Risteys · CD2_INSITU

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions not C3_STOMACH	518250
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D00.2& Hospital discharge: ICD-9 — 2302A Cause of death: ICD-10 — D00.2& Cause of death: ICD-9 — 2302A Cancer registry: Topography ICD-O-3 — C16 Cancer registry: Morphology ICD-O-3 — ANY Cancer registry: Behaviour codes — 2 3 out of 7 registries used, show all original rules.	26
4. Check minimum number of events None	26
5. Include endpoints None	26
6. Filter based on genotype QC (FinnGen only)	26

Summary Statistics

↥

-FinRegistry-

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	26	6	20
Unadjusted period prevalence (%)	0.01	0.00	0.01
Median age at first event (years)	75.60	76.39	75.37

-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 (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

(40768797) Stomach Pathology biopsy report

18.21

12.99

4.9

1.3

—

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

9.06

7.38

4.3

2.0

—

(3044640) Blood type and Crossmatch panel - Blood

10.74

7.19

4.2

2.2

—

(3002256) Pathology report gross observation

10.21

6.85

1.6

1.2

—

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

8.63

6.83

6.4

5.5

104.9

102.4

mmol/l

0.78

(4035726)

8.93

6.14

1.4

—

(3013742) Prealbumin [Mass/volume] in Serum or Plasma

22.05

5.83

2.3

2.8

0.2

g/l

—

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

15.25

4.57

5.1

8.5

25.1

22.7

mmol/l

—

(3014218) Bicarbonate [Moles/volume] standard in Arterial blood

13.05

4.29

7.1

7.6

24.0

23.9

mmol/l

—

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

5.72

4.15

4.2

3.4

—

(3000991) Gas panel - Venous blood

9.04

4.02

6.5

5.3

—

(40768804) Tissue Pathology biopsy report

5.11

3.99

3.2

2.2

—

(42870588) Differential panel, method unspecified - Blood

5.11

3.99

7.5

5.7

—

(3021347) Calcium.ionized [Moles/volume] in Serum or Plasma

5.12

3.86

6.3

1.2

mmol/l

1.33

(3014111) Lactate [Moles/volume] in Serum or Plasma

8.22

3.44

7.3

5.7

0.8

1.3

mmol/l

—

(3033658) Prothrombin time (PT) actual/Normal

4.58

3.39

8.3

3.5

84.5

80.1

0.20

(3024561) Albumin [Mass/volume] in Serum or Plasma

4.53

3.35

8.4

4.4

35.6

35.2

g/l

0.10

(3014007) Fractional oxyhemoglobin in Arterial blood

7.51

3.26

7.1

7.9

95.9

91.8

—

(40762366) Oxygen capacity [Volume Fraction] in Arterial blood

9.30

3.24

8.0

9.8

—

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

6.28

3.22

6.5

7.2

121.0

122.9

g/l

—

(3013826) Glucose [Moles/volume] in Serum or Plasma

110

4.52

3.09

9.9

4.9

7.5

6.8

mmol/l

0.95

103

(3018010) Neutrophils/100 leukocytes in Blood

4.15

3.07

9.6

7.2

56.6

59.6

0.35

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

106

3.92

2.75

13.1

4.9

9.2

11.0

umol/l

0.85

100

(3025941) Bacteria identified in Stool by Culture

6.71

2.71

1.2

1.4

—

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

8.48

2.67

1.8

1.9

—

(3006418) Campylobacter sp identified in Tissue by Organism specific culture

8.48

2.67

1.0

1.1

—

(42529406) Shigella sp [Presence] in Stool by Culture

8.48

2.67

1.0

1.1

—

(3014765) Yersinia sp identified in Stool by Organism specific culture

8.48

2.67

1.0

1.1

—

(3042936) Bacteria identified in Isolate by Culture

4.54

2.52

2.3

1.4

—

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

7.40

2.48

1.8

1.1

—

(3003396) Base excess in Arterial blood by calculation

4.34

2.42

6.5

5.9

-0.3

0.8

mmol/l

—

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

4.63

2.34

2.9

1.6

—

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

6.56

2.32

1.0

1.4

—

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

6.56

2.32

1.8

—

(3007853) Bacteria identified in Skin by Aerobe culture

4.16

2.14

2.6

1.3

—

(36304419) Bacteria [Presence] in Urine

3.19

2.06

4.3

2.8

—

(3018095) Leukocytes [#/volume] in Urine

3.11

2.03

5.4

3.7

7.0

50.0

e6/l

—

(3023368) Bacteria identified in Blood by Culture

2.94

1.84

8.4

4.1

—

(3006315) Basophils [#/volume] in Blood

2.81

1.71

9.9

7.1

0.0

e9/l

—

(3001604) Monocytes [#/volume] in Blood

2.81

1.71

9.9

7.1

0.7

0.6

e9/l

—

(3035995) Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma

139

2.89

1.63

17.9

7.0

98.5

78.2

u/l

1.15

129

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

2.71

1.61

3.0

2.4

94.6

84.8

pmol/l

—

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

2.42

1.30

4.4

3.0

—

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

2.56

1.08

2.8

2.1

—

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

2.06

0.93

1.5

2.3

1.2

1.9

mg/l

—

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

167

2.33

0.89

48.5

17.3

25.5

27.7

mg/l

0.18

138

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

170

2.22

0.89

47.7

20.8

139.2

139.4

mmol/l

0.06

165

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

171

2.18

0.88

48.0

20.6

4.0

mmol/l

0.10

