Risteys · F5

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions None	520210
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — F04 Hospital discharge: ICD-9 — 2940 Cause of death: ICD-10 — F04 Cause of death: ICD-9 — 2940 2 out of 7 registries used, show all original rules.	44
4. Check minimum number of events None	44
5. Include endpoints None	44
6. Filter based on genotype QC (FinnGen only)	44

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	618	287	325
Only index persons	392	179	213
Unadjusted period prevalence (%)
Whole population	0.01	0.01	0.01
Only index persons	0.01	0.01	0.01
Median age at first event (years)
Whole population	61.45	66.15	57.14
Only index persons	58.87	62.16	56.10

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	44	14	30
Unadjusted period prevalence (%)	0.01	0.00	0.01
Median age at first event (years)	56.85	58.26	56.20

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

No data

-FinnGen-

Cumulative Incidence Function

Not a core endpoint, no data to show.

CodeWAS (R11)

↥

CodeWAS is a tool for exploring the associations between an endpoint and all of the medical codes and drug codes.

This is a new tool, please reach out using the contact form for feedback and improvement ideas.

First, a cohort is built by matching controls to the endpoint cases using year of birth and sex. Then, a Fisher test is done for all the medical codes and drug codes between the cases and controls of this cohort. Codes are reported in the table below if they have −log₁₀(p-value) ≥ 6.

No data available

LabWAS

↥

(ID) Name

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(3044938) Influenza virus A RNA [Presence] in Specimen by NAA with probe detection

3.00

2.48

2.6

1.6

—

(3023368) Bacteria identified in Blood by Culture

102

2.52

2.21

6.5

3.8

—

(3032080) INR in Blood by Coagulation assay

141

2.32

1.95

12.5

10.6

1.7

1.3

inr

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

4.55

1.87

2.0

3.7

—

(3026008) Bacteria identified in Urine by Culture

101

2.32

1.85

3.1

3.0

—

(3012544) pH of Venous blood

3.27

1.81

2.6

2.7

—

(3026782) Osmolality of Urine

2.35

1.67

4.3

2.8

499.2

528.8

mosm/kgh2o

0.26

(3006140) Bilirubin.total [Moles/volume] in Serum or Plasma

167

2.15

1.64

5.7

6.3

11.2

11.8

umol/l

0.16

160

(3025941) Bacteria identified in Stool by Culture

3.38

1.48

2.0

1.2

—

(40768797) Stomach Pathology biopsy report

0.00

1.40

0.0

1.2

—

(3037467) Urinalysis macro (dipstick) panel - Urine

206

1.99

1.31

5.9

4.9

—

(3029937) Albumin [Presence] in Urine by Test strip

2.04

1.28

7.0

4.4

0.0

estimate

—

(40763086) Leukocyte esterase [Presence] in Urine by Automated test strip

123

1.96

1.28

6.7

4.4

—

(3019902) Methicillin resistant Staphylococcus aureus [Presence] in Specimen by Organism specific culture

2.49

1.16

3.7

3.9

—

(1761868) Lipid panel - Serum or Plasma

118

0.43

1.16

2.8

—

(3000850) Epithelial cells [#/volume] in Urine

1.95

1.06

4.6

2.8

3.2

5.5

e6/l

0.74

(3043924) Respiratory syncytial virus RNA [Identifier] in Specimen by NAA with probe detection

2.12

1.02

3.4

1.6

—

(3001079) Blood group antibody screen [Presence] in Serum or Plasma

133

1.75

0.96

4.2

4.0

—

(3029287) Urinalysis microscopic panel [#/volume] - Urine by Automated count

126

1.73

0.90

4.3

3.2

—

(3019060) Gas panel - Arterial blood

2.08

0.88

7.3

3.7

—

(3035350) Ketones [Presence] in Urine by Test strip

155

1.68

0.86

6.2

4.2

0.0

estimate

—

(3021601) Nitrite [Presence] in Urine by Test strip

156

1.66

0.83

7.3

5.5

0.0

estimate

—

(4010399)

