{
  "id": "AIBD-0048",
  "title": "Fabric GEM AI ranked the causal ANTXR2 variant, diagnosing infantile hyaline fibromatosis in a six-month-old",
  "summary": "AI-assisted rapid genome sequencing scored a homozygous ANTXR2 variant at 4.7, diagnosing an infant within five days and changing her care plan.",
  "date_observed": "2023-01-10",
  "date_basis": "unassessed",
  "date_precision": "unassessed",
  "benefit_status": null,
  "source_collection": null,
  "source_entry": null,
  "account": "The report's abstract describes a six-month-old infant with a history of painful extremity contractures. Its case presentation opens with a four-month-old girl referred to the pediatric emergency department at Robert Wood Johnson University Hospital. She was referred for failure to thrive with abdominal distension and global developmental delay. The paper dates her abnormal neurological development to two months of age. It included bilateral upper-extremity hypotonia, a weak palmar grasp, pain with all passive and active extremity movement and bilateral contractures. A bleeding, ulcerated infantile hemangioma in the center of the neck was managed from three months of age. The diminishing appetite and abdominal distension were noted at four months. Rapid whole-genome sequencing at Rady Children's Institute for Genomic Medicine used the Fabric GEM artificial-intelligence analysis tool with Phevor re-ranking. The sample was shipped on 5 January 2023 and preliminary results were returned on 10 January 2023. GEM scored a homozygous ANTXR2 variant, c.652T>C (p.Cys218Arg), at 4.7. That gave a diagnosis of infantile hyaline fibromatosis syndrome. A multidisciplinary meeting held the same day conveyed the implications, coordinated gastrostomy tube placement and discussed long-term goals. Treating clinicians reported the case in Cureus on 9 June 2024.",
  "category": "benefit created",
  "unexpected": false,
  "purpose": "Rank candidate variants from rapid whole-genome sequencing against the patient's phenotype so that clinicians can reach a molecular diagnosis quickly.",
  "system": "Fabric GEM artificial-intelligence variant interpretation tool with Phevor phenotype-driven re-ranking",
  "model_version": null,
  "developer": "Fabric Genomics, Oakland, California",
  "deployer": "Rady Children's Institute for Genomic Medicine and Robert Wood Johnson University Hospital",
  "location": "New Brunswick, New Jersey, United States",
  "domain": "Clinical genomics / rare disease diagnosis",
  "segment": "Critically ill infant undergoing rapid whole-genome sequencing",
  "benefit_type": "Improved Physical Health",
  "taxonomy_note": null,
  "registry_ids": {},
  "ratings": [
    {
      "group": "personal",
      "depth": 3,
      "reason": "An identifiable infant received a definitive molecular diagnosis of a disorder the authors describe as frequently causing early death before age two. This triggered a same-day multidisciplinary meeting that conveyed the implications, coordinated gastrostomy tube placement and discussed long-term goals. The authors add that extensive genetic counseling is essential for parents desiring future children, given a 25% risk for the offspring of carrier parents. They do not report that counseling was delivered."
    },
    {
      "group": "organizational",
      "depth": 1,
      "reason": "A single case in which preliminary results returned five days after the sample shipped, on 5 January 2023, with results on 10 January 2023. Genomic panels and a microarray sent from the institution were still pending and anticipated to take longer than one month. The report does not say what became of those tests."
    }
  ],
  "ai_role": {
    "status": "assessed",
    "statement": "GEM scored and surfaced the homozygous ANTXR2 variant at 4.7. The paper says Bayes factor scores greater than 2 are considered strong support. Phevor also identified the variant but scored it 1. That is below the Phevor score of 5 or above that the paper treats as further guidance on what to prioritize. The clinicians then confirmed and interpreted the finding and made the diagnosis. The report is written by the treating clinicians and a Rady clinical genomics scientist, not by the tool's vendor."
  },
  "evidence": [
    {
      "kind": "case report",
      "citation": "Ye GX, Ontiveros E, Ivander A, Velinov M, Simotas C (2024). Autosomal Recessive Infantile Hyaline Fibromatosis Identified Using Artificial Intelligence-Assisted Rapid Whole Genome Sequencing. Cureus.",
      "title": "Autosomal Recessive Infantile Hyaline Fibromatosis Identified Using AI-Assisted Rapid Whole Genome Sequencing",
      "url": "https://europepmc.org/article/PMC/PMC11234061",
      "date": "2024-06-09",
      "written_by": "deployer",
      "quote": "Variants with a GEM score ≥ 0 were reviewed for this proband leading to the identification of a homozygous c.652T>C (p.Cys218Arg) variant in the ANTXR2 gene"
    },
    {
      "kind": "peer-reviewed study",
      "citation": "Owen MJ, Kingsmore SF, et al. (2022). An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun. Led from Rady Children's Institute for Genomic Medicine, with Fabric Genomics and Illumina staff among the co-authors.",
      "title": "An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9325884/",
      "date": "2022-07-26",
      "written_by": "makers",
      "quote": "The average rank of the correct diagnosis was 1, 2 and 1 for MOON, GEM and TSS, respectively"
    }
  ],
  "replication": {
    "produced_by": [
      "Rapid whole-genome sequencing of a critically ill infant",
      "Structured phenotype terms entered for the patient",
      "AI ranking of candidate variants reviewed and confirmed by clinicians"
    ],
    "must_hold": [
      "Rapid whole-genome sequencing of the proband",
      "Structured phenotype terms entered for the patient",
      "Clinician review and confirmation of the ranked variant"
    ],
    "echoes": [
      {
        "date": "2022-07-26",
        "setting": "Rady Children's automated 13.5-hour diagnosis system, four retrospective infant cases",
        "model_version": "GEM (Fabric Genomics)",
        "outcome": "recurred",
        "source": "Owen MJ, et al. Nat Commun 2022. https://pmc.ncbi.nlm.nih.gov/articles/PMC9325884/"
      }
    ]
  },
  "paired_incident": {
    "database": "AI Incident Database",
    "identifier": "123",
    "title": "Epic Systems’s Sepsis Prediction Algorithms Revealed to Have High Error Rates on Seriously Ill Patients",
    "url": "https://incidentdatabase.ai/cite/123",
    "severity": null,
    "group": "personal",
    "basis": "Both are hospital decision-support systems meant to flag a life-threatening condition in a critically ill patient; Epic's false negatives and false positives left seriously ill inpatients unrecognised by their clinicians."
  },
  "headline": "Fabric GEM flags ANTXR2 and diagnoses an infant in five days",
  "metric": "scored a homozygous ANTXR2 variant at 4.7, diagnosing an infant within five days",
  "comparator": {
    "against": "chromosomal microarray and targeted gene panels",
    "before": "one to two weeks for much more limited results from chromosomal microarray and four to six weeks for targeted gene panels",
    "after": "less than five days",
    "basis": "assumed",
    "quote": "Using a combination of next-generation sequencing and these novel artificial intelligence methods, Rady has been able to lower the total turnaround time for commercial rWGS to less than five days, compared to one to two weeks for much more limited results from chromosomal microarray and four to six weeks for targeted gene panels",
    "url": "https://europepmc.org/article/PMC/PMC11234061"
  },
  "later": {
    "status": "unknown",
    "date": null,
    "note": "No later development found.",
    "quote": null,
    "url": null
  },
  "value": null,
  "developer_country": "United States",
  "deployer_country": "United States",
  "unrated_because": null,
  "brief_notes": null,
  "brief": null,
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    {
      "date": "2026-10-20",
      "change": "Record drafted from the cited sources.",
      "source": null,
      "editor": "AIBD"
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    {
      "date": "2026-10-20",
      "change": "Paired with AI Incident Database incident 123 (medium confidence); severity not given by the source.",
      "source": "https://incidentdatabase.ai/cite/123",
      "editor": "AIBD"
    },
    {
      "date": "2026-10-20",
      "change": "Dropped the claim that the diagnosis ended further investigation at the treating hospital, restated the GEM and Phevor thresholds as the paper gives them (greater than 2, and 5 or above), dated the presenting findings as the paper dates them, recast the 25% recurrence risk as the authors' recommendation that counseling is essential rather than counseling delivered, and marked the 13.5-hour Nature Communications paper as not vendor-authored, because each of those statements went further than the sources do.",
      "source": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11234061/ ; https://pmc.ncbi.nlm.nih.gov/articles/PMC9325884/",
      "editor": "AIBD"
    },
    {
      "date": "2026-10-21",
      "change": "Added what the benefit is measured against from the cited sources.",
      "source": "https://europepmc.org/article/PMC/PMC11234061",
      "editor": "AIBD"
    },
    {
      "date": "2026-10-21",
