Table 1.

Summary information

Review Categorya	n (%)b	Chart Review Summary
T2DM (n = 84 821; cases = 9301, controls = 23 776)
Cases with probability <50%	675 (0.80)	7 cases: none had T2DM diagnosis codes, but they did have a history of diabetes in clinical notes with medication and elevated blood glucose measurements.
		3 could not be determined: no mention of T2DM in clinical notes but they had medication and elevated blood glucose measurements.
Controls with probability ≥50%	24 (0.03)	1 case: clinical notes indicate well-controlled T2DM.
		9 non-cases: no evidence that suggests T2DM, but they had other features that inflated the phenotype score, like blood glucose measurements or hypoglycemia.
Unclassified with probability <50%	39 611 (46.69)	10 non-cases: no evidence that suggests T2DM.
Unclassified with probability ≥50%	12 133 (14.31)	6 cases: history of T2DM in clinical notes.
		4 non-cases: 3 have no evidence that suggests T2DM; 1 has prediabetes.
Dementia (n = 84 821; cases = 2989, controls = 77 688)
Cases with probability <50%	1339 (1.58)	4 cases: history of dementia in clinical notes with no dementia diagnosis codes but they were identified as cases by the presence of an associated medication.
		6 non-cases or could not be determined: no evidence that suggests dementia; identified as cases by the presence of an associated medication, where the medication was prescribed for reasons unrelated to dementia
Controls with probability ≥50%	0 (0.00)	0 cases
Unclassified with probability <50%	2894 (3.41)	10 non-cases: 7 diagnosed with delirium, but not dementia.
		3 with a persistent mental disorder, but not dementia
Unclassified with probability ≥50%	1250 (1.47)	5 cases: history of dementia in clinical notes but excluded from a case group for not having >5 diagnosis codes.
		5 non-cases: persistent mental disorder, but not dementia
Hypothyroidism (n = 84 821; cases = 5170, controls = 27 926)
Cases with probability <50%	16 (0.02)	10 cases: history of hypothyroidism in clinical notes, but specific diagnosis code were not captured or assigned a lower score by PheMap
Controls with probability ≥50%	133 (0.16)	5 non-cases: goiter, but no hypothyroidism
		5 non-cases: coma (assigned a high score by PheMap), but unrelated to hypothyroidism
Unclassified with probability <50%	45 499 (55.64)	10 non-cases: no evidence that suggests hypothyroidism
Unclassified with probability ≥50%	11 492 (13.55)	3 cases: history of hypothyroidism in clinical notes
		3 cases: postsurgical or secondary due to recent contrast exposure
		4 non-cases: goiter or coma (see “Controls with probability ≥50%”)

Note: Data are of subjects with inconsistent PheMap phenotype probabilities, eMERGE-defined case-control status, and results of chart reviews of randomly selected 10 samples per group. eMERGE: Electronic Medical Records and Genomics; T2DM: type 2 diabetes mellitus; XPRESS: eXtraction of Phenotypes from Records using Silver Standards.

^aCase, control, and unclassified refer to a patient’s eMERGE-defined case-control status.

^bReporting as percentage of total patients (N = 84 821)