165

(3044889) 12 lead EKG panel

116

1.99

0.83

5.1

4.7

—

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

1.96

0.78

2.4

2.2

—

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

2.23

0.77

2.8

2.1

—

(40761511) CBC panel - Blood by Automated count

172

2.14

0.73

27.6

14.4

—

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

176

2.00

0.72

52.7

20.0

89.9

83.7

umol/l

0.30

176

(40758558) Short blood count panel - Blood

1.96

0.72

12.9

8.2

—

(3015736) pH of Urine

1.78

0.61

3.6

4.5

—

(3026361) Erythrocytes [#/volume] in Blood

181

1.83

0.57

61.7

24.5

4.3

4.4

e12/l

0.53

175

(3010813) Leukocytes [#/volume] in Blood

181

1.83

0.57

62.0

24.5

14.2

7.1

e9/l

0.53

174

(3007461) Platelets [#/volume] in Blood

181

1.83

0.57

61.7

24.5

237.0

232.9

e9/l

0.11

175

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

1.80

0.56

1.7

4.2

—

(1761868) Lipid panel - Serum or Plasma

1.62

0.52

3.1

3.5

—

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

1.55

0.46

2.1

2.4

182.3

428.1

u/l

—

(3025839) Triglyceride [Moles/volume] in Serum or Plasma

1.55

0.39

1.3

1.9

1.2

mmol/l

—

(3041096) Erythrocytes [Presence] in Urine by Automated

1.47

0.35

5.6

4.4

—

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

1.27

0.23

1.0

1.5

—

(3020891) Body temperature

0.00

0.22

0.0

5.4

—

(3022313) Gas panel - Capillary blood

0.00

0.21

0.0

2.9

—

(3013512) EKG study

1.25

0.19

9.1

5.4

—

(3037467) Urinalysis macro (dipstick) panel - Urine

133

1.30

0.18

5.1

4.9

—

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

1.22

0.10

4.4

2.6

—

(3026008) Bacteria identified in Urine by Culture

0.80

0.09

4.8

3.1

—

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

109

1.19

0.08

5.6

2.8

184.3

54.9

u/l

0.62

101

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

0.00

0.0

2.2

—

(3020565) Legionella pneumophila DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.8

—

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

0.00

0.0

2.0

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.5

—

(40765161) Human bocavirus DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.7

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.2

—

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

0.98

0.00

5.4

4.7

—

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

0.00

0.0

1.2

—

(3042194) Human metapneumovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.4

—

(21494890) Protein electrophoresis panel - 24 hour Urine

0.00

0.0

1.4

—

(44790049)

0.00

0.0

1.0

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.2

—

(3005570) Glucose [Moles/volume] in Urine

0.00

0.0

1.0

—

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

0.00

0.0

1.7

—

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

0.00

0.0

1.4

—

(3003181) Sodium [Moles/volume] in Urine

0.00

0.0

1.2

—

53.2

—

(4024509)

0.00

0.0

1.0

—

(44790047)

0.00

0.0

1.0

—

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

0.00

0.0

1.7

—

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

0.00

0.0

1.6

—

1.3

—

(44790048)

0.00

0.0

1.0

—

(3009340) Metanephrine [Moles/volume] in Serum or Plasma

0.00

0.0

1.4

—

(3040853) Adenovirus DNA [Identifier] in Specimen by NAA with probe detection

0.00

0.0

1.4

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.0

7.1

—

(3042111) Morphology [Interpretation] in Bone marrow Narrative

0.00

0.0

1.4

—

(42868544) Hantavirus puumala IgM Ab [Presence] in Serum or Plasma by Immunofluorescence

0.00

0.0

1.2

—

(44806118)

0.00

0.0

1.0

—

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

0.00

-0.00

0.0

7.8

—

(3030692) Respiratory virus DNA+RNA [Identifier] in Specimen by NAA with probe detection

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

1.6

—

Mortality – FinRegistry

↥

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

Relationships between endpoints

↥

Index endpoint: CD2_INSITU_STOMACH – Carcinoma in situ of stomach

GWS hits: -

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

NAME	CD2_INSITU_STOMACH
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS	!C3_STOMACH
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D002
HD_ICD_9	2302A
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	D002
COD_ICD_9	2302A
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	C16
CANC_TOPO_EXCL
CANC_MORPH	ANY
CANC_MORPH_EXCL
CANC_BEHAV	2

≡ Risteys

FG R12 + FR

FinnGen R11 + FinRegistry

FinnGen R10 + FinRegistry

FinnGen R10

FinnGen R9

FinnGen R8

FinnGen R7

FinnGen R6

FinnGen R5

FinnGen R4

FinnGen R3

Carcinoma in situ of stomach

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

Summary Statistics

-FinRegistry-

-FinnGen-

Key figures

-FinnGen-

Age distribution of first events

-FinnGen-

Year distribution of first events

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

LabWAS

Mortality – FinRegistry

Relationships between endpoints