      "change": "Benefit type set to Improved Physical Health under Trustible's full taxonomy of 23 types; it was Improved Knowledge Discovery among the six first used.",
      "source": "https://trustible.ai/post/a-framework-for-measuring-the-benefits-of-ai/",
      "editor": "AIBD"
    },
    {
      "date": "2026-10-21",
      "change": "Country of the developer and the deployer added from the organization's own site or a registry.",
      "source": "https://fabricgenomics.com/privacy-policy/; https://radygenomics.org/contact-us/",
      "editor": "AIBD"
    },
    {
      "date": "2026-10-21",
      "change": "Prose pass: a rating reason, account, the system's part rewritten in shorter sentences with abbreviations expanded; facts, figures and quotations unchanged.",
      "source": null,
      "editor": "AIBD"
    },
    {
      "date": "2026-10-25",
      "change": "Clarified the displayed field answers and placed measurements and limitations in their respective fields.",
      "source": null,
      "editor": "AIBD"
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  ],
  "confidence": "claimed",
  "shade": "low",
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      "evaluations[].exposure": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial",
        "family": "evaluations"
      },
      "evaluations[].id": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial",
        "family": "evaluations"
      },
      "evaluations[].measurement_method": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial",
        "family": "evaluations",
        "display": {
          "answer": "The researchers recorded the GEM score, the interval between sample shipment and preliminary results, and the resulting changes to care."
        }
      },
      "evaluations[].metric": {
        "state": "not_assessed",
        "provenance": {
          "kind": "legacy_record",
          "basis": "Mapped from the existing case description without a new external source review.",
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            "metric"
          ],
          "source_refs": []
        },
        "review_state": "not_assessed",
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        "family": "evaluations",
        "display": {
          "answer": "The GEM score and the time from sample shipment to preliminary results."
        }
      },
      "evaluations[].reproduction_materials": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial",
        "family": "evaluations"
      },
      "evaluations[].setting_sample": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial",
        "family": "evaluations"
      },
      "evaluations[].uncertainty_limitations": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial",
        "family": "evaluations",
        "display": {
          "answer": "The clinicians did not report the eventual results of the slower genetic tests or whether the parents received genetic counseling. The report documents a diagnosis and care decisions, without establishing longer survival."
        }
      },
      "external_references[]": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "paired_incident": {
              "database": "AI Incident Database",
              "identifier": "123",
              "title": "Epic Systems’s Sepsis Prediction Algorithms Revealed to Have High Error Rates on Seriously Ill Patients",
              "url": "https://incidentdatabase.ai/cite/123",
              "group": "personal",
              "basis": "Both are hospital decision-support systems meant to flag a life-threatening condition in a critically ill patient; Epic's false negatives and false positives left seriously ill inpatients unrecognised by their clinicians."
            }
          }
        },
        "provenance": {
          "kind": "legacy_record",
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        "review_state": "record_mapped",
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      },
      "follow_up[]": {
        "state": "value_present",
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          "kind": "record_fields",
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              "status": "unknown",
              "note": "No later development found."
            }
          }
        },
        "provenance": {
          "kind": "legacy_record",
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          ],
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        },
        "review_state": "record_mapped",
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      },
      "human_oversight": {
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        "review_state": "not_assessed",
        "coverage": "partial"
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        "state": "value_present",
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          "kind": "record_fields",
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        },
        "review_state": "record_mapped",
        "coverage": "partial"
      },
      "infrastructure_dependencies[]": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "outcomes[].beneficiaries": {
        "state": "value_present",
        "value": {
          "kind": "text",
          "text": "An infant and the clinicians who investigated her condition."
        },
        "provenance": {
          "kind": "legacy_record",
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        },
        "review_state": "record_mapped",
        "coverage": "partial",
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          "answer": "An infant and the clinicians who investigated her condition."
        }
      },
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          "kind": "text",
          "text": "One infant."
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          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial",
        "display": {
          "answer": "One infant."
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      },
      "outcomes[].benefit_type": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "benefit_type": "Improved Physical Health"
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        },
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          "kind": "legacy_record",
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      },
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        "state": "value_present",
        "value": {
          "kind": "record_fields",
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            "account": "The report's abstract describes a six-month-old infant with a history of painful extremity contractures. Its case presentation opens with a four-month-old girl referred to the pediatric emergency department at Robert Wood Johnson University Hospital. She was referred for failure to thrive with abdominal distension and global developmental delay. The paper dates her abnormal neurological development to two months of age. It included bilateral upper-extremity hypotonia, a weak palmar grasp, pain with all passive and active extremity movement and bilateral contractures. A bleeding, ulcerated infantile hemangioma in the center of the neck was managed from three months of age. The diminishing appetite and abdominal distension were noted at four months. Rapid whole-genome sequencing at Rady Children's Institute for Genomic Medicine used the Fabric GEM artificial-intelligence analysis tool with Phevor re-ranking. The sample was shipped on 5 January 2023 and preliminary results were returned on 10 January 2023. GEM scored a homozygous ANTXR2 variant, c.652T>C (p.Cys218Arg), at 4.7. That gave a diagnosis of infantile hyaline fibromatosis syndrome. A multidisciplinary meeting held the same day conveyed the implications, coordinated gastrostomy tube placement and discussed long-term goals. Treating clinicians reported the case in Cureus on 9 June 2024.",
            "benefit_type": "Improved Physical Health"
          }
        },
        "provenance": {
          "kind": "legacy_record",
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            "benefit_type"
          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial",
        "display": {
          "answer": "An infant received a diagnosis of infantile hyaline fibromatosis within five days, and her clinicians changed her care plan."
        }
      },
      "outcomes[].distribution": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "outcomes[].duration": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "outcomes[].id": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "outcomes[].stakeholder_group": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "ratings": [
              {
                "group": "personal",
                "depth": 3,
                "reason": "An identifiable infant received a definitive molecular diagnosis of a disorder the authors describe as frequently causing early death before age two. This triggered a same-day multidisciplinary meeting that conveyed the implications, coordinated gastrostomy tube placement and discussed long-term goals. The authors add that extensive genetic counseling is essential for parents desiring future children, given a 25% risk for the offspring of carrier parents. They do not report that counseling was delivered."
              },
              {
                "group": "organizational",
                "depth": 1,
                "reason": "A single case in which preliminary results returned five days after the sample shipped, on 5 January 2023, with results on 10 January 2023. Genomic panels and a microarray sent from the institution were still pending and anticipated to take longer than one month. The report does not say what became of those tests."
              }
            ]
          }
        },
        "provenance": {
          "kind": "legacy_record",
          "basis": "Preserved from the existing AIBD record; external sources were not rechecked.",
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          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
      },
      "outcomes[].status": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "outcomes[].tradeoffs": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "outcomes[].unexpected": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
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            "purpose": "Rank candidate variants from rapid whole-genome sequencing against the patient's phenotype so that clinicians can reach a molecular diagnosis quickly."
          }
        },
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          "kind": "legacy_record",
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          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
      },
      "places[]": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "location": "New Brunswick, New Jersey, United States",
            "developer_country": "United States",
            "deployer_country": "United States"
          }
        },
        "provenance": {
          "kind": "legacy_record",
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            "deployer_country"
          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
      },
      "purpose": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "purpose": "Rank candidate variants from rapid whole-genome sequencing against the patient's phenotype so that clinicians can reach a molecular diagnosis quickly."
