[ { "phenotype_id": "PH1691", "phenotype_version_id": 3622, "name": "Chronic paediatric conditions: Cystic Fibrosis", "definition": "This code list is part of a set of harmonised code lists to identify chronic paediatric\nconditions across primary and secondary care datasets across the UK.\n\nPublished ICD-10 and Read v2 code lists were combined with SNOMED codes derived using\nCALIBERas below:\n\n- Read v2 cystic fibrosis code list: [https://phenotypes.healthdatagateway.org/phenotypes/PH14/version/28/detail/](https://phenotypes.healthdatagateway.org/phenotypes/PH14/version/28/detail/)\n- ICD-10 cystic fibrosis diagnoses as per Hardelid 2014 mapped through CALIBER to produce SNOMED code list.\n\n### Methods\n\nChronic paediatric conditions were defined as health problems requiring medical follow-up\nfor more than 12 months in 50% or more of cases. Code lists were produced by mapping\nexisting ICD-10 codes for chronic paediatric conditions to SNOMED and Read v2 codes\nusing the CALIBER R package, with review by paediatric sub-specialists.\n\nAn established ICD-10 code list of chronic paediatric conditions (Hardelid 2014)\nwas used as the basis for the new lists.1 Chronic paediatric conditions were defined\nas any health problem requiring medical follow-up (hospital admission, outpatient\nfollow up or use of support services such as physiotherapy) for more than 12 months\nin 50% or more of cases.[1] A Chronic Paediatric Conditions Committee of paediatric\nsub-specialists was established. The original ICD-10 list was screened by two paediatricians\nand acute conditions removed, with disagreements resolved by a third paediatrician.\nConditions which were likely acute and would not fulfil our chronic disease definition\nwere excluded, including skeletal injuries and self-harm. Drug-induced conditions\nwere excluded as chronicity was not known. Infections other than human immunodeficiency\nvirus (HIV), hepatitis B or C, or congenital infections (syphilis / toxoplasmosis\n/ rubella / herpes simplex virus / cytomegalovirus) were excluded. Chronic sequelae\nof infections were retained.\n\nPublished code lists were then identified for Read v2 and SNOMED codes for well-characterised\nconditions including asthma, diabetes, cystic fibrosis and cancer. The remaining\nICD-10 codes were mapped to SNOMED and Read v2 codes using the CALIBER R package\nand Technology Reference Update Distribution NHS Data Migration tables [2] to produce\nnew code lists suitable for primary care data. These resulting code lists were screened\nby two sub-specialists to ensure conditions were chronic and in the correct subgroup\nwith disagreements resolved by a third clinician.\n\n### References:\n\n1. Hardelid P, Dattani N, Gilbert R. Estimating the prevalence of chronic conditions in children who die in England, Scotland and Wales: a data linkage cohort study. BMJ Open 2014; 4: e005331.\n2. CALIBER codelists-package: Generate ICD, Read and OPCS codelists in CALIBER codelists: Generate ICD10, Read and OPCS codelists, [https://rdrr.io/rforge/CALIBERcodelists/man/CALIBERcodelists-package.html](https://rdrr.io/rforge/CALIBERcodelists/man/CALIBERcodelists-package.html) (accessed 19 October 2022).\n\n", "implementation": "We have considered conditions to be active if they had been coded for in the preceding\nfive years. In addition, conditions from the following subgroups were considered\nto be permanent, therefore active if coded for at any time: metabolic, diabetes,\ncystic fibrosis, transplant, receiving palliative care, other congenital multisystem\nsyndromes and chromosomal abnormalities, immunological and cerebral palsy / paralysis\n(a subgroup of \"Other neurology\" code list).\n", "publications": [], "validation": "", "citation_requirements": "To our knowledge, these are the first set of harmonised code lists for chronic paediatric\nconditions that span commonly used primary and secondary care coding systems in the\nUK. We hope they will prove a valuable resource for the paediatric research community\nand welcome suggestions for further development ([Olivia.Swann@ed.ac.uk](mailto:Olivia.Swann@ed.ac.uk)).