Risteys · AB1_TUBERCU

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 — A17 Hospital discharge: ICD-9 — 01[3] Hospital discharge: ICD-8 — 01[3] Cause of death: ICD-10 — A17 Cause of death: ICD-9 — 01[3] Cause of death: ICD-8 — 01[3] 2 out of 7 registries used, show all original rules.	52
4. Check minimum number of events None	52
5. Include endpoints None	52
6. Filter based on genotype QC (FinnGen only)	52

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	600	293	286
Only index persons	340	181	159
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	58.42	59.18	58.14
Only index persons	50.32	47.69	53.31

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	52	27	25
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	50.43	42.04	59.49

-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

unit

cases

controls

-log₁₀(p)

N cases

N controls

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

9.70

8.32

3.5

1.9

—

(3000991) Gas panel - Venous blood

4.54

4.04

10.1

11.8

—

(40758558) Short blood count panel - Blood

113

3.09

3.78

8.6

8.5

—

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

3.12

3.73

8.9

3.3

—

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

111

2.92

3.40

3.9

2.0

u/l

170.0

150.2

0.11

106

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

194

2.92

3.38

7.5

7.0

mmol/l

1.2

0.59

173

(3042936) Bacteria identified in Isolate by Culture

3.29

3.31

2.3

2.0

—

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

3.60

3.21

2.3

1.6

—

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

8.28

3.14

1.2

1.1

g/l

1.3

1.2

—

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

8.28

3.14

1.2

1.1

g/l

0.2

—

(3012544) pH of Venous blood

3.72

3.14

9.0

3.0

—

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

10.86

3.04

3.6

1.6

—

(36660697) Celiac disease serology panel - Serum

3.63

2.81

1.3

—

(3043109) Cytology report of Tissue fine needle aspirate Cyto stain

9.04

2.81

1.0

—

(3005702) Mycobacterium sp identified in Specimen by Organism specific culture

7.74

2.60

2.4

1.0

—

(3001604) Monocytes [#/volume] in Blood

215

2.46

16.8

5.4

e9/l

0.7

0.6

0.60

183

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

6.77

2.42

1.6

g/l

1.1

0.4

—

(3006315) Basophils [#/volume] in Blood

216

2.44

2.42

16.8

5.5

e9/l

0.0

1.60

185

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

2.64

2.39

2.2

1.7

—

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

2.69

2.39

2.3

1.9

—

(3018095) Leukocytes [#/volume] in Urine

156

2.33

2.29

5.7

3.1

e6/l

41.7

69.1

0.38

115

(3052851) Hemolysis interference index of Serum or Plasma

4.69

2.22

3.7

4.1

—

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

2.82

2.22

1.8

1.6

—

(40768797) Stomach Pathology biopsy report

2.82

2.22

1.2

1.4

—

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

261

2.45

2.21

18.0

10.0

e9/l

4.8

4.0

1.07

223

(42870588) Differential panel, method unspecified - Blood

125

2.32

2.17

14.5

4.7

—

(3020891) Body temperature

4.37

2.10

28.2

5.1

—

(3046870) Tissue transglutaminase IgG Ab [Units/volume] in Serum

4.37

2.10

1.3

1.1

—

(3023368) Bacteria identified in Blood by Culture

111

2.30

2.07

5.8

4.3

—

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

153

2.22

2.05

4.6

3.9

ng/l

14.4

31.3

1.95

108

(3000494) Fungus identified in Specimen by Culture

2.76

2.01

1.5

1.3

—

(3014007) Fractional oxyhemoglobin in Arterial blood

3.51

1.96

17.4

15.6

93.0

94.3

—

(3007164) IgA [Mass/volume] in Serum or Plasma

2.34

1.90

1.8

1.3

g/l

1.8

2.3

—

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

4.48

1.87

1.4

1.8

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

3.20

1.79

17.4

14.4

0.5

0.8

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

3.20

1.79

17.4

14.5

1.4

1.5

—

(3031040) Bacteria [#/volume] in Urine by Automated count

274

2.21

1.79

10.8

4.1

—

30.0

—

(3043723) Beta 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

4.13

1.75

2.0

1.0

—

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

4.13

1.75

1.6

1.5

—

(3004588) Protein electrophoresis panel - Serum or Plasma

2.95

1.64

2.6

2.7

—

(36031861) Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection

2.95

1.64

1.4

1.6

—

(3015736) pH of Urine

165

1.99

1.59

7.9

3.3

—

(3019060) Gas panel - Arterial blood

2.83

1.58

16.3

4.2

—

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

2.41

