Genes&Health_PHENOTYPES

	A	B	C	D	E
1	v008 custom binary traits
2	release: 2024_02_05
3
4	Our custom binary trait data includes ICD10, OPCS, SNOMED. Codes are not mapped between datatypes, the individual must have the precise code/code type to be counted as a Case. The codelists are in the next sheet.
5	The custom traits/phenotypes are precise and accurate for the intended purpose. Note that there can still be wide definitions (e.g. patient history of heart attack) versus narrow definitions (e.g. require ECG evidence of heart attack)
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7	We also have 3digit ICD10 simple binary traits (where 4digitICD10, SNOMED mapped back to 3 digit ICD10), performed in the same way as UK Biobank https://biobank.ndph.ox.ac.uk/ukb/ukb/docs/first_occurrences_outcomes.pdf
8	The 3digit ICD10 are intended to be a wide sweep of all human disease. They are less accurate than custom phenotypes as a) OPCS codes not used and b) codes with many SNOMED: many ICD10 mapping are discarded. if b) is not done, then implausible numbers of cases of Anthrax and some other disease appear. UK Biobank did the same.
9
10	We also have quantitative trait phenotypes e.g. blood test pathology results and clinical measurements, see separate sheet v007 release
11
12	There are 11 new traits since v005
13	For this v008 release, we have removed some of the calculated/logic traits e.g. 'type 1 diabetes but NOT type 2 diabetes', these can easily be calculated from the caselists in the TRE if required.
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16	phenotype	5 Feb 2024 tre-tools with NHSD Cancer Registry missing HES 2022 v008 Count of Cases (of 52,808 uniq NHS numbers for data linkage)	codelist_source	phenotype class	comments
17	GNH0001_AtrialFibrillationFlutter	735	GenomicsPLC	simple binary	Atrial Fibrillation and Flutter - Genomics PLC/Vincent Plagnol 2021
18	GNH0002_CoronaryArteryDisease_narrow	3556	GenomicsPLC	simple binary	Coronary Artery Disease narrow - Genomics PLC/Vincent Plagnol 2021
19	GNH0003_CoronaryArteryDisease_broad	4636	GenomicsPLC	simple binary	Coronary Artery Disease broad - Genomics PLC/Vincent Plagnol 2021
20	GNH0004_MyocardialInfarction_narrow	2251	GenomicsPLC	simple binary	Myocardial Infarction - Genomics PLC/Vincent Plagnol 2021
21	GNH0005_MyocardialInfarction_extended	2657	GenomicsPLC	simple binary	Myocardial Infarction extended - Genomics PLC/Vincent Plagnol 2021
22	GNH0006_IschaemicStroke	823	GenomicsPLC	simple binary	Ischaemic Stroke - Genomics PLC/Vincent Plagnol 2021
23	GNH0007_Type2Diabetes	13425	GenomicsPLC	simple binary	Type 2 Diabetes - Genomics PLC/Vincent Plagnol 2021
24	GNH0008_PrimaryOpenAngleGlaucoma	223	Consortium	simple binary	Primary Open Angle Glaucoma - GlobalBiobankMetaAnalysis 2020
25	GNH0009_Asthma	8038	Consortium	simple binary	Asthma - GlobalBiobankMetaAnalysis 2020
26	GNH0010_Gout	1110	Consortium	simple binary	Gout - GlobalBiobankMetaAnalysis 2020
27	GNH0011_COPD	1274	Consortium	simple binary	COPD - GlobalBiobankMetaAnalysis 2020
28	GNH0012_Stroke	858	Consortium	simple binary	Stroke - GlobalBiobankMetaAnalysis 2020
29	GNH0013_HeartFailure	1424	Consortium	simple binary	Heart Failure - GlobalBiobankMetaAnalysis 2020, and further extended
30	GNH0014_IdiopathicPulmonaryFibrosis	209	Consortium	simple binary	Idiopathic Pulmonary Fibrosis - GlobalBiobankMetaAnalysis 2020
31	GNH0015_AcuteAppendicitis	653	Consortium	simple binary	Acute Appendicitis - GlobalBiobankMetaAnalysis 2020
32	GNH0016_HospitalisedVenousThromboEmbolism	388	Consortium	simple binary	Hospitalised for Venous Thrombo-Embolism - GlobalBiobankMetaAnalysis 2020
33	GNH0017_COPD	955	Custom-QMUL	simple binary	COPD, based on HDR-UK Nov 2011 (#as a test of these HDR-UK phenotypes) (note: second flavour of COPD) https://phenotypes.healthdatagateway.org/phenotypes/PH11/version/22/detail/
34	GNH0018_EssentialHypertension	12999	Custom-QMUL	simple binary	Essential Hypertension, based on HDR-UK, Nov 2021
35	GNH0032_ProstateCancer	158	Custom-QMUL	simple binary	obvious ICD10 codes, MULTIPLY SNOMED Codelists, Barts Health actual data, HDR-UK Phenotype Library
36	GNH0033_LungCancer_OpenSafelyCodelist	141	Custom-QMUL	simple binary	obvious ICD10 codes, then opensafely SNOMED https://www.opencodelists.org/codelist/opensafely/lung-cancer-snomed/2020-04-15/#full-list
37	GNH0034_LungCancer_CRPDAurumCodelist	112	Custom-QMUL	simple binary	obvious ICD10 codes, then MULTIPLY SNOMED Codelists
38	GNH0035_BreastCancer	358	Custom-QMUL	simple binary	obvious ICD10 codes, then MULTIPLY SNOMED Codelists
39	GNH0036_ColorectalCancer	777	Custom-QMUL	simple binary	obvious ICD10 codes, then MULTIPLY SNOMED Codelists
40	GNH0037_RheumatoidArthritis	1573	Custom-QMUL	simple binary	obvious ICD10 codes, then MULTIPLY SNOMED Codelists
41	GNH0038_Depression	12241	Custom-QMUL	simple binary	obvious ICD10 codes, then MULTIPLY SNOMED Codelists
42	ADHD_and_hyperkinetic_disorders	109	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
