Risteys · CD2_INSITU

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions not C3_BRONCHUS_LUNG	511876
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D02.2& Hospital discharge: ICD-9 — 2312 Cause of death: ICD-10 — D02.2& Cause of death: ICD-9 — 2312 Cancer registry: Topography ICD-O-3 — C34 Cancer registry: Morphology ICD-O-3 — ANY Cancer registry: Behaviour codes — 2 3 out of 7 registries used, show all original rules.	44
4. Check minimum number of events None	44
5. Include endpoints None	44
6. Filter based on genotype QC (FinnGen only)	44

Summary Statistics

↥

-FinRegistry-

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

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	44	16	28
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	69.10	68.65	69.36

-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

(4035726)

7.07

7.84

1.5

1.1

—

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

4.37

5.40

3.3

2.1

—

(40768804) Tissue Pathology biopsy report

126

4.36

5.34

2.9

2.3

—

(3014444) EGFR gene mutations tested for in Blood or Tissue by Molecular genetics method Nominal

+∞

5.30

1.2

0.0

—

(4010399)

5.52

5.20

1.3

—

(3018559) Microscopic observation [Identifier] in Buccal smear by Cyto stain

16.24

4.74

1.3

1.2

—

(3003785) Carcinoembryonic Ag [Mass/volume] in Serum or Plasma

4.33

4.56

7.7

5.4

3.6

95.2

ug/l

0.54

(3002256) Pathology report gross observation

4.34

3.94

1.5

1.2

—

(3032080) INR in Blood by Coagulation assay

164

3.61

3.89

10.8

8.5

1.3

inr

—

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

166

3.54

3.77

5.3

4.0

—

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

161

3.35

3.56

6.4

4.9

35.1

34.4

g/l

0.37

152

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

6.71

3.52

1.4

1.1

—

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

6.25

3.37

3.5

1.7

—

(3042936) Bacteria identified in Isolate by Culture

3.41

3.16

1.7

2.0

—

(3042631) Mycobacterium sp identified in Specimen

11.03

3.05

2.6

2.8

—

(3019225) pH of Specimen

3.88

2.98

4.1

4.2

—

(3044640) Blood type and Crossmatch panel - Blood

115

2.83

2.82

3.5

2.1

—

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

9.18

2.82

2.0

1.5

—

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

297

3.75

2.50

14.8

8.1

75.4

80.5

u/l

0.40

276

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

213

2.84

2.45

9.8

12.2

4.6

4.4

e9/l

0.11

183

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

4.01

2.40

4.8

9.7

27.6

24.8

mmol/l

—

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

205

2.73

2.37

11.9

7.1

19.8

11.3

umol/l

0.45

194

(3018418) pH of Serum or Plasma

116

2.55

2.32

3.7

5.2

7.4

—

(3023368) Bacteria identified in Blood by Culture

127

2.46

2.19

3.6

4.4

—

(3000494) Fungus identified in Specimen by Culture

2.93

2.12

1.1

1.5

—

(3049717) Cytology report of Urine Cyto stain

3.76

2.06

2.1

2.8

—

(3018010) Neutrophils/100 leukocytes in Blood

165

2.19

1.71

4.1

5.1

62.5

59.0

0.75

153

(42870588) Differential panel, method unspecified - Blood

121

2.20

1.70

3.4

4.6

—

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

3.88

1.66

1.0

1.4

—

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

158

2.14

1.63

2.1

3.6

—

(3022096) Basophils/100 leukocytes in Blood

159

2.12

1.60

4.7

4.9

0.7

0.6

0.48

144

(3007930) Methemoglobin/Hemoglobin.total in Blood

3.38

1.48

9.8

4.4

0.8

0.9

—

(3019069) Monocytes/100 leukocytes in Blood

164

2.02

1.42

4.7

5.3

9.5

8.6

0.67

151

(3006504) Eosinophils/100 leukocytes in Blood

164

2.02

1.42

4.5

5.0

3.2

2.4

1.17

151

(40760892) CBC W Ordered Manual Differential panel - Blood

2.13

1.37

4.1

6.4

—

(3000492) Spirometry study

2.73

1.35

1.2

1.6

—

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

2.61

1.29

18.7

7.8

—

(3033658) Prothrombin time (PT) actual/Normal

2.01

1.24

4.9

3.2

87.2

84.7

0.20

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

229

1.97

1.23

8.4

5.2

7.5

6.9

mmol/l

1.17

217

(3012544) pH of Venous blood

2.28

1.23

2.3

4.5

—

(40768797) Stomach Pathology biopsy report

2.25

1.14

1.6

1.1

—

(3037467) Urinalysis macro (dipstick) panel - Urine

255

1.93

1.09

5.2

4.9

—

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

2.05

0.94

9.6

11.1

113.9

119.2

g/l

—

(3019060) Gas panel - Arterial blood

2.08

0.88

9.5

4.9

—

(3003458) Phosphate [Moles/volume] in Serum or Plasma

1.86

0.86

2.4

7.0

1.0

1.1

mmol/l

—

(3003396) Base excess in Arterial blood by calculation

1.92

0.83

15.9

9.9

3.9

1.4

mmol/l

—

(3018095) Leukocytes [#/volume] in Urine

148

1.64

0.80

2.6

4.0

573.6

73.4

e6/l

0.43

112

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

1.70

0.69

1.6

1.9

—

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

0.00

0.62

0.0

6.9

—

(3000330) Specific gravity of Urine by Test strip

0.00

0.62

0.0

6.7

—

(3021337) Troponin I.cardiac [Mass/volume] in Serum or Plasma

1.65

0.60

7.5

3.1

12.9

157.4

ng/l

0.96

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

1.66

0.60

2.0

—

(3000991) Gas panel - Venous blood

1.72

0.58

16.0

12.1

—

(3048816) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Blood

1.72

0.58

5.2

5.7

1.2

mmol/l

—

(3001122) Ferritin [Mass/volume] in Serum or Plasma

130

1.50

0.55

2.8

109.1

157.5

ug/l

0.59

118

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

1.62

0.51

1.6

2.0

—

(36304419) Bacteria [Presence] in Urine

115

1.46

0.47

2.5

2.9

—

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

352

0.67

0.46

5.5

5.7

2.4

2.5

mmol/l

0.51

315

(3021589) Normoblasts [#/volume] in Blood

163

1.42

0.46

11.7

12.3

0.0

e9/l

0.47

133

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

1.43

0.44

1.8

2.8

2.4

2.3

g/l

—

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

1.63

0.44

1.2

8.3

9.1

11.1

mmol/l

—

(3020961) Endomysium IgA Ab [Titer] in Serum

0.00

0.42

0.0

1.0

—

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

165

1.39

0.42

2.3

1.9

108.1

94.6

pmol/l

0.59

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

165

1.39

0.42

2.6

2.3

—

(36660697) Celiac disease serology panel - Serum

0.00

0.41

0.0

1.2

—

(3009542) Hematocrit [Volume Fraction] of Blood

294

0.72

0.41

33.9

17.8

36.6

39.3

0.48

183

(3008230) Borrelia burgdorferi IgM Ab [Units/volume] in Serum

0.00

0.41

0.0

1.8

—

(3036481) Cortisol [Moles/volume] in Serum or Plasma

1.48

0.41

2.6

1.8

441.0

328.4

nmol/l

—

(3023602) Cholesterol in HDL [Moles/volume] in Serum or Plasma

339

0.71

0.37

5.2

5.1

1.4

mmol/l

0.11

300

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

339

0.71

0.37

5.0

5.1

4.2

4.3

mmol/l

0.20

305

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

1.43

0.36

1.4

1.3

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.42

0.36

1.2

1.7

—

(3027945) Reticulocytes/100 erythrocytes in Blood

1.35

0.32

2.1

1.7

—

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

1.38

0.30

1.9

2.8

8.0

13.1

umol/l

—

(3048773) Triglyceride [Moles/volume] in Serum or Plasma --fasting

326

0.75

0.30

4.8

4.5

1.2

1.3

mmol/l

0.43

289

(3041096) Erythrocytes [Presence] in Urine by Automated

105

1.34

0.29

6.8

4.7

—

(3004410) Hemoglobin A1c/Hemoglobin.total in Blood

338

1.36

0.24

7.0

6.7

42.2

41.7

mmol/mol

0.11

308

(3005785) Creatine kinase.MB [Mass/volume] in Serum or Plasma

1.36

0.24

2.2

2.7

2.6

7.9

ug/l

—

(3003338) MCHC [Mass/volume]

273

0.80

0.22

46.9

22.7

328.6

331.7

g/l

0.93

273

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

0.00

0.21

0.0

1.4

—

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

0.00

0.21

0.0

3.4

—

4.0

—

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

0.00

0.21

0.0

3.4

—

107.8

—

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

0.00

0.21

0.0

3.4

—

(3002109) Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma

0.00

0.21

0.0

2.0

—

(3045414) Leukocytes [Presence] in Urine

0.00

0.21

0.0

1.5

—

(3052851) Hemolysis interference index of Serum or Plasma

0.00

0.21

0.0

4.3

—

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

0.00

0.21

0.0

1.1

—

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

0.00

0.21

0.0

1.0

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.00

0.21

0.0

1.4

—

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

0.00

0.20

0.0

1.0

—

(3006184) Hemoglobin [Mass/volume] in Capillary blood

0.00

0.20

0.0

2.9

—

126.7

—

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

374

1.38

0.18

37.0

20.2

87.2

84.8

umol/l

0.19

374

(3006923) Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma

374

1.38

0.18

19.1

11.8

23.8

24.1

u/l

0.05

357

(40761511) CBC panel - Blood by Automated count

363

1.34

0.17

28.8

16.5

—

(1761868) Lipid panel - Serum or Plasma

108

0.79

0.15

4.4

3.4

—

(40761535) Cells panel - Urine sediment

1.18

0.10

4.8

3.7

—

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

194

0.88

0.09

6.5

4.6

0.0

estimate

—

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

378

1.28

0.09

35.7

19.7

138.7

139.8

mmol/l

1.09

365

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

381

1.21

0.09

35.7

19.6

4.0

mmol/l

0.32

368

(3020682) Albumin/Creatinine [Ratio] in Urine

139

0.91

0.04

4.3

3.9

0.7

10.6

mg/mmol

—

(40758558) Short blood count panel - Blood

103

1.09

0.02

4.5

6.2

—

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

157

1.03

0.00

7.1

5.0

—

(3044889) 12 lead EKG panel

275

1.05

0.00

5.9

4.2

—

(3013512) EKG study

116

1.05

0.00

3.9

4.7

—

(3012516) Albumin [Mass/volume] in Urine

126

1.05

0.00

3.2

7.9

76.2

mg/l

—

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

195

0.95

0.00

6.2

4.7

0.0

estimate

—

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

194

0.96

0.00

9.3

6.4

0.0

estimate

—

(3009508) Creatinine [Moles/volume] in Urine

128

1.02

0.00

3.2

3.1

8.0

7.8

mmol/l

—

105

(42868674) Cholesterol in HDL/Cholesterol.total [Molar ratio] in Serum or Plasma

0.94

0.00

3.0

5.1

—

32.7

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.0

1.7

—

(3050380) Cytology report of Cervical or vaginal smear or scraping Cyto stain

0.00

0.0

1.1

—

(3001019) Free T4 and TSH panel - Serum or Plasma

0.00

0.0

2.1

—

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

0.00

0.0

4.4

—

(3023150) Myeloperoxidase Ab [Units/volume] in Serum

0.00

0.0

2.3

—

(3007844) Epstein Barr virus capsid IgM Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.0

—

(3015635) Cytomegalovirus IgM Ab [Units/volume] in Serum or Plasma

0.00

0.0

1.4

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.1

—

(40763082) Lactate dehydrogenase [Enzymatic activity/volume] in Pleural fluid by Lactate to pyruvate reaction

0.00

0.0

1.6

—

167.3

—

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

0.00

0.0

1.2

—

371.5

—

(3016543) Leukocytes [#/volume] in Cerebral spinal fluid

0.00

0.0

1.0

—

3.3

—

(3007461) Platelets [#/volume] in Blood

383

1.16

0.00

43.6

24.9

242.2

237.5

e9/l

0.19

372

(4094501)

0.00

0.0

1.3

—

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

0.00

0.0

1.7

—

(3051611) Lipemic interference index of Serum or Plasma

0.00

0.0

2.6

—

(3026361) Erythrocytes [#/volume] in Blood

383

1.16

0.00

43.4

24.9

4.3

4.5

e12/l

0.77

370

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

0.00

0.0

1.4

—

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

1.00

0.00

2.8

4.3

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.9

—

(3029511) Human papilloma virus DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.1

—

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

0.00

0.0

7.0

—

(3010813) Leukocytes [#/volume] in Blood

383

1.16

0.00

43.6

25.0

7.3

6.7

e9/l

1.14

370

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

0.00

0.0

1.1

—

(3000963) Hemoglobin [Mass/volume] in Blood

383

1.16

0.00

45.1

25.0

131.4

134.5

g/l

0.63

375

(3026008) Bacteria identified in Urine by Culture

140

1.00

0.00

4.9

3.5

—

(3043849) Epstein Barr virus DNA [Units/volume] (viral load) in Serum or Plasma by NAA with probe detection

0.00

0.0

4.3

—

(3035941) MCH [Entitic mass]

383

1.16

0.00

43.3

24.8

30.7

30.5

0.33

375

(3009214) Lutropin [Units/volume] in Serum or Plasma

0.00

0.0

1.2

—

5.4

—

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

0.92

0.00

3.2

9.4

—

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

0.00

0.0

1.3

—

(3024731) MCV [Entitic volume]

383

1.16

0.00

43.4

24.9

92.5

91.7

0.49

375

(3027475) Erythrocytes [#/volume] in Cerebral spinal fluid

0.00

0.0

1.3

—

315.5

—

(3048929) Epstein Barr virus Ab [Presence] in Serum

0.00

0.0

1.0

—

(3042111) Morphology [Interpretation] in Bone marrow Narrative

0.00

0.0

2.2

—

(46237023) Hepatitis B virus core and surface Ab and surface Ag panel - Serum

0.00

0.0

1.2

—

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

0.00

0.0

1.2

—

(3036086) Jo-1 extractable nuclear Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.4

—

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

0.00

0.0

1.2

—

(3051651) Icteric interference index of Serum or Plasma

0.00

0.0

2.0

—

(3006588) Cancer Ag 15-3 [Units/volume] in Serum or Plasma

0.00

0.0

4.2

—

20.0

—

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

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

1.4

—

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

0.00

-0.00

0.0

1.1

—

(3021901) Oxygen saturation in Capillary blood

0.00

-0.00

0.0

3.0

—

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

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

1.1

—

Mortality – FinRegistry

↥

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

Relationships between endpoints

↥

Index endpoint: CD2_INSITU_BRONCHUSLUNG – Carcinoma in situ of bronchus and lung

GWS hits: -

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

NAME	CD2_INSITU_BRONCHUSLUNG
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS	!C3_BRONCHUS_LUNG
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D022
HD_ICD_9	2312
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	D022
COD_ICD_9	2312
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	C34
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 bronchus and lung

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 Carcinoma in situ of bronchus and lung (CD2_INSITU_BRONCHUSLUNG)

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