1.58

2.0

1.7

—

(3037467) Urinalysis macro (dipstick) panel - Urine

292

2.12

1.56

8.8

3.4

—

(3029879) Epithelial cells.squamous [#/volume] in Urine by Automated count

2.30

1.53

4.2

2.6

e6/l

0.4

4.8

—

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

214

1.95

1.50

7.4

3.5

estimate

0.0

—

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

214

1.95

1.50

9.3

4.3

estimate

0.0

—

(3018405) Lactate [Moles/volume] in Arterial blood

3.34

1.47

22.2

5.2

mmol/l

1.1

1.6

—

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

216

1.92

1.44

7.4

3.4

estimate

0.0

—

(36304419) Bacteria [Presence] in Urine

117

1.98

1.44

5.3

2.7

—

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

152

1.92

1.43

8.8

3.0

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.26

1.35

2.4

1.5

—

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

2.18

1.28

1.7

—

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

2.58

1.28

2.3

1.5

—

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

1.94

1.25

2.8

1.9

—

(40761535) Cells panel - Urine sediment

2.24

1.21

13.3

3.3

—

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

2.18

1.18

2.0

1.9

—

(1761868) Lipid panel - Serum or Plasma

144

0.48

1.16

2.1

2.8

—

(3026008) Bacteria identified in Urine by Culture

134

1.80

1.15

5.5

2.5

—

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

171

1.75

1.12

3.2

1.8

pmol/l

87.1

91.6

0.19

(3022621) pH of Urine by Test strip

2.52

1.11

1.2

2.4

—

(3025941) Bacteria identified in Stool by Culture

2.40

1.06

1.0

1.1

—

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

2.03

0.98

17.4

10.6

g/l

117.6

118.4

—

(3017732) Neutrophils [#/volume] in Blood

2.29

0.95

7.0

1.9

e9/l

4.1

2.8

—

(3000492) Spirometry study

2.20

0.93

4.0

1.5

—

(3012516) Albumin [Mass/volume] in Urine

120

1.62

0.77

4.5

3.3

mg/l

4117.1

84.4

0.46

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

2.19

0.77

1.2

1.4

—

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

2.19

0.77

4.2

6.8

mmol/l

23.5

25.4

—

(3008152) Bicarbonate [Moles/volume] in Arterial blood

2.10

0.75

43.6

7.8

mmol/l

26.7

23.8

—

(3004716) Salmonella sp identified in Stool by Organism specific culture

2.02

0.73

1.2

1.3

—

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

1.76

0.71

1.2

1.4

—

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

238

1.49

0.66

2.7

3.0

—

(3002256) Pathology report gross observation

1.71

0.65

1.1

1.2

—

(40768804) Tissue Pathology biopsy report

171

1.50

0.65

2.5

2.0

—

(3021589) Normoblasts [#/volume] in Blood

181

1.49

0.64

17.6

9.0

e9/l

0.0

0.50

150

(3032080) INR in Blood by Coagulation assay

172

1.48

0.63

9.4

9.3

inr

1.3

—

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

1.81

0.60

4.3

1.8

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

1.75

0.59

1.0

1.5

—

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

1.65

0.56

3.7

2.9

—

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

1.61

0.55

5.0

2.0

—

(3013512) EKG study

117

0.63

0.53

2.4

3.8

—

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

1.49

0.48

9.9

8.9

—

(3022217) INR in Platelet poor plasma by Coagulation assay

1.49

0.48

62.3

21.0

—

1.4

—

(3010156) C reactive protein [Mass/volume] in Serum or Plasma by High sensitivity method

0.00

0.42

0.0

1.5

—

1.2

—

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

1.46

0.42

1.3

1.6

—

(3041096) Erythrocytes [Presence] in Urine by Automated

120

0.70

0.41

2.8

3.2

—

(3044640) Blood type and Crossmatch panel - Blood

138

1.34

0.37

3.2

2.0

—

(3020564) Creatinine [Moles/volume] in Serum or Plasma

436

0.72

0.33

35.9

16.4

umol/l

79.3

78.6

0.05

436

(3026910) Gamma glutamyl transferase [Enzymatic activity/volume] in Serum or Plasma

268

1.28

0.32

4.9

2.7

u/l

42.8

46.7

0.19

248

(3009542) Hematocrit [Volume Fraction] of Blood

356

1.25

0.22

32.6

14.6

40.0

39.9

0.03

256

(4035726)

1.21

0.22

1.2

—

(3050129) First trimester maternal screen panel - Serum or Plasma

0.00

0.21

0.0

1.5

—

(40768800) Prostate Pathology biopsy report

0.00

0.21

0.0

1.3

—

(3008037) Lactate [Moles/volume] in Venous blood

0.00

0.21

0.0

2.5

—

1.4

—

(3016407) Fibrinogen [Mass/volume] in Platelet poor plasma by Coagulation assay

0.00

0.21

0.0

2.0

—

3.9

—

(37019628) Gastrointestinal bacterial pathogens panel - Stool by NAA with probe detection