43	Adrenal_insufficiency_and_Addisons_disease	90	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
44	Alcohol_dependence_and_related_disease	4892	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
45	Allergic_and_chronic_rhinitis	14844	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
46	Alopecia_areata_and_scarring_alopecia	859	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
47	Ankylosing_spondylitis	151	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
48	Anxiety_and_phobia	9695	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
49	Aortic_aneurysm	263	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
50	Aplastic_anaemias	113	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
51	Asbestosis	8	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
52	Asthma	8016	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
53	Atrial_fibrillation_and_flutter	762	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
54	Autism_and_Aspergers_syndrome	52	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
55	Autoimmune_liver_disease	60	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
56	Barretts_oesophagus	122	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
57	Bipolar_affective_disorder_and_mania	336	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
58	Blistering_autoimmune_skin_conditions	57	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
59	Bronchiectasis	390	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
60	Cardiac_conduction_defects	904	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
61	Cardiomyopathy_other	259	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
62	Cerebral_Palsy	33	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
63	Cerebrovascular_disease	1391	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
64	Cervical_carcinoma_in_situ	438	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
65	Cholelithiasis	2815	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
66	Chronic_fatigue	3053	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
67	Chronic_Kidney_Disease	3068	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
68	Chronic_sinusitis	9559	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
69	Chronic_ulcer_of_the_skin	1077	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
70	Chronic_viral_hepatitis	900	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
71	Coeliac_disease	167	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
72	Collapsed_vertebra	60	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
73	Congenital_cardiac_disease	532	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
74	Constipation	11841	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
75	COPD	1174	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
76	Coronary_heart_disease	4825	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
77	Crohns_disease	368	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
78	Cystic_Fibrosis	16	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
79	Cystic_renal_disease	67	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
80	Dementia	570	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
81	Depression	12241	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
82	Dermatitis_atopc_contact_other_unspecified	15408	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
83	Diabetic_eye_disease	5924	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
84	Diabetic_neurological_complications	624	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
85	Disorders_of_autonomic_nervous_system	224	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
86	Diverticular_disease_of_intestine	1053	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
87	Downs_syndrome	3	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
88	Dysmenorrhoea	2655	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
89	Eating_disorders	945	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
90	End_stage_renal_disease	323	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
91	Endometriosis	1419	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
92	Enteropathic_arthropathy	18	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
93	Enthesopathies__synovial_disorders	11970	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
94	Epilepsy	608	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
95	Erectile_dysfunction	4237	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
96	Female_genital_prolapse	1571	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
97	Female_infertility	2470	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
98	Fibromyalgia	1148	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
99	Folate_deficiency_with_and_without_anaemia	3667	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022
100	Fracture_of_hip	106	MULTIPLY-Initiative	simple binary	updated MULTIPLY codelist downloaded 8 Jun 2022