0.00

0.80

0.0

1.4

—

(3002109) Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma

0.00

0.80

0.0

2.0

—

(43054903) Holo-transcobalamin II [Moles/volume] in Serum

121

1.66

0.78

2.1

1.9

93.9

93.8

pmol/l

0.00

(3009261) Glucose [Presence] in Urine by Test strip

159

1.61

0.75

6.2

4.2

0.0

estimate

—

(3016431) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Serum or Plasma

150

1.61

0.74

6.4

5.5

1.2

mmol/l

0.17

123

(3038288) Influenza virus B RNA [Presence] in Specimen by NAA with probe detection

1.84

0.74

3.4

1.6

—

(36304419) Bacteria [Presence] in Urine

1.67

0.73

4.9

3.1

—

(40764999) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)

307

0.63

0.70

23.8

14.0

87.9

77.3

ml/min/173m2

1.00

247

(3013512) EKG study

106

1.63

0.70

3.7

4.3

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.88

0.68

1.8

1.5

—

(3017143) Hepatitis C virus Ab [Presence] in Serum

1.88

0.68

2.2

1.3

—

(3051552) Clostridioides difficile toxin genes [Presence] in Stool by NAA with probe detection

1.81

0.66

2.6

1.2

—

(40761535) Cells panel - Urine sediment

1.81

0.66

4.2

3.6

—

(40761536) Microorganisms panel - Urine sediment

1.75

0.63

9.8

3.9

—

(3008230) Borrelia burgdorferi IgM Ab [Units/volume] in Serum

0.00

0.62

0.0

2.4

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.62

0.0

1.3

—

(42870588) Differential panel, method unspecified - Blood

100

1.59

0.62

9.0

5.4

—

(3045783) Sodium and Potassium panel [Moles/volume] - Serum or Plasma

1.72

0.58

13.2

11.7

—

(3009508) Creatinine [Moles/volume] in Urine

111

1.53

0.56

3.8

2.9

6.2

8.1

mmol/l

—

(3000494) Fungus identified in Specimen by Culture

1.62

0.55

2.0

1.4

—

(46235355) HIV 1 and 2 tests - Meaningful Use set

1.62

0.55

2.3

1.5

—

(3006923) Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma

346

0.65

0.54

14.6

10.4

36.0

24.5

u/l

0.48

331

(3011397) Hemoglobin [Presence] in Urine by Test strip

1.61

0.52

7.1

4.1

—

(3042936) Bacteria identified in Isolate by Culture

1.62

0.51

2.3

2.1

—

(3044640) Blood type and Crossmatch panel - Blood

1.50

0.49

1.4

2.0

—

(3035941) MCH [Entitic mass]

353

0.66

0.49

44.4

21.2

30.5

30.4

0.12

346

(3024731) MCV [Entitic volume]

353

0.66

0.49

44.4

21.3

92.1

91.3

0.42

346

(3000963) Hemoglobin [Mass/volume] in Blood

353

0.66

0.49

44.8

21.5

131.8

137.1

g/l

1.01

345

(3048773) Triglyceride [Moles/volume] in Serum or Plasma --fasting

306

0.70

0.46

3.6

4.0

1.4

1.2

mmol/l

0.33

272

(3023520) Reticulocytes [#/volume] in Blood

1.69

0.45

2.4

3.4

67.6

61.5

e9/l

—

(3006315) Basophils [#/volume] in Blood

154

1.41

0.44

8.7

5.9

0.0

e9/l

0.52

133

(3001604) Monocytes [#/volume] in Blood

154

1.41

0.44

8.7

5.8

0.7

0.6

e9/l

1.31

133

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.42

0.0

1.5

—

(3044491) Cholesterol non HDL [Mass/volume] in Serum or Plasma

0.00

0.42

0.0

1.4

—

(40758558) Short blood count panel - Blood

1.48

0.41

7.2

6.1

—

(3020682) Albumin/Creatinine [Ratio] in Urine

118

1.41

0.41

5.5

3.6

11.1

8.6

mg/mmol

—

(3019198) Lymphocytes [#/volume] in Blood

156

1.38

0.40

8.8

6.2

1.9

1.7

e9/l

0.20

137

(40768804) Tissue Pathology biopsy report

132

0.69

0.39

2.2

1.9

—

(3021589) Normoblasts [#/volume] in Blood

139

1.36

0.36

16.4

11.2

0.0

e9/l

0.00

107

(40761511) CBC panel - Blood by Automated count

329

0.72

0.36

35.8

13.7

—

(3015736) pH of Urine

112

1.37

0.34

4.9

3.8

—

(3030467) Casts [#/volume] in Urine by Automated count

103

1.37

0.33

5.2

3.1

0.2

0.4

e6/l

0.60

(3002582) Erythrocytes [#/volume] in Urine

113

1.35

0.32

4.7

3.1

17.2

628.3

e6/l

0.53

(3012516) Albumin [Mass/volume] in Urine

106

1.32

0.27

3.9

2.9

72.1

60.3

mg/l

—

(3001784) Prostate Specific Ag Free/Prostate specific Ag.total in Serum or Plasma