0.00

0.21

0.0

1.3

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.21

0.0

1.5

—

(40761511) CBC panel - Blood by Automated count

430

0.78

0.21

27.1

12.7

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3044889) 12 lead EKG panel

289

1.18

0.17

5.1

3.6

—

(3020682) Albumin/Creatinine [Ratio] in Urine

131

1.20

0.17

5.2

3.8

mg/mmol

3.6

10.2

—

(40760892) CBC W Ordered Manual Differential panel - Blood

104

1.20

0.14

13.3

4.9

—

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

114

0.85

0.11

1.5

1.4

—

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

169

1.01

0.00

10.1

3.7

—

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

191

0.99

0.00

4.6

3.5

—

(3009201) Thyrotropin [Units/volume] in Serum or Plasma

372

0.98

0.00

7.3

4.4

mu/l

1.7

2.0

1.09

328

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

0.00

0.0

3.2

—

(3021901) Oxygen saturation in Capillary blood

0.00

0.0

3.8

—

(3005988) Vibrio sp identified in Specimen by Organism specific culture

0.00

0.0

1.3

—

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

0.00

0.0

1.0

—

1.3

—

(21493466) Plesiomonas shigelloides DNA [Presence] in Stool by NAA with non-probe detection

0.00

0.0

1.3

—

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

0.00

0.0

3.2

—

107.5

—

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

0.00

0.0

3.2

—

4.0

—

(3018572) Chloride [Moles/volume] in Blood

0.00

0.0

3.8

—

104.7

—

(3024522) Salmonella sp identified in Specimen by Organism specific culture

0.00

0.0

1.3

—

(3012568) Campylobacter sp identified in Specimen by Organism specific culture

0.00

0.0

1.3

—

(3039000) Anion gap in Blood

0.00

0.0

3.8

—

11.2

—

(4094501)

0.00

0.0

1.3

—

(40760847) Basement membrane Ab [Titer] in Serum by Immunofluorescence

0.00

0.0

1.4

—

(3011985) Renin [Units/volume] in Plasma

0.00

0.0

1.2

—

22.0

—

(21492888) Glucose tolerance 2 hours gestational panel - Serum or Plasma

0.00

0.0

1.1

—

(3025468) Yersinia sp identified in Specimen by Organism specific culture

0.00

0.0

1.3

—

(3038515) Glucose [Moles/volume] in Venous blood

0.00

0.0

2.7

—

7.0

—

(3019601) Blood group antibody investigation [Interpretation] in Plasma or RBC

0.00

0.0

1.0

—

(3045716) Anion gap in Serum or Plasma

0.00

0.0

2.2

—

6.4

—

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

0.00

0.0

1.4

—

(3005570) Glucose [Moles/volume] in Urine

0.00

0.0

3.0

—

(42868716) Shigella species+EIEC invasion plasmid antigen H ipaH gene [Presence] in Stool by NAA with probe detection

0.00

0.0

1.4

—

(3023419) Bacteria identified in Sputum by Culture

0.00

0.0

2.4

—

(1002102) Choriogonadotropin.intact+Beta subunit [Mass/volume] in Serum or Plasma

0.00

0.0

1.4

—

(3010566) Parathyrin.intact [Moles/volume] in Serum or Plasma

0.00

0.0

4.4

—

(3028707) Methadone [Presence] in Urine by Screen method

0.00

0.0

1.3

—

(42529200) Cancer Ag 15-3 [Units/volume] in Serum or Plasma by Immunoassay

0.00

0.0

3.8

—

100.4

—

(3038177) Helicobacter pylori Ab [Presence] in Serum

0.00

0.0

1.6

—

(3030408) 3-Methoxytyramine [Moles/volume] in Serum or Plasma

0.00

0.0

1.4

—

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

0.00

0.0

1.3

—

(4146454)

0.00

0.0

2.8

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.4

—

Mortality – FinRegistry

↥

Association

Association between endpoint AB1_TUBERCU_NEU and mortality.

Females

No data

Males

Parameter	HR [95% CI]	p-value
AB1_TUBERCU_NEU	3.102 [1.98, 4.86]	< 0.001
Birth year	0.985 [0.98, 1.0]	0.003

During the follow-up period (1.1.1998 — 31.12.2019), 59 out of 121 males with AB1_TUBERCU_NEU died.

Mortality risk

Mortality risk for people of age

years, who have AB1_TUBERCU_NEU.

N-year risk	Females	Males
1	No data	0.547%
5	No data	3.433%
10	No data	8.635%
15	No data	15.568%
20	No data	24.871%

Relationships between endpoints

↥

Index endpoint: AB1_TUBERCU_NEU – Tuberculosis of nervous system

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

Extremity

rg [CI]

Extremity

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

NAME	AB1_TUBERCU_NEU
CONTROL_EXCLUDE	AB1_TUBERCULOSIS
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	A17
HD_ICD_9	01[3]
HD_ICD_8	01[3]
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	A17
COD_ICD_9	01[3]
COD_ICD_8	01[3]
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

Tuberculosis of nervous system

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