DHX9

monarch-initiative · Jan 8, 2025 · f4fc1ed · f4fc1ed
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diff --git a/notebooks/DHX9/DHX9_MRD75_individuals.ipynb b/notebooks/DHX9/DHX9_MRD75_individuals.ipynb
diff --git a/notebooks/DHX9/input/DHX9_MRD75_individuals.xlsx b/notebooks/DHX9/input/DHX9_MRD75_individuals.xlsx
diff --git a/notebooks/DHX9/phenopackets/PMID_37369308_patient.json b/notebooks/DHX9/phenopackets/PMID_37369308_patient.json
@@ -0,0 +1,260 @@
+{
+  "id": "PMID_37369308_patient",
+  "subject": {
+    "id": "patient",
+    "timeAtLastEncounter": {
+      "age": {
+        "iso8601duration": "P8Y"
+      }
+    },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
+    "sex": "FEMALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0002020",
+        "label": "Gastroesophageal reflux"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003593",
+          "label": "Infantile onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001508",
+        "label": "Failure to thrive"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003593",
+          "label": "Infantile onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0011968",
+        "label": "Feeding difficulties"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003593",
+          "label": "Infantile onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001263",
+        "label": "Global developmental delay"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000286",
+        "label": "Epicanthus"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001999",
+        "label": "Abnormal facial shape"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000219",
+        "label": "Thin upper lip vermilion"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000582",
+        "label": "Upslanted palpebral fissure"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000369",
+        "label": "Low-set ears"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000278",
+        "label": "Retrognathia"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0004322",
+        "label": "Short stature"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001518",
+        "label": "Small for gestational age"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000252",
+        "label": "Microcephaly"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000431",
+        "label": "Wide nasal bridge"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000319",
+        "label": "Smooth philtrum"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0045025",
+        "label": "Narrow palpebral fissure"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000316",
+        "label": "Hypertelorism"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0012817",
+        "label": "Noncompaction cardiomyopathy"
+      }
+    }
+  ],
+  "interpretations": [
+    {
+      "id": "patient",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:620988",
+          "label": "Intellectual developmental disorder, autosomal dominant 75"
+        },
+        "genomicInterpretations": [
+          {
+            "subjectOrBiosampleId": "patient",
+            "interpretationStatus": "CAUSATIVE",
+            "variantInterpretation": {
+              "variationDescriptor": {
+                "id": "var_qrVJgNtcUwIlLCZIMsTkscJMU",
+                "geneContext": {
+                  "valueId": "HGNC:2750",
+                  "symbol": "DHX9"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_001357.5:c.1240G>A"
+                  },
+                  {
+                    "syntax": "hgvs.g",
+                    "value": "NC_000001.11:g.182860092G>A"
+                  }
+                ],
+                "vcfRecord": {
+                  "genomeAssembly": "hg38",
+                  "chrom": "chr1",
+                  "pos": "182860092",
+                  "ref": "G",
+                  "alt": "A"
+                },
+                "moleculeContext": "genomic",
+                "allelicState": {
+                  "id": "GENO:0000135",
+                  "label": "heterozygous"
+                }
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "diseases": [
+    {
+      "term": {
+        "id": "OMIM:620988",
+        "label": "Intellectual developmental disorder, autosomal dominant 75"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003623",
+          "label": "Neonatal onset"
+        }
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2025-01-08T06:54:05.534396886Z",
+    "createdBy": "ORCID:0000-0002-0736-9199",
+    "resources": [
+      {
+        "id": "geno",
+        "name": "Genotype Ontology",
+        "url": "http://purl.obolibrary.org/obo/geno.owl",
+        "version": "2022-03-05",
+        "namespacePrefix": "GENO",
+        "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+      },
+      {
+        "id": "hgnc",
+        "name": "HUGO Gene Nomenclature Committee",
+        "url": "https://www.genenames.org",
+        "version": "06/01/23",
+        "namespacePrefix": "HGNC",
+        "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
+      },
+      {
+        "id": "omim",
+        "name": "An Online Catalog of Human Genes and Genetic Disorders",
+        "url": "https://www.omim.org",
+        "version": "January 4, 2023",
+        "namespacePrefix": "OMIM",
+        "iriPrefix": "https://www.omim.org/entry/"
+      },
+      {
+        "id": "so",
+        "name": "Sequence types and features ontology",
+        "url": "http://purl.obolibrary.org/obo/so.obo",
+        "version": "2021-11-22",
+        "namespacePrefix": "SO",
+        "iriPrefix": "http://purl.obolibrary.org/obo/SO_"
+      },
+      {
+        "id": "hp",
+        "name": "human phenotype ontology",
+        "url": "http://purl.obolibrary.org/obo/hp.owl",
+        "version": "2024-12-12",
+        "namespacePrefix": "HP",
+        "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+      }
+    ],
+    "phenopacketSchemaVersion": "2.0",
+    "externalReferences": [
+      {
+        "id": "PMID:37369308",
+        "reference": "https://pubmed.ncbi.nlm.nih.gov/37369308",
+        "description": "Heterozygous loss-of-function DHX9 variants are associated with neurodevelopmental disorders: Human genetic and experimental evidences"
+      }
+    ]
+  }
+}