Risteys · F5

Endpoint definition steps	FinnGen
Phenotype data	557745
1. Apply sex-specific rule None	557745
2. Check conditions None	557745
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.	51
4. Check minimum number of events None	51
5. Include endpoints None	51
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

↥

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

↥

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(3023368) Bacteria identified in Blood by Culture

106

2.84

2.87

7.0

4.2

—

(40767503) Oxygen content in Capillary blood by calculation

7.84

2.61

7.4

3.6

17.82

16.23

—

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

2.59

1.94

3.3

1.7

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

4.54

1.87

2.0

3.8

—

(40768797) Stomach Pathology biopsy report

0.00

1.83

0.0

1.2

—

(3025941) Bacteria identified in Stool by Culture

3.17

1.40

2.0

1.2

—

(3026008) Bacteria identified in Urine by Culture

112

2.01

1.36

3.6

3.3

—

(3014162) Mycobacterium tuberculosis DNA [Presence] in Specimen by NAA with probe detection

2.99

1.32

4.8

2.0

—

(1761868) Lipid panel - Serum or Plasma

132

0.44

1.25

3.0

3.5

—

(3026782) Osmolality of Urine

2.03

1.23

4.8

3.1

516.64

513.94

mosm/kgh2o

0.02

(4010399) Spirometry for bronchospasm with prolonged evaluation after bronchodilator