          }
        },
        "provenance": {
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      },
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        "value": {
          "kind": "record_fields",
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                "date": "2026-10-20",
                "change": "Record drafted from the cited sources.",
                "editor": "AIBD"
              },
              {
                "date": "2026-10-20",
                "change": "Paired with AI Incident Database incident 123 (medium confidence); severity not given by the source.",
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                "editor": "AIBD"
              },
              {
                "date": "2026-10-20",
                "change": "Dropped the claim that the diagnosis ended further investigation at the treating hospital, restated the GEM and Phevor thresholds as the paper gives them (greater than 2, and 5 or above), dated the presenting findings as the paper dates them, recast the 25% recurrence risk as the authors' recommendation that counseling is essential rather than counseling delivered, and marked the 13.5-hour Nature Communications paper as not vendor-authored, because each of those statements went further than the sources do.",
                "source": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11234061/ ; https://pmc.ncbi.nlm.nih.gov/articles/PMC9325884/",
                "editor": "AIBD"
              },
              {
                "date": "2026-10-21",
                "change": "Added what the benefit is measured against from the cited sources.",
                "source": "https://europepmc.org/article/PMC/PMC11234061",
                "editor": "AIBD"
              },
              {
                "date": "2026-10-21",
                "change": "Benefit type set to Improved Physical Health under Trustible's full taxonomy of 23 types; it was Improved Knowledge Discovery among the six first used.",
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                "editor": "AIBD"
              },
              {
                "date": "2026-10-21",
                "change": "Country of the developer and the deployer added from the organization's own site or a registry.",
                "source": "https://fabricgenomics.com/privacy-policy/; https://radygenomics.org/contact-us/",
                "editor": "AIBD"
              },
              {
                "date": "2026-10-21",
                "change": "Prose pass: a rating reason, account, the system's part rewritten in shorter sentences with abbreviations expanded; facts, figures and quotations unchanged.",
                "editor": "AIBD"
              },
              {
                "date": "2026-10-25",
                "change": "Clarified the displayed field answers and placed measurements and limitations in their respective fields.",
                "editor": "AIBD"
              }
            ]
          }
        },
        "provenance": {
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        "review_state": "record_mapped",
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        "value": {
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                "AI ranking of candidate variants reviewed and confirmed by clinicians"
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              "must_hold": [
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                "Clinician review and confirmation of the ranked variant"
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                {
                  "date": "2022-07-26",
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                  "model_version": "GEM (Fabric Genomics)",
                  "outcome": "recurred",
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              ]
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              ]
            }
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        },
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        },
        "review_state": "record_mapped",
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        "display": {
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      },
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        "value": {
          "kind": "record_fields",
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                "date": "2026-10-20",
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              },
              {
                "date": "2026-10-20",
                "change": "Paired with AI Incident Database incident 123 (medium confidence); severity not given by the source.",
                "source": "https://incidentdatabase.ai/cite/123",
                "editor": "AIBD"
              },
              {
                "date": "2026-10-20",
                "change": "Dropped the claim that the diagnosis ended further investigation at the treating hospital, restated the GEM and Phevor thresholds as the paper gives them (greater than 2, and 5 or above), dated the presenting findings as the paper dates them, recast the 25% recurrence risk as the authors' recommendation that counseling is essential rather than counseling delivered, and marked the 13.5-hour Nature Communications paper as not vendor-authored, because each of those statements went further than the sources do.",
                "source": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11234061/ ; https://pmc.ncbi.nlm.nih.gov/articles/PMC9325884/",
                "editor": "AIBD"
              },
              {
                "date": "2026-10-21",
                "change": "Added what the benefit is measured against from the cited sources.",
                "source": "https://europepmc.org/article/PMC/PMC11234061",
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              },
              {
                "date": "2026-10-21",
                "change": "Benefit type set to Improved Physical Health under Trustible's full taxonomy of 23 types; it was Improved Knowledge Discovery among the six first used.",
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              },
              {
                "date": "2026-10-21",
                "change": "Country of the developer and the deployer added from the organization's own site or a registry.",
                "source": "https://fabricgenomics.com/privacy-policy/; https://radygenomics.org/contact-us/",
                "editor": "AIBD"
              },
              {
                "date": "2026-10-21",
                "change": "Prose pass: a rating reason, account, the system's part rewritten in shorter sentences with abbreviations expanded; facts, figures and quotations unchanged.",
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              },
              {
                "date": "2026-10-25",
                "change": "Clarified the displayed field answers and placed measurements and limitations in their respective fields.",
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            ]
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        },
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        },
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        "state": "value_present",
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          "kind": "record_fields",
          "fields": {
            "domain": "Clinical genomics / rare disease diagnosis",
            "segment": "Critically ill infant undergoing rapid whole-genome sequencing"
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        "review_state": "record_mapped",
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          "kind": "record_fields",
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                "kind": "case report",
                "citation": "Ye GX, Ontiveros E, Ivander A, Velinov M, Simotas C (2024). Autosomal Recessive Infantile Hyaline Fibromatosis Identified Using Artificial Intelligence-Assisted Rapid Whole Genome Sequencing. Cureus.",
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                "url": "https://europepmc.org/article/PMC/PMC11234061",
                "date": "2024-06-09",
                "written_by": "deployer",
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              },
              {
                "kind": "peer-reviewed study",
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                "title": "An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases",
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            ]
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          "kind": "identifiers",
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        },
        "provenance": {
          "kind": "curatorial",
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        "review_state": "record_mapped",
        "coverage": "complete"
      },
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        "state": "not_assessed",
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                "kind": "case report",
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                "date": "2024-06-09",
                "written_by": "deployer",
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              },
              {
                "kind": "peer-reviewed study",
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                "title": "An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases",
                "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9325884/",
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                "written_by": "makers",
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              }
            ]
          }
        },
        "provenance": {
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          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
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      "sources[].upstream_sources": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "strategic_assessments[]": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial",
        "family": "strategic assessments"
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      "summary": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "summary": "AI-assisted rapid genome sequencing scored a homozygous ANTXR2 variant at 4.7, diagnosing an infant within five days and changing her care plan.",
            "account": "The report's abstract describes a six-month-old infant with a history of painful extremity contractures. Its case presentation opens with a four-month-old girl referred to the pediatric emergency department at Robert Wood Johnson University Hospital. She was referred for failure to thrive with abdominal distension and global developmental delay. The paper dates her abnormal neurological development to two months of age. It included bilateral upper-extremity hypotonia, a weak palmar grasp, pain with all passive and active extremity movement and bilateral contractures. A bleeding, ulcerated infantile hemangioma in the center of the neck was managed from three months of age. The diminishing appetite and abdominal distension were noted at four months. Rapid whole-genome sequencing at Rady Children's Institute for Genomic Medicine used the Fabric GEM artificial-intelligence analysis tool with Phevor re-ranking. The sample was shipped on 5 January 2023 and preliminary results were returned on 10 January 2023. GEM scored a homozygous ANTXR2 variant, c.652T>C (p.Cys218Arg), at 4.7. That gave a diagnosis of infantile hyaline fibromatosis syndrome. A multidisciplinary meeting held the same day conveyed the implications, coordinated gastrostomy tube placement and discussed long-term goals. Treating clinicians reported the case in Cureus on 9 June 2024."
