Risteys · CD2_INSITU_STOMACH

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

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	-	-	-
Only index persons	-	-	-
Unadjusted period prevalence (%)
Whole population	-	-	-
Only index persons	-	-	-
Median age at first event (years)
Whole population	-	-	-
Only index persons	-	-	-

-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

-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

cases

controls

unit

-log₁₀(p)

N cases

N controls

(40768797) Stomach Pathology biopsy report

20.29

13.97

4.9

1.2

—

(3002256) Pathology report gross observation

15.63

9.24

1.6

1.1

—

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

10.86

8.67

4.3

2.0

—

(3044640) Blood type and Crossmatch panel - Blood

13.15

8.24

4.2

2.1

—

(4035726)

25.67

7.45

1.4

1.0

—

(40768804) Tissue Pathology biopsy report

9.07

7.37

3.2

1.5

—

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

6.98

5.20

4.2

3.9

—

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

18.32

4.88

5.1

6.4

25.1

24.3

mmol/l

—

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

6.18

4.67

6.3

5.7

1.2

mmol/l

1.17

(42870588) Differential panel, method unspecified - Blood

5.83

4.66

7.5

6.0

—

(3033658) Prothrombin time (PT) actual/Normal

5.51

4.22

8.3

2.6

84.5

87.0

0.11

(3000991) Gas panel - Venous blood

9.90

4.22

6.5

3.9

—

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

5.10

3.70

13.1

3.1

9.2

10.7

umol/l

0.75

(3018010) Neutrophils/100 leukocytes in Blood

4.90

3.69

9.6

6.3

56.6

58.4

0.19

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

101

5.22

3.59

9.9

4.1

7.5

7.1

mmol/l

0.43

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

4.94

3.50

8.4

3.4

35.6

35.0

g/l

0.15

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

10.65

3.45

8.0

7.7

—

(3014007) Fractional oxyhemoglobin in Arterial blood

7.51

3.26

7.1

6.2

95.9

93.1

—

(3023368) Bacteria identified in Blood by Culture

4.31

3.21

8.4

3.9

—

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

11.91

3.11

1.8

2.2

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

6.91

3.10

7.1

5.8

1.0

1.7

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

6.91

3.10

7.1

5.8

0.7

0.9

—

(3027946) Carbon dioxide [Partial pressure] in Arterial blood

5.91

3.09

6.5

5.9

5.3

4.8

kpa

—

(3027801) Oxygen [Partial pressure] in Arterial blood

5.91

3.09

6.4

5.9

14.3

10.1

kpa

—

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

5.58

2.96

6.5

5.3

121.0

125.4

g/l

—

(3016502) Oxygen saturation in Arterial blood

5.58

2.96

6.5

5.4

96.6

95.6

—

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

5.95

2.82

2.9

1.4

—

(36304419) Bacteria [Presence] in Urine

3.88

2.74

4.3

2.9

—

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

8.48

2.67

1.8

2.0

—

(3018095) Leukocytes [#/volume] in Urine

3.65

2.59

5.4

4.0

7.0

53.1

e6/l

—

(3025941) Bacteria identified in Stool by Culture

6.13

2.56

1.2

—

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

7.40

2.48

1.8

1.1

—

(3042936) Bacteria identified in Isolate by Culture

4.15

2.33

2.3

1.7

—

(3006315) Basophils [#/volume] in Blood

3.30

2.22

9.9

5.9

0.0

e9/l

—

(3001604) Monocytes [#/volume] in Blood

3.30

2.22

9.9

5.9

0.7

0.6

e9/l

—

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

5.89

2.17

1.0

1.1

—

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

5.89

2.17

1.0

1.1

—

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

5.89

2.17

1.0

1.1

—

(3007853) Bacteria identified in Skin by Aerobe culture

4.16

2.14

2.6

1.7

—

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

3.12

2.04

3.0

2.1

94.6

81.2

pmol/l

—

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

5.33

2.04

1.0

1.2

—

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

3.00

1.90

4.4

2.9

—

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

132

3.22

1.89

17.9

5.2

98.5

72.5

u/l

1.71

118

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

3.16

1.65

2.4

2.3

—

