence and phenotype data with researchers, allowing development of a Critical Assessment of Genome Interpretation (CAGI) community challenge, placing variant prioritization models head-to-head in a real-life clinical diagnostic setting. Methods Predictors were provided a dataset of phenotype terms and variant calls from GS of 175 RGP individuals (65 families), including 35 solved training set families, with causal variants specified, and 30 test set families (14 solved, 16 unsolved). The challenge tasked teams with identifying the causal variants in as many test set families as possible. Ranked variant predictions were submitted with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on rank position of true positive causal variants and maximum F-measure, based on precision and recall of causal variants across EPCR thresholds. Results Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performing teams recalled the causal variants in up to 13 of 14 solved families by prioritizing high quality variant calls that were rare, predicted deleterious, segregating correctly, and consistent with reported phenotype. In unsolved families, newly discovered diagnostic variants were returned to two families following confirmatory RNA sequencing, and two prioritized novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant, in an unsolved proband with phenotype overlap with asparagine synthetase deficiency. Conclusions By objective assessment of variant predictions, we provide insights into current state-of-the-art algorithms and platforms for genome sequencing analysis for rare disease diagnosis and explore areas for future optimization. Identification of diagnostic variants in unsolved families promotes synergy between researchers with clinical and computational expertise as a means of advancing the field of clinical genome interpretation.
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Affiliation(s)
- Sarah L. Stenton
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Melanie O’Leary
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace E. VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie DiTroia
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay S. Ganesh
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily O’Heir
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Mangilog
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lynn S. Pais
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jillian Serrano
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marwa Abdelhakim
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Azza Althagafi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Department, College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Giulia Babbi
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Riccardo Bellazzi
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Maria Giulia Carta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Manavalan Gajapathy
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Hoehndorf
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Julius O.B. Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Thomas Joseph
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Panagiotis Katsonis
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Olivier Lichtarge
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Yulan Lu
- Center for molecular medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Paolo Magni
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Tarun Karthik Kumar Mamidi
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Mulargia
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | | | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yisu Peng
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Thi Hong Cam Pham
- Anatomy and Surgical Training Department, University of Medicine and Pharmacy, Hue University, Vietnam
| | - Maurizio S. Podda
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Aditya Rao
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | | | - Vangala G Saipradeep
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, USA
| | - Naveen Sivadasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | | | - Rajgopal Srinivasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Uma Sunderam
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Naina Tiwari
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Xiao Wang
- Center for molecular medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Yaqiong Wang
- Center for molecular medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Amanda Williams
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth A. Worthey
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rujie Yin
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Yuning You
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Daniel Zeiberg
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Constantina Bakolitsa
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
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5
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Abstract
Here we report a consanguineous Egyptian family with two siblings presented with congenital microcephaly, early-onset epileptic encephalopathy, feeding difficulties, and early lethality. The condition was initially diagnosed as molybdenum cofactor deficiency as the brain imaging for one of them showed brain edema and intracranial hemorrhage in addition to the hypoplastic corpus callosum, vermis hypoplasia, and small-sized pons. Subsequently, whole exome sequencing identified a novel homozygous missense variant in exon 4 of ASNS gene c.397_398GT > CA (p.Val133Gln) confirming the diagnosis of asparagine synthetase deficiency syndrome. No discernible alternative cause for the intracranial hemorrhage was found. Our patient is the second to show asparagine synthetase deficiency and intracranial hemorrhage, thus confirming the involvement of ASNS gene. As such, it is important to consider asparagine synthetase deficiency syndrome in patients with microcephaly, brain edema, and neonatal intracranial hemorrhage.
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Affiliation(s)
- Ghada M H Abdel-Salam
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Mohamed S Abdel-Hamid
- Human Genetics and Genome Research Division, Medical Molecular Department, National Research Centre, Cairo, Egypt
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6
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Surasiang T, Noree C. Effects of A6E Mutation on Protein Expression and Supramolecular Assembly of Yeast Asparagine Synthetase. Biology (Basel) 2021; 10:biology10040294. [PMID: 33916846 PMCID: PMC8065433 DOI: 10.3390/biology10040294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Certain mutations causing extremely low abundance of asparagine synthetase (the enzyme responsible for producing asparagine, one of the amino acids required for normal growth and development) have been identified in humans with neurological problems and small head and brain size. Currently, yeast is becoming more popular in modeling many human diseases. In this study, we incorporate a mutation, associated with human asparagine synthetase deficiency, into the yeast asparagine synthetase gene to demonstrate that this mutation can also show similar effects as those observed in humans, leading to very low abundance of yeast asparagine synthetase and slower yeast growth rate. This suggests that our yeast system can be alternatively used to initially screen for any drugs that can help rescue the protein levels of asparagine synthetase before applying them to further studies in mammals and humans. Furthermore, this mutation might specifically be introduced into the asparagine synthetase gene of the target cancer cells in order to suppress the overproduction of asparagine synthetase within these abnormal cells, therefore inhibiting the growth of cancer, which might be helpful for patients with blood cancer to prevent them developing any resistance to the conventional asparaginase treatment. Abstract Asparagine synthetase deficiency (ASD) has been found to be caused by certain mutations in the gene encoding human asparagine synthetase (ASNS). Among reported mutations, A6E mutation showed the greatest reduction in ASNS abundance. However, the effect of A6E mutation has not yet been tested with yeast asparagine synthetase (Asn1/2p). Here, we constructed a yeast strain by deleting ASN2 from its genome, introducing the A6E mutation codon to ASN1, along with GFP downstream of ASN1. Our mutant yeast construct showed a noticeable decrease of Asn1p(A6E)-GFP levels as compared to the control yeast expressing Asn1p(WT)-GFP. At the stationary phase, the A6E mutation also markedly lowered the assembly frequency of the enzyme. In contrast to Asn1p(WT)-GFP, Asn1p(A6E)-GFP was insensitive to changes in the intracellular energy levels upon treatment with sodium azide during the log phase or fresh glucose at the stationary phase. Our study has confirmed that the effect of A6E mutation on protein expression levels of asparagine synthetase is common in both unicellular and multicellular eukaryotes, suggesting that yeast could be a model of ASD. Furthermore, A6E mutation could be introduced to the ASNS gene of acute lymphoblastic leukemia patients to inhibit the upregulation of ASNS by cancer cells, reducing the risk of developing resistance to the asparaginase treatment.
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7
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Tabari D, Scholl C, Steffens M, Weickhardt S, Elgner F, Bender D, Herrlein ML, Sabino C, Semkova V, Peitz M, Till A, Brüstle O, Hildt E, Stingl J. Impact of Zika Virus Infection on Human Neural Stem Cell MicroRNA Signatures. Viruses 2020; 12:E1219. [PMID: 33121145 PMCID: PMC7693339 DOI: 10.3390/v12111219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/09/2020] [Accepted: 10/23/2020] [Indexed: 12/11/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne virus, which can cause brain abnormalities in newborns, including microcephaly. MicroRNAs (miRNAs) are small non-coding RNAs, which post- transcriptionally regulate gene expression. They are involved in various processes including neurological development and host responses to viral infection, but their potential role in ZIKV pathogenesis remains poorly understood. MiRNAs can be incorporated into extracellular vesicles (EVs) and mediate cell-to-cell communication. While it is well known that in viral infections EVs carrying miRNAs can play a crucial role in disease pathogenesis, ZIKV effects on EV-delivered miRNAs and their contribution to ZIKV pathogenesis have not been elucidated. In the present study, we profiled intracellular and EV-derived miRNAs by next generation sequencing and analyzed the host mRNA transcriptome of neural stem cells during infection with ZIKV Uganda and French Polynesia strains. We identified numerous miRNAs, including miR-4792, which were dysregulated at the intracellular level and had altered levels in EVs during ZIKV infection. Integrated analyses of differentially expressed genes and miRNAs showed that ZIKV infection had an impact on processes associated with neurodevelopment and oxidative stress. Our results provide insights into the roles of intracellular and EV-associated host miRNAs in ZIKV pathogenesis.