0.00

1.22

0.0

1.4

—

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

2.21

1.19

4.1

3.8

—

(3019060) Gas panel - Arterial blood

2.57

1.18

8.6

4.0

—

(3037467) Urinalysis macro (dipstick) panel - Urine

223

1.85

1.09

6.4

5.0

—

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

143

1.72

0.92

7.5

4.6

0.00

estimate

—

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

191

1.70

0.90

6.4

6.5

11.56

11.69

umol/l

0.03

181

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

2.08

0.88

2.3

1.3

—

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

147

1.65

0.81

2.9

2.6

—

estimate

—

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

318

0.62

0.72

4.0

4.4

1.42

1.24

mmol/l

0.33

288

(40761535) Cells panel - Urine sediment

1.96

0.71

4.0

3.7

—

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

134

1.57

0.67

5.2

3.5

—

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

352

0.62

0.67

16.6

12.3

30.19

24.85

u/l

0.38

341

(3044640) Blood type and Crossmatch panel - Blood

107

1.60

0.67

1.4

2.0

—

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

1.69

0.65

2.1

1.6

—

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

108

1.58

0.64

8.5

4.7

0.00

estimate

—

(3042936) Bacteria identified in Isolate by Culture

1.65

0.64

2.1

—

(3009542) Hematocrit [Volume Fraction] of Blood by calculation

359

0.62

50.3

25.9

38.64

40.71

0.75

354

(3000963) Hemoglobin [Mass/volume] in Blood

359

0.62

50.6

25.5

131.72

136.43

g/l

0.86

354

(21494755) Public health laboratory ask at order entry panel

0.00

0.62

0.0

1.3

—

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

1.82

0.60

13.2

12.2

—

(3014576) Chloride [Moles/volume] in Serum or Plasma

1.59

0.59

4.2

7.7

99.89

104.61

mmol/l

—

(40768804) Tissue Pathology biopsy report

142

0.62

0.58

2.2

2.0

—

(3023520) Reticulocytes [#/volume] in Blood

1.67

0.57

2.5

3.6

70.67

62.29

e9/l

—

(40761511) CBC panel - Blood by Automated count

339

0.65

0.56

39.6

15.3

—

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

1.56

0.56

5.8

2.9

3.57

4.40

e6/l

0.25

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

1.66

0.52

4.6

1.7

—

(36304419) Bacteria [Presence] in Urine

104

1.50

0.51

5.4

3.3

—

estimate

—

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

1.58

0.50

4.6

1.7

—

(40761536) Microorganisms panel - Urine sediment

1.63

0.44

11.4

4.1

—

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

184

1.38

0.42

7.0

4.4

0.00

estimate

—

(3045424) Erythrocytes [Presence] in Urine

0.00

0.42

0.0

2.1

—

0.00

—

(1002224) Polysomnography panel

0.00

0.42

0.0

1.2

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.42

0.0

1.5

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.53

0.42

1.8

1.6

—

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

185

1.37

0.40

7.1

4.5

0.00

estimate

—

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

1.44

0.39

2.6

1.3

—

(3000494) Fungus identified in Specimen by Culture

1.45

0.37

2.0

1.5

—

(3022145) Colonoscopy Study observation

1.42

0.36

2.3

1.2

—

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

111

1.38

0.35

5.8

3.4

0.16

0.25

e6/l

0.38

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

188

1.33

0.35

7.1

4.5

0.00

estimate

—

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

152

1.31

0.30

2.3

2.0

90.92

94.09

pmol/l

0.13

(40758558) Short blood count panel - Blood

105

1.33

0.29

8.1

5.9

—

(3003338) MCHC [Entitic Mass/volume] in Red Blood Cells

258

0.78

0.29

41.3

22.8

331.52

331.91

g/l

0.09

258

(3015736) pH of Urine

135

1.29

0.26

4.7

3.8

6.55

6.38

—

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

175

1.26

0.24

8.8

7.1

1.21

1.20

mmol/l

0.21

151

(42870588) Differential panel, method unspecified - Blood

117

1.29

0.24

9.5

5.1

—

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

342

0.78

0.23

36.3

20.6

4.05

4.01

mmol/l

0.50

337

(3019284) Hepatitis B virus surface Ag [Presence] in Serum

1.25

0.23

2.0

1.4

—

(3002582) Erythrocytes [#/volume] in Urine

128

1.26

0.22

5.6

3.3

17.45

549.77

e6/l

0.53

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

341

0.79

0.22

35.9

20.6

138.88

139.77

mmol/l

0.79

335

(3008898) HLA-B27 [Presence]

0.00

0.21

0.0

1.0

—

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

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.2

—

(3021589) Normoblasts [#/volume] in Blood

160

1.21

0.18

19.5

13.7

0.00

e9/l

0.50

127

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

0.73

0.17

1.0

2.0

—

(3020682) Albumin/Creatinine [Ratio] in Urine

134

1.18

0.13

6.6

3.9

8.58

12.59

mg/mmol

—

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

154

1.17

0.12

3.4

2.6

—

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

135

1.17

0.11

3.8

4.8

24.90

23.45

—

(3006315) Basophils [#/volume] in Blood

175

1.15

0.11

9.7

6.2

0.03

0.04

e9/l

0.77

147

(3001604) Monocytes [#/volume] in Blood

175

1.15

0.11

9.6

6.1

0.71

0.60

e9/l

1.08

147

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

0.83

0.09

4.6

2.5

1.81

2.33

g/l

—

(3019198) Lymphocytes [#/volume] in Blood

177

1.13

0.08

9.8

6.5

1.84

1.69

e9/l

0.24

153

(3041096) Erythrocytes [Presence] in Urine by Automated

113

1.08

0.02

6.4

3.9

0.00

estimate

—

(3012516) Albumin [Mass/volume] in Urine

124

1.07

0.01

5.2

3.2

56.83

72.75

mg/l

—

(3007220) Creatine kinase [Enzymatic activity/volume] in Serum or Plasma

123

0.97

0.00

3.2

2.0

196.25

322.81

u/l

0.38

117

(3002030) Lymphocytes/Leukocytes in Blood

165

0.95

0.00

11.2

6.2

19.94

25.93

1.12

159

(3011985) Renin [Units/volume] in Plasma

0.00

-0.00

0.0

1.2

—

14.08

—

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

0.00

-0.00

0.0

1.3

—

(4062490) Immunoglobulin typing, IgG

0.00

-0.00

0.0

1.2

—

(3012413) Glucose [Moles/volume] in Serum or Plasma --2 hours post meal

0.00

-0.00

0.0

1.2

—

9.78

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.00

-0.00

10.1

5.8

—

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

1.03

-0.00

1.4

—

(3026285) Alpha 1 antitrypsin [Mass/volume] in Serum or Plasma

0.00

-0.00

0.0

1.0

—

1.39

—

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

0.00

-0.00

0.0

1.4

—

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

0.00

-0.00

0.0

2.6

—

116.28

—

(3044941) Cell count panel - Synovial fluid

0.00

-0.00

0.0

1.0

—

(4024509) Urine culture

0.00

-0.00

0.0

1.8

—

(3000093) Morphology [Interpretation] in Blood Narrative

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.6

—

1.17

—

(3017766) Complement C4 [Mass/volume] in Serum or Plasma

0.00

-0.00

0.0

1.5

—

0.25

—

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

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.7

—

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

0.00

-0.00

0.0

1.0

—

(3010838) Calcium [Moles/time] in 24 hour Urine

0.00

-0.00

0.0

1.3

—

6.83

—

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

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.3

—

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

0.00

-0.00

0.0

1.4

—

(40768800) Prostate Pathology biopsy report

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

1.3

—

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

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

3.0

—

0.89

—

(40763571) Iron/Transferrin [Ratio] in Serum or Plasma

0.90

-0.00

4.6

2.5

18.80

22.05

—

(4094501) Cardiovascular stress test using bicycle ergometer

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

1.4

—

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

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

1.2

—

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

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints