Cholera

AB1_CHOLERA

No definition available.

Endpoint definition

↥

Report an error or suggest an improvement for this endpoint codes

Endpoint definition steps	FinnGen
Phenotype data	519972
1. Apply sex-specific rule None	519972
2. Check conditions None	519972
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — A00 Hospital discharge: ICD-9 — 00[1] Hospital discharge: ICD-8 — 00001\|00010\|00097\|00099 Cause of death: ICD-10 — A00 Cause of death: ICD-9 — 00[1] Cause of death: ICD-8 — 00001\|00010\|00097\|00099 2 out of 7 registries used, show all original rules.	46
4. Check minimum number of events None	46
5. Include endpoints None	46
6. Filter based on genotype QC (FinnGen only)	46

Control definitions (FinnGen only)

Control exclude: AB1_INTESTINAL_INFECTIONS

Extra metadata

Level in the ICD hierarchy: 3
First used in FinnGen datafreeze: DF5

NAME	AB1_CHOLERA
CONTROL_EXCLUDE	AB1_INTESTINAL_INFECTIONS
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	A00
HD_ICD_9	00[1]
HD_ICD_8	00001\|00010\|00097\|00099
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	A00
COD_ICD_9	00[1]
COD_ICD_8	00001\|00010\|00097\|00099
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

Similar endpoints

↥

List of similar endpoints to Cholera based on the number of shared cases.

Similar with more cases:

Similar with less cases:

None

Case counts by codes

↥

FinnGen case counts by registry codes:

Upset plot

Full data table

Summary Statistics

↥

-FinRegistry-

This endpoint is excluded (different definition than used in FinnGen).

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	46	22	24
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	54.65	36.85	70.97

-FinnGen-

Age distribution of first events

-FinnGen-

Year distribution of first events

-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

4.04

5.08

8.8

3.1

—

(3017895) Helicobacter pylori Ab [Units/volume] in Serum

13.49

3.87

1.7

1.8

—

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

113

3.07

3.39

4.7

3.1

—

(3022217) INR in Platelet poor plasma by Coagulation assay

163

3.11

3.36

19.6

14.7

1.15

1.25

inr

0.38

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

3.10

3.19

5.2

2.0

—

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

10.98

3.05

1.2

1.0

—

(3044640) Blood type and Crossmatch panel - Blood

107

2.77

2.79

4.4

2.1

—

(3021447) Carbon dioxide [Partial pressure] in Venous blood

4.21

2.75

2.9

5.7

5.39

5.69

kpa

—

(36304419) Bacteria [Presence] in Urine

2.72

2.55

3.8

2.8

—

(3027315) Oxygen [Partial pressure] in Blood

5.56

2.48

5.5

2.8

8.22

8.65

kpa

—

(3013290) Carbon dioxide [Partial pressure] in Blood

5.56

2.48

5.5

2.8

5.13

4.92

kpa

—

(3051714) Fibrin D-dimer FEU [Mass/volume] in Platelet poor plasma

2.79

2.43

1.6

1.19

1.04

mg/l

—

(3028271) Lactate [Moles/volume] in Capillary blood

6.84

2.43

2.8

1.6

1.62

1.57

mmol/l

—

(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma

130

2.54

2.42

4.4

3.7

22.47

24.65

ng/l

0.14

(40771025) 25-Hydroxyvitamin D3+25-Hydroxyvitamin D2 [Moles/volume] in Serum or Plasma

132

2.48

2.32

3.3

2.4

78.48

73.22

nmol/l

0.37

118

(3022806) Fractional oxyhemoglobin in Capillary blood

5.45

2.12

2.8

1.4

89.44

90.43

—

(3003284) Neutrophil cytoplasmic Ab.perinuclear [Titer] in Serum by Immunofluorescence

5.45

2.12

2.0

1.5

—

(3022313) Gas panel - Capillary blood

5.45

2.12

1.6

—

(3021589) Normoblasts [#/volume] in Blood

164

2.35

2.07

20.9

10.0

0.01

0.00

e9/l

0.48

131

(3013115) Eosinophils [#/volume] in Blood

196

2.30

1.91

10.3

4.5

0.15

0.18

e9/l

0.59

173

(3007628) Bicarbonate [Moles/volume] standard in Venous blood

4.53

1.87

2.8

6.7

23.00

23.65

mmol/l

—

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

3.67

1.81

4.5

1.1

—

(3025941) Bacteria identified in Stool by Culture

4.17

1.76

2.4

1.2

—

(3042936) Bacteria identified in Isolate by Culture

2.69

1.72

2.3

2.0

—

(40760892) CBC W Ordered Manual Differential panel - Blood

173

2.16

1.72

11.5

4.9

—

(43055554) Base excess.100% oxygenated [Moles/volume] standard in Capillary blood by calculation

3.47

1.72

2.3

3.47

1.33

mmol/l

—

(3002256) Pathology report gross observation

2.62

1.69

1.2

1.3

—

(3016293) Bicarbonate [Moles/volume] in Serum or Plasma

2.99

1.65

6.1

5.8

26.44

24.48

mmol/l

—

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

157

2.11

1.64

7.2

1.20

1.21

mmol/l

0.23

132

(3013512) EKG study

2.23

1.59

4.9

4.2

—

(3027273) Bicarbonate [Moles/volume] in Venous blood

3.60

1.56

2.4

4.5

22.70

23.33

mmol/l

—

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

2.41

1.53

2.8

1.5

—

(3015399) Transferrin receptor.soluble [Mass/volume] in Serum or Plasma

2.13

1.49

3.6

1.8

2.70

2.82

mg/l

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

3.37

1.48

1.2

1.3

—

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

101

2.08

1.46

6.1

3.7

0.00

estimate

—

(3018010) Neutrophils/100 leukocytes in Blood

181

2.00

1.45

10.3

4.6

63.10

58.55

1.42

170

(3019309) Folate [Moles/volume] in Red Blood Cells

2.27

1.43

1.8

1235.00

1301.19

nmol/l

—

(3002030) Lymphocytes/100 leukocytes in Blood

182

1.99

1.42

10.7

4.6

20.96

26.96

2.26

171

(3024354) Oxygen [Partial pressure] in Venous blood

2.84

1.42

2.0

3.8

4.70

4.13

kpa

—

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

137

1.98

1.39

2.7

1.9

76.94

100.23

pmol/l

—

(3022096) Basophils/100 leukocytes in Blood

174

1.96

1.37

10.4

4.4

0.62

0.65

0.11

158

(3037467) Urinalysis macro (dipstick) panel - Urine

233

2.01

1.35

7.4

4.2

—

(40761536) Microorganisms panel - Urine sediment

2.55

1.35

6.6

3.4

—

(3026008) Bacteria identified in Urine by Culture

104

2.01

1.34

6.8

2.9

—

(3006315) Basophils [#/volume] in Blood

187

1.90

1.26

11.1

4.6

0.03

0.04

e9/l

0.52

160

(3001604) Monocytes [#/volume] in Blood

187

1.90

1.26

11.1

4.6

0.59

0.58

e9/l

0.05

162

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

2.33

1.26

1.5

—

(3019069) Monocytes/100 leukocytes in Blood

178

1.89

1.25

10.6

5.0

8.54

8.52

0.01

166

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

2.27

1.22

1.5

—

(3006504) Eosinophils/100 leukocytes in Blood

179

1.87

1.22

10.4

4.6

2.22

2.76

0.84

165

(3000991) Gas panel - Venous blood

2.57

1.18

4.0

13.5

—

(40758558) Short blood count panel - Blood

1.94

1.15

11.8

4.3

—

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

164

1.80

1.11

4.7

2.3

—

(43054914) Glucose tolerance 2 hours panel - Serum or Plasma

2.24

1.08

1.6

—

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

2.11

1.02

9.4

11.1

102.57

105.17

mmol/l

—

(3022145) Colonoscopy Study observation

2.05

0.99

2.0

1.3

—

(4035726) Immunohistochemistry procedure

2.40

0.97

1.2

1.1

—

(3019900) Cholesterol [Moles/volume] in Serum or Plasma

336

2.05

0.96

4.4

4.2

4.19

4.44

mmol/l

0.94

312

(3048689) Calprotectin [Mass/mass] in Stool

2.09

0.95

7.6

2.0

160.13

113.95

ug/g

—

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

170

1.71

0.94

6.8

5.7

0.00

estimate

—

(3020682) Albumin/Creatinine [Ratio] in Urine

1.79

0.93

3.8

3.9

22.50

14.63

mg/mmol

—

(3020779) Urea [Moles/volume] in Serum or Plasma

2.22

0.93

16.5

6.9

7.93

10.73

mmol/l

—

(3009508) Creatinine [Moles/volume] in Urine

107

1.76

0.92

2.9

2.8

7.40

8.11

mmol/l

—

(3021879) Hepatitis B virus core Ab [Presence] in Serum

2.15

0.90

1.0

1.3

—

(3018418) pH of Serum or Plasma

108

1.74

0.89

3.8

4.2

7.40

—

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

172

1.67

0.89

5.7

4.0

0.00

estimate

—

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

173

1.66

0.86

5.7

4.0

0.20

0.00

estimate

—

(3044889) 12 lead EKG panel

242

1.69

0.86

4.7

3.8

—

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

137

1.66

0.83

5.5

4.3

—

(3001308) Cholesterol in LDL [Moles/volume] in Serum or Plasma

345

1.86

0.82

4.7

4.6

2.42

2.60

mmol/l

0.62

318

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

1.81

0.80

1.6

1.5

—

(3019225) pH of Specimen

2.31

0.79

4.2

—

(3019060) Gas panel - Arterial blood

2.31

0.79

9.8

3.6

—

(3012516) Albumin [Mass/volume] in Urine

1.68

0.75

3.2

3.0

144.75

115.06

mg/l

—

(3020630) Protein [Mass/volume] in Serum or Plasma

2.12

0.75

4.2

3.0

67.60

67.65

g/l

—

(3013721) Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma

105

1.64

0.72

4.7

3.1

36.87

30.19

u/l

0.48

100

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

1.69

0.65

1.5

1.4

—

(3013650) Neutrophils [#/volume] in Blood by Automated count

222

1.52

0.63

17.8

8.2

5.24

4.23

e9/l

0.63

196

(3005772) Bilirubin.conjugated [Moles/volume] in Serum or Plasma

1.76

0.59

4.8

2.3

11.67

4.79

umol/l

—

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

245

1.50

0.58

3.5

3.3

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.62

0.55

2.3

1.5

—

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

1.62

0.55

10.8

6.2

—

(3000494) Fungus identified in Specimen by Culture

1.65

0.52

1.9

1.4

—

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

1.56

0.51

3.8

3.2

—

(3022948) Iron [Moles/volume] in Serum or Plasma

1.49

0.45

2.6

12.82

16.83

umol/l

—

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

1.46

0.44

2.1

2.5

2.20

2.40

g/l

—

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

1.49

0.43

1.8

1.9

—

(3016502) Oxygen saturation in Arterial blood

1.58

0.43

10.8

11.0

94.52

95.77

—

(3000330) Specific gravity of Urine by Test strip

0.00

0.42

0.0

7.1

—

(4034850) Laboratory test

0.00

0.42

0.0

9.7

—

(3002173) Hemoglobin [Mass/volume] in Arterial blood

1.53

0.42

10.8

10.7

126.60

120.53

g/l

—

(3024889) Methemoglobin/Hemoglobin.total in Venous blood

0.00

0.41

0.0

3.1

—

0.74

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

0.00

0.41

0.0

3.0

—

1.62

—

(3041096) Erythrocytes [Presence] in Urine by Automated

102

1.38

0.35

6.3

4.2

—

(1761482) Bacteria [#/volume] in Urine by Culture

0.00

0.21

0.0

7.9

—

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

0.00

0.21

0.0

1.0

—

(3008898) HLA-B27 [Presence]

0.00

0.21

0.0

1.0

—

(3020321) Streptococcus agalactiae [Presence] in Vaginal fluid by Organism specific culture

0.00

0.21

0.0

1.3

—

(3020961) Endomysium IgA Ab [Titer] in Serum

0.00

0.21

0.0

1.2

—

(1002224) Polysomnography panel

0.00

0.21

0.0

1.0

—

(3003510) Neisseria gonorrhoeae DNA [Presence] in Urine by NAA with probe detection

1.27

0.19

2.3

2.2

—

(3024950) Chlamydia trachomatis DNA [Presence] in Urine by NAA with probe detection

1.17

0.18

2.1

2.4

—

(3024135) Streptococcus.beta-hemolytic [Presence] in Throat by Organism specific culture

1.17

0.16

1.7

1.6

—

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

1.19

0.11

1.5

1.4

—

(40768804) Tissue Pathology biopsy report

135

1.16

0.11

2.6

2.1

—

(3018006) Microscopic observation [Identifier] in Cervix by Cyto stain.thin prep

1.12

0.10

1.2

1.6

—

(40768797) Stomach Pathology biopsy report

1.10

0.10

2.2

1.3

—

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

1.07

0.10

5.6

3.0

—

(3019832) Treponema pallidum Ab [Presence] in Serum

1.07

0.10

2.0

1.7

—

(1761868) Lipid panel - Serum or Plasma

129

1.12

0.06

3.7

2.9

—

(3027544) Mycobacterium sp identified in Sputum by Organism specific culture

0.00

-0.00

0.0

2.4

—

(3037756) Immunofixation for Serum or Plasma

0.00

-0.00

0.0

2.4

—

(3035285) Chloride [Moles/volume] in Venous blood

0.00

-0.00

0.0

2.7

—

109.71

—

(3033705) Calcium.ionized [Moles/volume] in Venous blood

0.00

-0.00

0.0

2.7

—

(3019473) Protein [Mass/volume] in Cerebral spinal fluid

0.00

-0.00

0.0

1.3

—

423.13

—

(3003740) Influenza virus B Ag [Presence] in Specimen

0.00

-0.00

0.0

1.5

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

-0.00

0.0

2.8

—

(3024403) Complement+Immunoglobulin [Units/volume] in Red Blood Cells

0.00

-0.00

0.0

1.1

—

(3003191) Choriogonadotropin (pregnancy test) [Presence] in Serum or Plasma

0.00

-0.00

0.0

1.5

—

(21494890) Protein electrophoresis panel - 24 hour Urine

0.00

-0.00

0.0

1.2

—

(3041354) Potassium [Moles/volume] in Venous blood

0.00

-0.00

0.0

2.7

—

4.00

—

(3015816) F5 gene p.Arg506Gln [Presence] in Blood or Tissue by Molecular genetics method

0.00

-0.00

0.0

1.2

—

(3028531) Enolase.neuron specific [Mass/volume] in Serum or Plasma

0.00

-0.00

0.0

2.2

—

14.46

—

(3050238) Crystals [Presence] in Synovial fluid by Light microscopy

0.00

-0.00

0.0

1.5

—

(3002482) Mycoplasma pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

1.0

—

(3024980) IgG subclass 4 [Mass/volume] in Serum

0.00

-0.00

0.0

1.5

—

0.55

—

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

0.00

-0.00

0.0

1.0

—

(3020287) Protein C actual/normal in Platelet poor plasma by Coagulation assay

0.00

-0.00

0.0

1.2

—

107.20

—

(21494670) JAK2 gene exon 14 targeted mutation analysis in Blood or Tissue by Molecular genetics method

0.00

-0.00

0.0

1.2

—

(44816844) Macroprolactin [Units/volume] in Serum or Plasma

0.00

-0.00

0.0

1.2

—

(3019150) Specific gravity of Urine by Refractometry

1.02

-0.00

4.8

4.1

—

1.01

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

-0.00

0.0

1.4

—

(40762119) U1 small nuclear ribonucleoprotein 70kD Ab [Units/volume] in Serum

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

4.5

—

0.67

—

(3032155) Metanephrine Free [Moles/volume] in Serum or Plasma

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

2.6

—

(3000855) Microscopic observation [Identifier] in Vaginal fluid by Gram stain

0.00

-0.00

0.0

1.6

—

(3017817) Protein [Mass] in Urine collected for unspecified duration

0.00

-0.00

0.0

1.7

—

(3031478) Chlamydophila pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

1.0

—

(3014973) Borrelia burgdorferi IgM Ab [Units/volume] in Cerebral spinal fluid

0.00

-0.00

0.0

1.4

—

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

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

1.0

—

(3000924) Streptococcus pyogenes [Presence] in Throat by Organism specific culture

0.00

-0.00

0.0

1.1

—

(3012477) Bordetella pertussis DNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

1.0

—

(3044290) Cell count panel - Cerebral spinal fluid

0.00

-0.00

0.0

1.3

—

(3011166) Borrelia burgdorferi Ab [Presence] in Cerebral spinal fluid

0.00

-0.00

0.0

1.4

—

(3015916) Alpha-1-Fetoprotein [Units/volume] in Serum or Plasma

0.00

-0.00

0.0

1.7

—

2.49

—

(3039162) Centromere protein B Ab [Units/volume] in Serum

0.00

-0.00

0.0

1.0

—

(3002523) Influenza virus A Ag [Presence] in Specimen

0.00

-0.00

0.0

1.5

—

(4094501) Cardiovascular stress test using bicycle ergometer

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

1.0

—

Mortality – FinRegistry

↥

This endpoint is excluded (different definition than used in FinnGen).

Relationships between endpoints

↥

Index endpoint: AB1_CHOLERA – Cholera

GWS hits: -

This endpoint is excluded (different definition than used in FinnGen).

≡ Risteys

R13

FinnGen R12 + FinRegistry

FinnGen R11 + FinRegistry

FinnGen R10 + FinRegistry

FinnGen R10

FinnGen R9

FinnGen R8

FinnGen R7

FinnGen R6

FinnGen R5

FinnGen R4

FinnGen R3

Cholera

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)

All original rules

Similar endpoints

Case counts by codes

Upset plot

Case counts by code for Cholera (AB1_CHOLERA)

Summary Statistics

-FinRegistry-

-FinnGen-

Key figures

-FinnGen-

Age distribution of first events

-FinnGen-

Year distribution of first events

-FinnGen-

Cumulative Incidence Function

CodeWAS

LabWAS

Mortality – FinRegistry

Relationships between endpoints