128

1.26

0.22

3.3

4.4

24.9

22.1

—

(3008898) HLA-B27 [Presence]

0.00

0.21

0.0

1.0

—

(3018095) Leukocytes [#/volume] in Urine

119

1.26

0.21

5.3

3.6

5.8

96.2

e6/l

1.66

(3022217) INR in Platelet poor plasma by Coagulation assay

1.26

0.21

22.2

37.9

—

1.4

—

(1002224) Polysomnography panel

0.00

0.21

0.0

1.1

—

(3045414) Leukocytes [Presence] in Urine

0.00

0.20

0.0

1.8

—

(46236098) ABO and Rh group [Type] in Blood by Confirmatory method

0.70

0.18

1.0

1.8

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.15

0.17

8.6

5.7

—

(3023103) Potassium [Moles/volume] in Serum or Plasma

337

0.82

0.16

30.8

16.7

4.0

mmol/l

0.59

328

(3041096) Erythrocytes [Presence] in Urine by Automated

1.23

0.15

5.3

3.8

—

(3020460) C reactive protein [Mass/volume] in Serum or Plasma

316

0.84

0.13

30.6

15.0

29.0

25.7

mg/l

0.29

252

(3019550) Sodium [Moles/volume] in Serum or Plasma

335

0.84

0.13

30.5

16.8

139.0

139.7

mmol/l

0.62

324

(3004789) Transferrin [Mass/volume] in Serum or Plasma

1.13

0.10

3.6

2.0

1.8

2.4

g/l

—

(3003694) ABO and Rh group [Type] in Blood

0.85

0.08

1.3

1.4

—

(3009542) Hematocrit [Volume Fraction] of Blood

280

1.10

0.05

27.9

15.8

39.1

40.3

0.14

195

(706163) SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory system specimen by NAA with probe detection

152

1.08

0.03

3.1

2.6

—

(3013603) Prostate specific Ag [Mass/volume] in Serum or Plasma

168

0.93

0.03

2.9

5.3

1.8

3.1

ug/l

0.71

145

(3002385) Erythrocyte distribution width [Ratio]

263

0.97

0.00

36.2

18.1

13.9

13.8

0.20

255

(3044889) 12 lead EKG panel

227

1.03

0.00

6.3

4.1

—

(40768793) Breast Pathology biopsy report

0.00

0.0

1.1

—

(3016881) Enterovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.0

—

(3016921) Smith extractable nuclear Ab [Units/volume] in Serum

0.00

0.0

1.3

—

(3027456) Digoxin [Moles/volume] in Serum or Plasma

0.00

0.0

2.6

—

0.7

—

(3006999) Ribonucleoprotein extractable nuclear Ab [Units/volume] in Serum

0.00

0.0

1.3

—

(3004383) Neutrophil cytoplasmic Ab.classic [Titer] in Serum by Immunofluorescence

0.00

0.0

1.4

—

(3027450) Sjogrens syndrome-B extractable nuclear Ab [Units/volume] in Serum

0.00

0.0

1.3

—

(3007778) Kappa light chains/Lambda light chains [Mass Ratio] in Serum

0.00

0.0

1.0

—

(40768800) Prostate Pathology biopsy report

0.00

0.0

1.1

—

(44790048)

0.00

0.0

1.1

—

(3008364) Apolipoprotein A-I [Mass/volume] in Serum or Plasma

0.00

0.0

1.6

—

(3029634) Reagin Ab [Titer] in Serum by VDRL

0.00

0.0

1.0

—

(3037551) Cancer Ag 125 [Units/volume] in Serum or Plasma

0.00

0.0

1.6

—

130.1

—

(4062490)

0.00

0.0

1.2

—

(3014791) Apolipoprotein B [Mass/volume] in Serum or Plasma

0.00

0.0

1.7

—

1.1

—

(3003327) Ova and parasites identified in Stool by Light microscopy

0.00

0.0

1.1

—

(3028369) Herpes simplex virus 1+2 DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.5

