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      Autosomal Recessive Infantile Hyaline Fibromatosis Identified Using Artificial Intelligence-Assisted Rapid Whole Genome Sequencing: A Rare, Multisystemic, Hereditary Disorder

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          Abstract

          Infantile hyaline fibromatosis syndrome (HFS) is an ultra-rare genetic condition characterized by the deposition of hyaline material in the skin, muscle, and viscera. Potential complications include debilitating joint contractures, coarse facial features, recurrent infections, failure to thrive, and death. Here, we present the case of a six-month-old infant with a history of painful extremity contractures, global developmental delay, neck hemangioma, and feeding intolerance presenting to our institution with abdominal distension. The multi-systemic, rapidly progressing, severe nature of her symptoms prompted consultation with inpatient pediatric genetics. Per their recommendation, rapid whole-genome sequencing (rWGS) was done with Fabric GEM®-assisted artificial intelligence (Fabric Genomics, Oakland, California, United States) at Rady Children’s Hospital Institute for Genomic Medicine (San Diego, California, United States), revealing homozygous pathogenic variant c.652T>C; P.Cys218Arg in the ANTXR2 gene consistent with HFS. This case was significant not only for its rarity, but also its early manifestation of symptoms, wide range of affected body systems, and severity of symptoms, which together present a fascinating diagnostic dilemma for future clinicians that should be taken into consideration. It also highlights the increasing utility of AI-assisted rWGS as a diagnostic tool for medically complex patients with unknown multisystemic hereditary conditions. 

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          Most cited references15

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          The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.

          GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It automatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. VarElect's capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. © 2016 by John Wiley & Sons, Inc.
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            Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.

            Phevor integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. Phevor works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant-prioritization tools. It does so by using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant-prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single-exome and family-trio-based diagnostic analyses, the most commonly occurring clinical scenarios and ones for which existing personal genome diagnostic tools are most inaccurate and underpowered. Here, we present a series of benchmark analyses illustrating Phevor's performance characteristics. Also presented are three recent Utah Genome Project case studies in which Phevor was used to identify disease-causing alleles. Collectively, these results show that Phevor improves diagnostic accuracy not only for individuals presenting with established disease phenotypes but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases or known disease-causing alleles. As we demonstrate, Phevor can also use latent information in ontologies to discover genes and disease-causing alleles not previously associated with disease. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
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              Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

              Background Clinical interpretation of genetic variants in the context of the patient’s phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artificial intelligence (AI) holds promise to greatly simplify and speed genome interpretation by integrating predictive methods with the growing knowledge of genetic disease. Here we assess the diagnostic performance of Fabric GEM, a new, AI-based, clinical decision support tool for expediting genome interpretation. Methods We benchmarked GEM in a retrospective cohort of 119 probands, mostly NICU infants, diagnosed with rare genetic diseases, who received whole-genome or whole-exome sequencing (WGS, WES). We replicated our analyses in a separate cohort of 60 cases collected from five academic medical centers. For comparison, we also analyzed these cases with current state-of-the-art variant prioritization tools. Included in the comparisons were trio, duo, and singleton cases. Variants underpinning diagnoses spanned diverse modes of inheritance and types, including structural variants (SVs). Patient phenotypes were extracted from clinical notes by two means: manually and using an automated clinical natural language processing (CNLP) tool. Finally, 14 previously unsolved cases were reanalyzed. Results GEM ranked over 90% of the causal genes among the top or second candidate and prioritized for review a median of 3 candidate genes per case, using either manually curated or CNLP-derived phenotype descriptions. Ranking of trios and duos was unchanged when analyzed as singletons. In 17 of 20 cases with diagnostic SVs, GEM identified the causal SVs as the top candidate and in 19/20 within the top five, irrespective of whether SV calls were provided or inferred ab initio by GEM using its own internal SV detection algorithm. GEM showed similar performance in absence of parental genotypes. Analysis of 14 previously unsolved cases resulted in a novel finding for one case, candidates ultimately not advanced upon manual review for 3 cases, and no new findings for 10 cases. Conclusions GEM enabled diagnostic interpretation inclusive of all variant types through automated nomination of a very short list of candidate genes and disorders for final review and reporting. In combination with deep phenotyping by CNLP, GEM enables substantial automation of genetic disease diagnosis, potentially decreasing cost and expediting case review. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00965-0.
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                Author and article information

                Journal
                Cureus
                Cureus
                2168-8184
                Cureus
                Cureus (Palo Alto (CA) )
                2168-8184
                9 June 2024
                June 2024
                : 16
                : 6
                : e62037
                Affiliations
                [1 ] Pediatrics, Rutgers Cancer Institute of New Jersey, New Brunswick, USA
                [2 ] Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, USA
                [3 ] Clinical Genomics, Rady Children's Hospital, San Diego, USA
                [4 ] Pediatrics, Robert Wood Johnson University Hospital, New Brunswick, USA
                Author notes
                Article
                10.7759/cureus.62037
                11234061
                38989346
                fa70fb2e-096b-4898-b17c-30e2abadcac6
                Copyright © 2024, Ye et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License CC-BY 4.0., which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 6 June 2024
                Categories
                Genetics
                Pediatrics
                Medical Education

                antxr2 gene,fabric gem®,rapid whole-genome sequencing,pediatric gastroenterology,pediatric rheumatology,rare case report,artificial intelligence,genetics,pediatrics

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