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Affiliation(s)
- Denna Tabari
- Research Division, Federal Institute for Drugs and Medical Devices, 53175 Bonn, Germany; (D.T.); (M.S.); (S.W.)
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices, 53175 Bonn, Germany; (D.T.); (M.S.); (S.W.)
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices, 53175 Bonn, Germany; (D.T.); (M.S.); (S.W.)
| | - Sandra Weickhardt
- Research Division, Federal Institute for Drugs and Medical Devices, 53175 Bonn, Germany; (D.T.); (M.S.); (S.W.)
| | - Fabian Elgner
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany; (F.E.); (D.B.); (M.-L.H.); (C.S.); (E.H.)
| | - Daniela Bender
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany; (F.E.); (D.B.); (M.-L.H.); (C.S.); (E.H.)
| | - Marie-Luise Herrlein
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany; (F.E.); (D.B.); (M.-L.H.); (C.S.); (E.H.)
| | - Catarina Sabino
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany; (F.E.); (D.B.); (M.-L.H.); (C.S.); (E.H.)
| | - Vesselina Semkova
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn Medical Faculty & University Hospital Bonn, 53127 Bonn, Germany; (V.S.); (M.P.); (A.T.); (O.B.)
| | - Michael Peitz
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn Medical Faculty & University Hospital Bonn, 53127 Bonn, Germany; (V.S.); (M.P.); (A.T.); (O.B.)
- Cell Programming Core Facility, Medical Faculty, University of Bonn, 53172 Bonn, Germany
| | - Andreas Till
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn Medical Faculty & University Hospital Bonn, 53127 Bonn, Germany; (V.S.); (M.P.); (A.T.); (O.B.)
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn Medical Faculty & University Hospital Bonn, 53127 Bonn, Germany; (V.S.); (M.P.); (A.T.); (O.B.)
| | - Eberhard Hildt
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany; (F.E.); (D.B.); (M.-L.H.); (C.S.); (E.H.)
| | - Julia Stingl
- Department of Clinical Pharmacology, University Hospital, RWTH Aachen University, 52074 Aachen, Germany;
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8
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Abstract
RATIONALE Asparagine synthetase deficiency (ASNSD) refers to a congenital metabolic abnormality caused by mutation in the asparagine synthetase (ASNS) gene encoded by chromosome 7q21. Herein, we report the first case of ASNSD in China, in which novel ASNS mutations were identified. PATIENT CONCERNS A 6-month-old boy presented with a 4-month history of microcephaly and psychomotor developmental retardation and a 2-month history of epilepsy. Four months after birth, magnetic resonance imaging demonstrated a giant cyst in the right lateral ventricle, and a ventriculoperitoneal shunt was placed. Video electroencephalography showed a hypsarrhythmia pattern with a string of tonic-clonic and myoclonic seizures. On admission, physical examination showed microcephaly. Neurologic examination showed a decreased tension in the trunk muscles and an increased tension in the extremity muscles; tendon hyperreflexia was noted, and bilateral pathologic reflexes were positive. DIAGNOSIS A diagnosed of congenital microcephaly was made. Whole-exome sequencing revealed a heterozygous deletion mutation c.666_667delCT (p.L2221Lfs*5) in exon 6 of the ASNS gene and a heterozygous missense mutation c.1424C>T (p.T457I) in exon 13 of the ASNS gene. INTERVENTIONS After admission, intravenous adrenocorticotropic hormone and oral topiramate was administrated for 4 weeks, while the seizures persisted. Then, levetiracetam and clonazepam were added. OUTCOMES After the follow-up period of 18 months, video electroencephalography showed that complex episodes disappeared with changes in multiple focal spike and sharp waves; 1 focal attack arising from the left occipital region and 2 focal attacks arising from the right middle temporal and the right occipital region were recorded. LESSONS This is the first case of ASNSD in China. We identified 2 novel mutations (c.666_667delCT and c.1424C>T) in the ASNS gene, which expands the ASNS gene mutation profile and will be beneficial for genetic diagnosis.
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Affiliation(s)
| | | | | | - Xuncan Liu
- Department of Rehabilitation, The First Hospital of Jilin University, Changchun, Jilin, China
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9
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Wang C, He G, Ge Y, Li R, Li Z, Lin Y. A novel compound heterozygous missense mutation in ASNS broadens the spectrum of asparagine synthetase deficiency. Mol Genet Genomic Med 2020; 8:e1235. [PMID: 32255274 PMCID: PMC7284041 DOI: 10.1002/mgg3.1235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/22/2020] [Accepted: 03/02/2020] [Indexed: 02/02/2023] Open
Abstract
Background Asparagine synthetase deficiency (ASNSD) is a rare pediatric congenital disorder that clinically manifests into severe progressive microcephaly, global developmental delay, spastic quadriplegia, and refractory seizures. ASNSD is caused by inheritable autosomal recessive mutations in the asparagine synthetase (ASNS) gene. Methods We performed whole‐exome sequencing using the patient's peripheral blood, and newly discovered mutations were subsequently verified in the patient's parents via Sanger sequencing. Software‐based bioinformatics analyses (protein sequence conservation analysis, prediction of protein phosphorylation sites, protein structure modeling, and protein stability prediction) were performed to investigate and deduce their downstream effects. Results In this article, we summarized all the previously reported cases of ASNSD and that of a Chinese girl who was clinically diagnosed with ASNSD, which was later confirmed via genetic testing. Whole‐exome sequencing revealed two compound heterozygous missense mutations within the ASNS (c.368T > C, p.F123S and c.1649G > A, p.R550H). The origin of the two mutations was also verified in the patient's parents via Sanger sequencing. The mutation c.368T > C (p.F123S) was discovered and confirmed to be novel and previously unreported. Using software‐based bioinformatics analyses, we deduced that the two mutation sites are highly conserved across a wide range of species, with the ability to alter different phosphorylation sites and destabilize the ASNS protein structure. The newly identified p.F123S mutation was predicted to be the most significantly destabilizing and detrimental mutation to the ASNS protein structure, compared to all other previously reported mutations. Conclusion Evidently, the presence of these compound heterozygous mutations could lead to severe clinical phenotypes and serve as a potential indicator for considerably higher risk with less optimistic prognosis in ASNSD patients.
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Affiliation(s)
- Chun Wang
- Department of NeurologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | - Guiyuan He
- Center for Reproductive and Genetic MedicineDalian Municipal Women and Children’s Medical CenterDalianChina
| | - Yusong Ge
- Department of NeurologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | - Runjie Li
- Department of RehabilitationDalian Municipal Women and Children’s Medical CenterDalianChina
| | - Zhenguo Li
- Clinical LaboratoryThe Second Hospital of Dalian Medical UniversityDalianChina
| | - Yongzhong Lin
- Department of NeurologyThe Second Hospital of Dalian Medical UniversityDalianChina
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10
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Schleinitz D, Kovacs P, Hirrlinger J. Letter to the Editor Regarding “Cyst-Peritoneal Shunt for the Treatment of a Progressive Intracerebral Cyst Associated with ASNS Mutation: Case Report and Literature Review”. World Neurosurg 2019; 130:564-566. [DOI: 10.1016/j.wneu.2019.05.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 11/30/2022]
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11
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Sprute R, Ardicli D, Oguz KK, Malenica-Mandel A, Daimagüler HS, Koy A, Coskun T, Wang H, Topcu M, Cirak S. Clinical outcomes of two patients with a novel pathogenic variant in ASNS: response to asparagine supplementation and review of the literature. Hum Genome Var 2019; 6:24. [PMID: 31123592 PMCID: PMC6531480 DOI: 10.1038/s41439-019-0055-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 11/09/2022] Open
Abstract