—

(44806118)

0.00

0.0

1.1

—

(3000620) Complement C3 [Mass/volume] in Serum or Plasma

0.00

0.0

1.4

—

1.2

—

(3001019) Free T4 and TSH panel - Serum or Plasma

0.00

0.0

1.4

—

(3025245) SCL-70 extractable nuclear Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.4

—

(3002434) Lupus erythematosus deoxynucleoproteins IgG Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.5

—

(3010521) Mycoplasma pneumoniae IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.3

—

(3024928) Oxygen saturation in Venous blood

0.00

0.0

1.3

—

(44790049)

0.00

0.0

1.1

—

(1175715) Chlamydophila pneumoniae IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.3

—

(3018387) Mycoplasma pneumoniae IgG Ab [Units/volume] in Serum

0.00

0.0

1.4

—

(3013527) Hepatitis B virus core IgM Ab [Presence] in Serum

0.00

0.0

1.2

—

(3027545) Mycoplasma pneumoniae Ab [Presence] in Serum by Immunoassay

0.00

0.0

2.0

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.0

1.0

—

(3025023) Rhinovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.0

—

(44790047)

0.00

0.0

1.1

—

(3006257) Acetylcholine receptor Ab [Moles/volume] in Serum

0.00

0.0

1.4

—

(3023150) Myeloperoxidase Ab [Units/volume] in Serum

0.00

0.0

2.7

—

(46237023) Hepatitis B virus core and surface Ab and surface Ag panel - Serum

0.00

0.0

1.1

—

(3023939) Sjogrens syndrome-A extractable nuclear Ab [Units/volume] in Serum

0.00

0.0

1.3

—

(3036086) Jo-1 extractable nuclear Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.3

—

(3014051) Protein [Presence] in Urine by Test strip

0.00

-0.00

0.0

2.2

—

(4094501)

0.00

-0.00

0.0

1.1

—

Mortality – FinRegistry

↥

Association

Association between endpoint F5_ORGAMN and mortality.

Females

Parameter	HR [95% CI]	p-value
F5_ORGAMN	2.828 [1.83, 4.37]	< 0.001
Birth year	0.996 [0.99, 1.0]	0.35

During the follow-up period (1.1.1998 — 31.12.2019), 104 out of 182 females with F5_ORGAMN died.

Males

Parameter	HR [95% CI]	p-value
F5_ORGAMN	3.338 [2.2, 5.06]	< 0.001
Birth year	0.991 [0.98, 1.0]	0.056

During the follow-up period (1.1.1998 — 31.12.2019), 116 out of 217 males with F5_ORGAMN died.

Mortality risk

Mortality risk for people of age

years, who have F5_ORGAMN.

N-year risk	Females	Males
1	0.201%	0.622%
5	1.661%	3.742%
10	4.01%	10.027%
15	7.3%	18.649%
20	13.199%	29.477%

Relationships between endpoints

↥

Index endpoint: F5_ORGAMN – Organic amnesic syndrome, not induced by alcohol and other psychoactive substances

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

rg [CI]

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

NAME	F5_ORGAMN
CONTROL_EXCLUDE	F5_ORGANIC
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	F04
HD_ICD_9	2940
HD_ICD_8	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	F04
COD_ICD_9	2940
COD_ICD_8	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
COD_ICD_10_EXCL
COD_ICD_9_EXCL
COD_ICD_8_EXCL
OPER_NOM
OPER_HL
OPER_HP1
OPER_HP2
KELA_REIMB
KELA_REIMB_ICD
KELA_ATC_NEEDOTHER
KELA_ATC
KELA_VNRO_NEEDOTHER
KELA_VNRO
CANC_TOPO
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

Organic amnesic syndrome, not induced by alcohol and other psychoactive substances

Endpoint definition

Endpoint definition steps

FinnGen

Phenotype data

1. Apply sex-specific rule

2. Check conditions

3. Check pre-conditions, main-only, mode, registry filters

4. Check minimum number of events

5. Include endpoints

6. Filter based on genotype QC (FinnGen only)

Similar endpoints

Case counts by codes

Summary Statistics

-FinRegistry-

Key figures

-FinnGen-

Key figures

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints