{
"id": "comprehensive-cohort-id",
"description": "A description of the example cohort.",
"members": [{
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"alternateIds": ["boy", "patient", "proband"],
"dateOfBirth": "1970-01-02T10:17:36.000000100Z",
"timeAtLastEncounter": {
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}
},
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"karyotypicSex": "XY",
"taxonomy": {
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}
},
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},
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}
},
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},
"reference": {
"id": "PMID:30808312",
"description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report."
}
}]
}, {
"type": {
"id": "HP:0031910",
"label": "Abnormal cranial nerve physiology"
},
"excluded": true,
"evidence": [{
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},
"reference": {
"id": "PMID:30808312",
"description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report."
}
}]
}, {
"type": {
"id": "HP:0011463",
"label": "Macroscopic hematuria"
},
"modifiers": [{
"id": "HP:0031796",
"label": "Recurrent"
}],
"onset": {
"age": {
"iso8601duration": "P14Y"
}
},
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"id": "ECO:0000033",
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"id": "PMID:30808312",
"description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report."
}
}]
}, {
"type": {
"id": "HP:0001270",
"label": "Motor delay"
},
"severity": {
"id": "HP:0012825",
"label": "Mild"
},
"onset": {
"ontologyClass": {
"id": "HP:0011463",
"label": "Childhood onset"
}
}
}],
"biosamples": [{
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"individualId": "14 year-old boy",
"description": "Muscle biopsy of 14 year-old boy",
"sampledTissue": {
"id": "UBERON:0003403",
"label": "skin of forearm"
},
"taxonomy": {
"id": "NCBITaxon:9606",
"label": "homo sapiens"
},
"timeOfCollection": {
"age": {
"iso8601duration": "P14Y"
}
},
"histologicalDiagnosis": {
"id": "NCIT:C38757",
"label": "Negative Finding"
},
"tumorProgression": {
"id": "NCIT:C3677",
"label": "Benign Neoplasm"
},
"tumorGrade": {
"id": "NCIT:C28076",
"label": "Disease Grade Qualifier"
},
"diagnosticMarkers": [{
"id": "NCIT:C68748",
"label": "HER2/Neu Positive"
}],
"materialSample": {
"id": "EFO:0009655",
"label": "abnormal sample"
}
}],
"interpretations": [{
"id": "comprehensive-phenopacket-id",
"progressStatus": "SOLVED",
"diagnosis": {
"disease": {
"id": "OMIM:101600",
"label": "PFEIFFER SYNDROME"
},
"genomicInterpretations": [{
"subjectOrBiosampleId": "14 year-old boy",
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"variationDescriptor": {
"expressions": [{
"syntax": "hgvs",
"value": "NM_001848.2:c.877G\u003eA"
}],
"allelicState": {
"id": "GENO:0000135",
"label": "heterozygous"
}
}
}
}]
}
}],
"diseases": [{
"term": {
"id": "OMIM:101600",
"label": "PFEIFFER SYNDROME"
},
"onset": {
"ontologyClass": {
"id": "HP:0003577",
"label": "Congenital onset"
}
}
}],
"files": [{
"uri": "file://data/genomes/P000001C",
"individualToFileIdentifiers": {
"14 year-old boy": "P000001C"
},
"fileAttributes": {
"genomeAssembly": "GRCh38.p13",
"fileFormat": "vcf",
"description": "Whole genome sequencing VCF output"
}
}],
"metaData": {
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"createdBy": "Peter R.",
"submittedBy": "PhenopacketLab",
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}, {
"subject": {
"id": "MOTHER",
"dateOfBirth": "1970-01-01T00:00:00Z",
"sex": "FEMALE"
}
}, {
"subject": {
"id": "FATHER",
"dateOfBirth": "1970-01-01T00:00:00Z",
"sex": "MALE"
}
}],
"files": [{
"uri": "file://data/genomes/FAM000001",
"individualToFileIdentifiers": {
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"MOTHER": "P000001M",
"FATHER": "P000001F"
},
"fileAttributes": {
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}],
"metaData": {
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}