Asparagine synthetase deficiency (ASNSD, OMIM #615574) is a rare autosomal recessive neurometabolic inborn error that leads to severe cognitive impairment. It manifests with microcephaly, intractable seizures, and progressive cerebral atrophy. Currently, there is no established treatment for this condition. In our pediatric cohort, we discovered, by whole-exome sequencing in two siblings from Turkey, a novel homozygous missense mutation in asparagine synthetase at NM_133436.3 (ASNS_v001): c.1108C>T that results in an amino acid exchange p.(Leu370Phe), in the C-terminal domain. After identification of the metabolic defect, treatment with oral asparagine supplementation was attempted in both patients for 24 months. Asparagine supplementation was well tolerated, and no further disease progression was observed during treatment. One of our patients showed mild developmental progress with increased levels of attention and improved nonverbal communication. These results support our hypothesis that asparagine supplementation should be further investigated as a treatment option for ASNSD. We further reviewed all previously reported ASNSD cases with regard for their clinical phenotypes and brain imaging findings to provide an essential knowledge base for rapid diagnosis and future clinical studies.
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Affiliation(s)
- Rosanne Sprute
- 1Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, 50931 Cologne, Germany.,2Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Didem Ardicli
- 3Department of Pediatric Neurology, Hacettepe University, 06100 Ankara, Turkey
| | - Kader Karli Oguz
- 4Department of Radiology, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Malenica-Mandel
- 1Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, 50931 Cologne, Germany.,2Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Hülya-Sevcan Daimagüler
- 1Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, 50931 Cologne, Germany.,2Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Anne Koy
- 1Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, 50931 Cologne, Germany
| | - Turgay Coskun
- 5Department of Pediatric Metabolism Unit, Hacettepe University, 06100 Ankara, Turkey
| | - Haicui Wang
- 1Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, 50931 Cologne, Germany.,2Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Meral Topcu
- 3Department of Pediatric Neurology, Hacettepe University, 06100 Ankara, Turkey
| | - Sebahattin Cirak
- 1Faculty of Medicine and University Hospital Cologne, Department of Pediatrics, University of Cologne, 50931 Cologne, Germany.,2Faculty of Medicine and the Faculty of Mathematics and Natural Sciences, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
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12
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Radha Rama Devi A, Naushad SM. Molecular diagnosis of asparagine synthetase (ASNS) deficiency in two Indian families and literature review of 29 ASNS deficient cases. Gene 2019; 704:97-102. [PMID: 30978478 DOI: 10.1016/j.gene.2019.04.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 11/27/2022]
Abstract
In the current study, we report three cases of Asparagine Synthetase (ASNS) Deficiency from two consanguineous families. Family 1 had two early neonatal deaths due to a novel mutation in the ASNS gene c.788C > T (p.S263F) and both the children presented with microcephaly and one of them had severe intracranial haemorrhage. The proband from the second family was homozygous for c.146G > A (p.R49Q) and manifested myoclonic seizures, developmental delay, coarse hair and diffuse cortical atrophy. Molecular docking studies of both the mutations revealed alteration in the ligand binding site. Till date, 26 mutations were reported in ASNS gene in 29 affected children indicating high degree of genetic heterogeneity and high mortality. Although asparagine depletion is not of diagnostic utility, multiple linear regression model suggested that asparagine levels vary to the extent of 20.6% based on glutamine and aspartate levels and ASNS deficiency results in depletion of asparagine synthesis. ASNS deficiency should be suspected in any neonate with microcephaly and epileptic encephalopathy.
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Affiliation(s)
- Akella Radha Rama Devi
- Rainbow Children's Hospital, Banjara Hills, Road No. 2, Hyderabad, India; Sandor Speciality Diagnostics Pvt Ltd, Banjara Hills, Road No.3, Hyderabad, India.
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