Risteys · CD2_INSITU

Endpoint definition steps	FinnGen
Phenotype data	519972
1. Apply sex-specific rule None	519972
2. Check conditions not C3_STOMACH	517816
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.	31
4. Check minimum number of events None	31
5. Include endpoints None	31
6. Filter based on genotype QC (FinnGen only)	28

Summary Statistics

↥

-FinRegistry-

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

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	28	7	21
Unadjusted period prevalence (%)	0.01	0.00	0.01
Median age at first event (years)	74.31	73.87	74.46

-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

(40768797) Stomach Pathology biopsy report

13.56

9.51

4.2

1.3

—

(3044640) Blood type and Crossmatch panel - Blood

7.60

6.53

3.5

2.5

—

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

5.76

5.50

3.6

2.4

—

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

6.44

4.73

5.1

7.5

105.62

102.71

mmol/l

1.00

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

103

4.89

4.24

3.3

2.7

—

(3016417) Amylase.pancreatic [Enzymatic activity/volume] in Serum or Plasma

6.18

3.83

4.4

2.5

26.30

27.94

u/l

—

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

144

4.78

3.58

8.6

5.5

7.08

6.62

mmol/l

0.75

135

(3016502) Oxygen saturation in Arterial blood

4.95

3.24

4.7

8.2

95.45

94.75

—

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

6.60

3.06

4.1

8.6

24.43

24.78

mmol/l

—

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

131

3.91

3.00

11.2

6.4

10.87

11.65

umol/l

0.18

124

(40760892) CBC W Ordered Manual Differential panel - Blood

103

3.65

2.96

6.9

7.7

—

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

6.11

2.91

6.0

9.7

—

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

4.63

2.85

5.1

8.5

119.67

122.64

g/l

—

(3003396) Base excess in Arterial blood by calculation

3.97

2.66

4.7

7.5

-0.20

1.53

mmol/l

—

(40768804) Tissue Pathology biopsy report

3.21

2.53

3.2

2.1

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

4.99

2.53

6.1

9.2

0.96

1.58

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

4.99

2.53

6.1

9.2

0.76

0.71

—

(3023368) Bacteria identified in Blood by Culture

3.17

2.47

6.2

4.2

—

(4035726) Immunohistochemistry procedure

4.12

2.38

1.1

1.6

—

(3000991) Gas panel - Venous blood

4.44

2.31

6.3

10.7

—

(3002256) Pathology report gross observation

3.94

2.28

1.3

—

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

108

2.96

2.17

2.7

2.2

84.18

89.96

pmol/l

0.17

(3025941) Bacteria identified in Stool by Culture

4.36

1.79

1.2

1.3

—

(3000492) Spirometry study

3.65

1.76

1.0

1.5

—

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

4.04

1.68

1.4

1.6

—

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

128

2.59

1.67

14.7

9.6

5.66

4.52

e9/l

1.21

116

(3006315) Basophils [#/volume] in Blood

110

2.52

1.65

8.8

6.8

0.04

e9/l

0.19

(3001604) Monocytes [#/volume] in Blood

110

2.52

1.65

8.8

6.8

0.67

0.60

e9/l

0.41

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

3.10

1.34

1.4

1.3

—

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

2.26

1.28

2.0

2.3

1298.00

525.06

u/l

0.28

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

2.93

1.26

1.4

1.6

—

(3022145) Colonoscopy Study observation

2.93

1.26

1.4

1.3

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.71

1.22

2.3

1.5

—

(36304419) Bacteria [Presence] in Urine

2.17

1.13

3.8

2.7

—

(3042936) Bacteria identified in Isolate by Culture

2.21

1.05

2.1

1.5

—

(3027945) Reticulocytes/100 erythrocytes in Blood

2.21

1.05

1.7

4.2

1.81

1.83

—

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

216

2.26

0.84

36.5

17.7

25.42

24.85

mg/l

0.04

183

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

2.39

0.80

2.4

1.6

—

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

2.28

0.78

1.2

1.3

—

(3023520) Reticulocytes [#/volume] in Blood

2.01

0.72

1.6

3.8

—

75.28

—

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

1.85

0.69

3.0

2.1

—

(40761511) CBC panel - Blood by Automated count

223

2.03

0.69

27.0

16.0

—

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

224

1.99

0.69

38.3

21.6

4.02

4.01

mmol/l

0.12

219

(3005013) Prostate Specific Ag Free [Mass/volume] in Serum or Plasma

1.75

0.64

2.3

3.1

1.31

0.72

ug/l

—

(3026782) Osmolality of Urine

1.77

0.63

3.7

3.0

618.67

534.60

mosm/kgh2o

—

(3037467) Urinalysis macro (dipstick) panel - Urine

160

1.70

0.63

5.1

4.5

—

(40758558) Short blood count panel - Blood

1.63

0.60

11.6

7.1

—

(3041096) Erythrocytes [Presence] in Urine by Automated

1.57

0.58

5.7

3.9

—

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

230

1.81

0.55

41.3

21.1

88.12

85.05

umol/l

0.17

230

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

1.59

0.50

3.8

2.9

—

(3012516) Albumin [Mass/volume] in Urine

1.63

0.49

2.1

