Table 1|. Summary of 10 inferred disease topics in the UK Biobank.

For each topic, we list its 3-letter acronym, disease systems, representative diseases, and number of associated diseases (defined as diseases with average diagnosis-specific topic probability >50% for that topic). Topics are ordered by the Phecode system (see Fig. 3). 316 of 348 diseases analyzed are associated with a topic; the remaining 32 diseases do not have a topic with average diagnosis-specific topic probability >50%. NOS, not otherwise specified.

Acronym	Disease systems	Representative diseases	Number of associated diseases
NRI	Neoplasms, respiratory, infectious diseases	Secondary malignancy of lymph nodes; Pneumococcal pneumonia; Bacterial infection NOS	53
CER	Circulatory system, endocrine/metabolic, respiratory	Type 2 diabetes; Obesity; Chronic airway obstruction	41
SRD	Sense organs, respiratory, dermatologic	Cataract; Septal Deviations/Turbinate Hypertrophy; Benign neoplasm of skin	38
CVD	Cardiovascular disease	Hypercholesterolemia; Coronary atherosclerosis; Myocardial infarction	27
UGI	Upper gastrointestinal disease	Diaphragmatic hernia; Benign neoplasm of other parts of digestive system; Gastritis and duodenitis	22
LGI	Lower gastrointestinal disease	Irritable Bowel Syndrome; Benign neoplasm of colon; Anal and rectal polyp	13
FGND	Female genitourinary, neoplasms, digestive	Uterine leiomyoma; Malignant neoplasm of female breast; Hypothyroidism NOS	34
MGND	Male genitourinary, neoplasms, digestive	Urinary tract infection; Cancer of prostate; Other disorders of bladder	33
MDS	Musculoskeletal, digestive, symptoms	Back pain; Cholelithiasis; Other disorders of soft tissues	29
ARP	Arthropathy-related disease	Arthropathy NOS; Rheumatoid arthritis; Enthesopathy	26