\n", "created": "2025-01-17T21:49:22.380717Z", "author": "Swann OV, Williams TC, Fraser LK, Farrell J, Parker M, Kennedy J, Seabourne M, Brophy S, Harrison EM, Docherty AB, Pollock L", "collections": [ { "name": "Phenotype Library", "value": 18 } ], "tags": null, "organisation": null, "world_access": 2, "updated": "2025-01-19T15:49:37.709710Z", "sex": [ { "name": "Both", "value": "3" } ], "type": [ { "name": "Disease or syndrome", "value": "2" } ], "ontology": [ { "name": "Paediatrics", "value": 842203 }, { "name": "Paediatric and Perinatal Pathology", "value": 842275 } ], "phenoflowid": "", "data_sources": [ { "name": "Hospital Episode Statistics Admitted Patient Care", "value": 2, "uid": "6599230a-df54-4615-937c-d724d239491f", "url": "https://healthdatagateway.org/en/dataset/875", "datasource_id": 875 }, { "name": "OpenSAFELY SNOMED CT", "value": 36, "datasource_id": 36 }, { "name": "Patient Episode Dataset for Wales (PEDW)", "value": 379, "uid": "4c33a5d2-164c-41d7-9797-dc2b008cc852", "url": "https://healthdatagateway.org/en/dataset/318", "datasource_id": 318 }, { "name": "Welsh Longitudinal General Practice Dataset (WLGP) - Welsh Primary Care", "value": 502, "uid": "33fc3ffd-aa4c-4a16-a32f-0c900aaea3d2", "url": "https://healthdatagateway.org/en/dataset/355", "datasource_id": 355 } ], "coding_system": [ { "name": "SNOMED CT codes", "value": 9 }, { "name": "ICD10 codes", "value": 4 }, { "name": "Read codes v2", "value": 5 } ], "event_date_range": "2021/01/01 - 2021/01/01", "concept_information": [ { "concept_id": 4044, "concept_version_id": 11399, "concept_name": "Cystic Fibrosis (ICD-10)", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH1691", "phenotype_version_id": 3622, "phenotype_name": "Chronic paediatric conditions: Cystic Fibrosis", "code_attribute_header": null, "codes": [ { "code": "E84", "description": "Cystic fibrosis", "attributes": null }, { "code": "E840", "description": "Cystic fibrosis with pulmonary manifestations", "attributes": null }, { "code": "E841", "description": "Cystic fibrosis with intestinal manifestations", "attributes": null }, { "code": "E848", "description": "Cystic fibrosis with other manifestations", "attributes": null }, { "code": "E849", "description": "Cystic fibrosis, unspecified", "attributes": null } ] }, { "concept_id": 4045, "concept_version_id": 11400, "concept_name": "Cystic Fibrosis (Read v2)", "coding_system": { "id": 5, "name": "Read codes v2", "description": "Read codes v2" }, "phenotype_id": "PH1691", "phenotype_version_id": 3622, "phenotype_name": "Chronic paediatric conditions: Cystic Fibrosis", "code_attribute_header": null, "codes": [ { "code": "C10N100", "description": "Cystic fibrosis related diabetes mellitus", "attributes": null }, { "code": "C370.00", "description": "Cystic fibrosis", "attributes": null }, { "code": "C370000", "description": "Cystic fibrosis with no meconium ileus", "attributes": null }, { "code": "C370100", "description": "Cystic fibrosis with meconium ileus", "attributes": null }, { "code": "C370111", "description": "Meconium ileus in cystic fibrosis", "attributes": null }, { "code": "C370200", "description": "Cystic fibrosis with pulmonary manifestations", "attributes": null }, { "code": "C370300", "description": "Cystic fibrosis with intestinal manifestations", "attributes": null }, { "code": "C370400", "description": "Arthropathy in cystic fibrosis", "attributes": null }, { "code": "C370500", "description": "Cystic fibrosis with distal intestinal obstruction syndrome", "attributes": null }, { "code": "C370700", "description": "Liver disease due to cystic fibrosis", "attributes": null }, { "code": "C370800", "description": "Cystic fibrosis related cirrhosis", "attributes": null }, { "code": "C370900", "description": "Exacerbation of cystic fibrosis", "attributes": null }, { "code": "C370y00", "description": "Cystic fibrosis with combined manifestations", "attributes": null }, { "code": "C370z00", "description": "Cystic fibrosis NOS", "attributes": null } ] }, { "concept_id": 4046, "concept_version_id": 11401, "concept_name": "Cystic Fibrosis (SNOMED-CT)", "coding_system": { "id": 9, "name": "SNOMED CT codes", "description": "SNOMED CT codes" }, "phenotype_id": "PH1691", "phenotype_version_id": 3622, "phenotype_name": "Chronic paediatric