3.4

53.88

88.00

mg/l

—

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

146

1.56

0.48

5.6

3.4

130.44

62.98

u/l

0.45

137

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

1.61

0.48

3.5

2.4

3.11

3.69

e6/l

—

(1761868) Lipid panel - Serum or Plasma

1.43

0.42

4.3

3.4

—

(3007461) Platelets [#/volume] in Blood

234

1.69

0.42

50.4

25.6

230.08

233.81

e9/l

0.14

228

(3026361) Erythrocytes [#/volume] in Blood

234

1.69

0.42

50.3

25.6

4.45

4.41

e12/l

0.13

228

(3010813) Leukocytes [#/volume] in Blood

234

1.69

0.42

50.6

25.6

12.82

6.99

e9/l

0.55

227

(3013512) EKG study

1.43

0.32

9.5

4.8

—

(3026493) Urate [Moles/volume] in Serum or Plasma

1.40

0.30

2.0

3.5

357.44

8242.73

umol/l

—

(3044889) 12 lead EKG panel

146

1.36

0.28

4.8

—

(3020059) Calcium [Moles/volume] corrected for albumin in Serum or Plasma

1.26

0.23

5.0

2.6

2.52

2.49

mmol/l

—

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

1.31

0.22

1.8

4.6

—

(3020891) Body temperature

0.00

0.22

0.0

3.0

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.22

0.0

4.9

—

(3043409) Potassium [Moles/volume] in Arterial blood

0.00

0.22

0.0

1.7

—

4.04

—

(3049717) Cytology report of Urine Cyto stain

0.00

0.21

0.0

1.8

—

(3022621) pH of Urine by Test strip

0.00

0.21

0.0

2.7

—

(3008909) Norovirus RNA [Presence] in Stool by NAA with probe detection

0.00

0.20

0.0

1.2

—

(3026008) Bacteria identified in Urine by Culture

0.74

0.17

3.6

3.1

—

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

1.08

0.10

1.0

1.3

—

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

118

1.18

0.09

3.7

2.4

—

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

1.08

0.08

5.6

4.6

—

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

1.15

0.05

3.4

2.6

68.40

75.23

nmol/l

—

(1002224) Polysomnography panel

0.00

-0.00

0.0

1.6

—

(3021901) Oxygen saturation in Capillary blood

0.00

-0.00

0.0

1.6

—

(3012447) Hantavirus puumala IgG Ab [Titer] in Serum

0.00

-0.00

0.0

1.2

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

-0.00

0.0

1.0

—

(42869457) Rotavirus RNA [Identifier] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.2

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

-0.00

0.0

2.5

—

32.33

—

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

0.00

-0.00

0.0

1.4

—

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

0.00

-0.00

0.0

3.8

—

1.32

—

(21494434) Karyotype in Bone marrow

0.00

-0.00

0.0

1.0

—

(3005570) Glucose [Moles/volume] in Urine

0.00

-0.00

0.0

1.0

—

(3020148) Glutamate decarboxylase 65 Ab [Units/volume] in Serum

0.00

-0.00

0.0

1.2

—

(3030905) Polymorphonuclear cells [#/volume] in Blood

0.00

-0.00

0.0

3.4

—

3.90

—

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

0.00

-0.00

0.0

2.0

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

-0.00

0.0

1.2

—

(40768800) Prostate Pathology biopsy report

0.00

-0.00

0.0

1.3

—

(21494890) Protein electrophoresis panel - 24 hour Urine

0.00

-0.00

0.0

1.4

—

(37020445) Astrovirus RNA [Presence] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.2

—

(1616796) Gas panel - Central venous blood

0.00

-0.00

0.0

2.4

—

(3036489) Thrombin time

0.00

-0.00

0.0

6.0

—

21.00

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

-0.00

0.0

4.3

—

5.03

—

(3017918) Cytomegalovirus IgG Ab [Titer] in Serum or Plasma

0.00

-0.00

0.0

1.4

—

(3019539) Treponema pallidum Ab [Titer] in Serum by Hemagglutination

0.00

-0.00

0.0

2.4

—

(3023183) Ammonium ion [Moles/volume] in Plasma

0.00

-0.00

0.0

2.0

—

46.00

—

(37020957) Sapovirus genogroups I+II+IV+V RNA [Presence] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.2

—

(3000012) Reticulocyte production index

0.00

-0.00

0.0

2.7

—

(37021247) Adenovirus 40+41 DNA [Presence] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

2.4

—

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

0.00

-0.00

0.0

1.4

—

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

0.00

-0.00

0.0

1.7

—

(40768795) Lymph node Pathology biopsy report

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.2

—

(3032035) Polymorphonuclear cells/100 leukocytes in Blood

0.00

-0.00

0.0

3.4

—

51.80

—

(3003181) Sodium [Moles/volume] in Urine

0.00

-0.00

0.0

1.8

—

45.11

—

(3042111) Morphology [Interpretation] in Bone marrow Narrative

0.00

-0.00

0.0

2.2

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

-0.00

0.0

4.3

—

7.76

—

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

0.00

-0.00

0.0

1.3

—

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

0.00

-0.00

0.0

1.2

—

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

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

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

Case counts by code for Carcinoma in situ of stomach (CD2_INSITU_STOMACH)

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