          }
        },
        "provenance": {
          "kind": "legacy_record",
          "basis": "Preserved from the existing AIBD record; external sources were not rechecked.",
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          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
      },
      "systems[].autonomy_permissions": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "systems[].component_role": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "systems[].deployment_configuration": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "systems[].inputs_outputs": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "systems[].model_name": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "systems[].model_version": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "systems[].product_name": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "system": "Fabric GEM artificial-intelligence variant interpretation tool with Phevor phenotype-driven re-ranking"
          }
        },
        "provenance": {
          "kind": "legacy_record",
          "basis": "Preserved from the existing AIBD record; external sources were not rechecked.",
          "record_fields": [
            "system"
          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
      },
      "systems[].provider": {
        "state": "value_present",
        "value": {
          "kind": "structured",
          "data": {
            "application_developer": "Fabric Genomics, Oakland, California"
          }
        },
        "provenance": {
          "kind": "legacy_record",
          "basis": "Mapped from the existing case description without a new external source review.",
          "record_fields": [
            "developer"
          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
      },
      "taxonomy_crosswalks[]": {
        "state": "not_assessed",
        "review_state": "not_assessed",
        "coverage": "partial"
      },
      "title": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "title": "Fabric GEM AI ranked the causal ANTXR2 variant, diagnosing infantile hyaline fibromatosis in a six-month-old",
            "headline": "Fabric GEM flags ANTXR2 and diagnoses an infant in five days"
          }
        },
        "provenance": {
          "kind": "legacy_record",
          "basis": "Preserved from the existing AIBD record; external sources were not rechecked.",
          "record_fields": [
            "title",
            "headline"
          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
      },
      "version": {
        "state": "value_present",
        "value": {
          "kind": "identifiers",
          "identifiers": [
            "a3075cb0abfb0ae85e7a06197875788a02a454737eaf475f4b55f59abb44644a"
          ],
          "role": "SHA-256 of normalized original case data"
        },
        "provenance": {
          "kind": "curatorial",
          "basis": "Deterministic content version assigned by the local migration.",
          "record_fields": [],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "complete"
      },
      "workflow": {
        "state": "value_present",
        "value": {
          "kind": "record_fields",
          "fields": {
            "account": "The report's abstract describes a six-month-old infant with a history of painful extremity contractures. Its case presentation opens with a four-month-old girl referred to the pediatric emergency department at Robert Wood Johnson University Hospital. She was referred for failure to thrive with abdominal distension and global developmental delay. The paper dates her abnormal neurological development to two months of age. It included bilateral upper-extremity hypotonia, a weak palmar grasp, pain with all passive and active extremity movement and bilateral contractures. A bleeding, ulcerated infantile hemangioma in the center of the neck was managed from three months of age. The diminishing appetite and abdominal distension were noted at four months. Rapid whole-genome sequencing at Rady Children's Institute for Genomic Medicine used the Fabric GEM artificial-intelligence analysis tool with Phevor re-ranking. The sample was shipped on 5 January 2023 and preliminary results were returned on 10 January 2023. GEM scored a homozygous ANTXR2 variant, c.652T>C (p.Cys218Arg), at 4.7. That gave a diagnosis of infantile hyaline fibromatosis syndrome. A multidisciplinary meeting held the same day conveyed the implications, coordinated gastrostomy tube placement and discussed long-term goals. Treating clinicians reported the case in Cureus on 9 June 2024.",
            "replication": {
              "produced_by": [
                "Rapid whole-genome sequencing of a critically ill infant",
                "Structured phenotype terms entered for the patient",
                "AI ranking of candidate variants reviewed and confirmed by clinicians"
              ],
              "must_hold": [
                "Rapid whole-genome sequencing of the proband",
                "Structured phenotype terms entered for the patient",
                "Clinician review and confirmation of the ranked variant"
              ],
              "echoes": [
                {
                  "date": "2022-07-26",
                  "setting": "Rady Children's automated 13.5-hour diagnosis system, four retrospective infant cases",
                  "model_version": "GEM (Fabric Genomics)",
                  "outcome": "recurred",
                  "source": "Owen MJ, et al. Nat Commun 2022. https://pmc.ncbi.nlm.nih.gov/articles/PMC9325884/"
                }
              ]
            }
          }
        },
        "provenance": {
          "kind": "legacy_record",
          "basis": "Preserved from the existing AIBD record; external sources were not rechecked.",
          "record_fields": [
            "account",
            "replication"
          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial",
        "display": {
          "answer": "Clinicians submitted the infant’s genome and symptoms for analysis. They reviewed the variants that GEM ranked and confirmed an ANTXR2 variant as the cause of her condition."
        }
      }
    },
    "summary": {
      "total": 91,
      "addressed": 91,
      "known": 33,
      "reviewed": 0,
      "record_mapped": 33,
      "not_assessed": 58,
      "complete": false,
      "by_state": {
        "value_present": 33,
        "not_reported": 0,
        "unresolved": 0,
        "not_assessed": 58,
        "not_applicable": 0,
        "withheld": 0,
        "source_unavailable": 0
      }
    }
  }
}