conditions: Cystic Fibrosis", "code_attribute_header": null, "codes": [ { "code": "190905008", "description": "Cystic fibrosis (disorder)", "attributes": null }, { "code": "206471004", "description": "Perinatal jaundice due to mucoviscidosis (disorder)", "attributes": null }, { "code": "235978006", "description": "Cystic fibrosis of pancreas (disorder)", "attributes": null }, { "code": "426705001", "description": "Diabetes mellitus co-occurrent and due to cystic fibrosis (disorder)", "attributes": null }, { "code": "427022004", "description": "Liver disease due to cystic fibrosis (disorder)", "attributes": null }, { "code": "427089005", "description": "Diabetes mellitus due to cystic fibrosis (disorder)", "attributes": null }, { "code": "445090007", "description": "Fibrosing colonopathy (disorder)", "attributes": null }, { "code": "698940002", "description": "Arthropathy associated with cystic fibrosis (disorder)", "attributes": null }, { "code": "707418001", "description": "Male infertility due to cystic fibrosis (disorder)", "attributes": null }, { "code": "707419009", "description": "Osteoporosis due to cystic fibrosis (disorder)", "attributes": null }, { "code": "707420003", "description": "Portal hypertension due to cystic fibrosis (disorder)", "attributes": null }, { "code": "707450006", "description": "Pancreatic insufficiency due to cystic fibrosis of pancreas (disorder)", "attributes": null }, { "code": "707536003", "description": "Digestive system manifestation co-occurrent and due to cystic fibrosis (disorder)", "attributes": null }, { "code": "707542004", "description": "Otorhinolaryngological manifestation co-occurrent and due to cystic fibrosis (disorder)", "attributes": null }, { "code": "707577004", "description": "Female infertility due to cystic fibrosis (disorder)", "attributes": null }, { "code": "707578009", "description": "Perforation of intestine due to cystic fibrosis with meconium ileus (disorder)", "attributes": null }, { "code": "707766007", "description": "Exocrine pancreatic manifestation co-occurrent and due to cystic fibrosis (disorder)", "attributes": null }, { "code": "716088000", "description": "Follicular hamartoma with alopecia and cystic fibrosis syndrome (disorder)", "attributes": null }, { "code": "720401009", "description": "Cystic fibrosis with gastritis and megaloblastic anemia syndrome (disorder)", "attributes": null }, { "code": "721197001", "description": "Polyneuropathy due to classical cystic fibrosis (disorder)", "attributes": null }, { "code": "725052002", "description": "Fetal cystic fibrosis (disorder)", "attributes": null }, { "code": "762269004", "description": "Classical cystic fibrosis (disorder)", "attributes": null }, { "code": "762270003", "description": "Atypical cystic fibrosis (disorder)", "attributes": null }, { "code": "762271004", "description": "Subclinical cystic fibrosis (disorder)", "attributes": null }, { "code": "81423003", "description": "Cystic fibrosis without meconium ileus (disorder)", "attributes": null }, { "code": "817966005", "description": "Distal intestinal obstruction syndrome due to cystic fibrosis (disorder)", "attributes": null }, { "code": "86092005", "description": "Cystic fibrosis with meconium ileus (disorder)", "attributes": null }, { "code": "86555001", "description": "Cystic fibrosis of the lung (disorder)", "attributes": null } ] } ], "status": 1, "doi": "https://doi.org/10.48533/z0df-2110", "is_deleted": false, "publish_status": 2, "owner": "farrellj", "template": { "id": 1, "name": "Clinical-Coded Phenotype", "description": "Phenotype definitions that are based on lists of clinical codes, or algorithms using clinical codes.", "version_id": 1 }, "versions": [ { "version_id": 3622, "version_name": "Chronic paediatric conditions: Cystic Fibrosis", "version_date": "2025-01-19T15:49:37.737584Z", "is_published": true, "is_latest": true }, { "version_id": 3621, "version_name": "Chronic paediatric conditions: Cystic Fibrosis", "version_date": "2025-01-19T15:47:25.907357Z", "is_published": true, "is_latest": false }, { "version_id": 3598, "version_name": "Cystic Fibrosis", "version_date": "2025-01-17T22:07:34.040019Z", "is_published": true, "is_latest": false } ] } ]