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

3.86

1.60

2.8

2.2

—

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

3.61

1.51

2.8

2.3

—

(40758558) Short blood count panel - Blood

2.67

1.36

12.9

6.0

—

(3026782) Osmolality of Urine

2.71

1.22

3.4

3.3

569.1

585.7

mosm/kgh2o

—

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

2.44

1.13

4.6

2.4

3.1

3.8

e6/l

—

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

2.30

1.01

1.5

1.7

1.3

mg/l

—

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

167

2.33

0.89

48.5

14.7

25.5

23.9

mg/l

0.12

133

(3044889) 12 lead EKG panel

115

2.02

0.86

5.1

4.5

—

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

2.02

0.79

1.7

3.5

—

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

173

2.11

0.73

47.7

17.6

139.2

139.3

mmol/l

0.04

166

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

174

2.07

0.73

48.0

17.5

4.0

mmol/l

0.44

166

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

176

2.00

0.72

52.7

16.6

89.9

85.3

umol/l

0.21

176

(40761511) CBC panel - Blood by Automated count

176

2.00

0.72

27.6

12.9

—

(3015736) pH of Urine

1.88

0.71

3.6

3.9

—

(3037467) Urinalysis macro (dipstick) panel - Urine

120

1.59

0.45

5.1

4.8

—

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

1.63

0.44

1.0

1.4

—

(3024731) MCV [Entitic volume]

183

1.76

0.44

62.1

20.5

91.8

91.0

0.29

176

(3007461) Platelets [#/volume] in Blood

184

1.73

0.44

61.7

20.5

237.0

237.1

e9/l

0.00

175

(3010813) Leukocytes [#/volume] in Blood

184

1.73

0.44

62.0

20.5

14.2

7.1

e9/l

0.53

175

(3035941) MCH [Entitic mass]

184

1.73

0.44

61.9

20.4

29.9

30.3

0.31

177

(3000963) Hemoglobin [Mass/volume] in Blood

184

1.73

0.44

62.5

20.6

125.0

135.2

g/l

1.97

177

(3026361) Erythrocytes [#/volume] in Blood

184

1.73

0.44

61.7

20.5

4.3

4.5

e12/l

0.80

175

(3041096) Erythrocytes [Presence] in Urine by Automated

1.44

0.35

5.6

3.7

—

(1761868) Lipid panel - Serum or Plasma

1.40

0.34

3.1

3.9

—

(3013512) EKG study

1.42

0.32

9.1

4.1

—

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

1.46

0.30

4.4

2.7

—

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

1.39

0.23

1.3

1.8

1.2

mmol/l

—

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

0.00

0.22

0.0

4.7

—

1.3

—

(3020891) Body temperature

0.00

0.21

0.0

4.1

—

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

106

1.25

0.13

5.6

2.7

184.3

37.6

u/l

0.74

100

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.0

1.2

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

0.0

1.2

—

(21494890) Protein electrophoresis panel - 24 hour Urine

0.00

0.0

1.0

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.0

—

37.0

—

(3026008) Bacteria identified in Urine by Culture

1.04

0.00

4.8

3.5

—

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

0.00

0.0

2.4

—

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

0.96

0.00

5.4

3.7

—

(3026389) Candida sp identified in Specimen by Organism specific culture

0.00

0.0

1.0

—

(3050449) Albumin [Mass/time] in Urine collected for unspecified duration

0.00

0.0

2.3

—

169.6

—

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

0.00

0.0

7.0

—

(1002224) Polysomnography panel

0.00

0.0

1.6

—

(3022313) Gas panel - Capillary blood

0.00

0.0

3.8

—

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

0.00

0.0

1.2

—

(3021901) Oxygen saturation in Capillary blood

0.00

0.0

1.4

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_INSITU_STOMACH_EXALLC and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have CD2_INSITU_STOMACH_EXALLC.

N-year risk	Females	Males
1	No data	No data
5	No data	No data
10	No data	No data
15	No data	No data
20	No data	No data

Relationships between endpoints

↥

Index endpoint: CD2_INSITU_STOMACH_EXALLC – Carcinoma in situ of stomach

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	CD2_INSITU_STOMACH_EXALLC
CONTROL_EXCLUDE	C3_CANCER\|C3_CANCER_WIDE
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-

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