Risteys · CD2_INSITU

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 — D09.7&, D09.9& Hospital discharge: ICD-9 — 234[8-9] Cause of death: ICD-10 — D09.7&, D09.9& Cause of death: ICD-9 — 234[8-9] 2 out of 7 registries used, show all original rules.	25
4. Check minimum number of events None	25
5. Include endpoints None	25
6. Filter based on genotype QC (FinnGen only)	25

Summary Statistics

↥

-FinRegistry-

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

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	25	10	15
Unadjusted period prevalence (%)	0.01	0.00	0.01
Median age at first event (years)	70.01	68.72	70.86

-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

unit

cases

controls

-log₁₀(p)

N cases

N controls

(3002256) Pathology report gross observation

7.60

3.27

2.1

1.6

—

(3044640) Blood type and Crossmatch panel - Blood

3.75

2.59

2.7

2.1

—

(40768804) Tissue Pathology biopsy report

3.70

2.54

3.1

2.4

—

(4035726)

4.58

2.07

1.5

1.1

—

(3030981) Hyaline casts [#/volume] in Urine by Automated count

4.58

2.07

7.7

4.4

e6/l

0.6

0.1

—

(3044254) Respiratory syncytial virus RNA [Presence] in Specimen by NAA with probe detection

5.37

2.04

1.6

2.0

—

(3000330) Specific gravity of Urine by Test strip

4.91

1.92

12.2

5.1

—

(46235759) Influenza virus B RNA [Presence] in Nasopharynx by NAA with probe detection

4.91

1.92

3.0

1.9

—

(3005772) Bilirubin.conjugated [Moles/volume] in Serum or Plasma

3.61

1.70

2.5

2.8

umol/l

5.0

10.0

—

(3026008) Bacteria identified in Urine by Culture

2.84

1.68

4.8

3.2

—

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

2.75

1.60

4.1

3.2

—

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

2.85

1.58

1.4

1.6

mg/l

3.2

1.9

—

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

2.77

1.55

2.2

2.0

—

(3000494) Fungus identified in Specimen by Culture

3.63

1.51

1.6

1.4

—

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

2.62

1.44

7.3

3.8

g/l

34.9

34.6

0.10

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

2.78

1.40

2.1

1.7

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.71

1.15

3.0

1.9

—

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

2.18

1.01

5.3

3.3

—

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

2.22

0.91

1.2

—

(3013512) EKG study

2.11

0.88

4.7

5.4

—

(3044889) 12 lead EKG panel

130

1.96

0.84

5.1

4.1

—

(3042936) Bacteria identified in Isolate by Culture

2.15

0.75

1.0

1.8

—

(3033658) Prothrombin time (PT) actual/Normal

1.93

0.72

6.1

3.6

75.9

81.2

—

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

1.86

0.69

1.8

2.2

pmol/l

81.9

89.1

—

(40761536) Microorganisms panel - Urine sediment

0.00

0.63

0.0

4.0

—

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

0.00

0.42

0.0

5.7

—

25.5

—

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

0.61

0.41

9.7

4.6

—

0.0

—

(3023368) Bacteria identified in Blood by Culture

1.59

0.40

3.9

4.1

—

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

127

1.45

0.30

6.5

4.5

mmol/l

6.5

6.6

0.13

120

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

100

0.71

0.28

8.6

4.4

—

0.0

—

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

0.72

0.28

16.3

6.0

—

0.0

—

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

0.00

0.22

0.0

2.0

—

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

0.00

0.22

0.0

1.8

—

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

0.00

0.22

0.0

1.8

—

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

0.00

0.21

0.0

5.7

—

(3037467) Urinalysis macro (dipstick) panel - Urine

132

1.34

0.20

9.2

5.5

—

(36304419) Bacteria [Presence] in Urine

1.20

0.20

4.4

3.0

—

(3009542) Hematocrit [Volume Fraction] of Blood

148

1.22

0.17

34.3

18.2

37.0

38.4

—

(40758558) Short blood count panel - Blood

1.14

0.10

20.4

7.0

—

(1761868) Lipid panel - Serum or Plasma

1.12

0.10

8.7

3.1

—

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

190

1.26

0.09

38.0

19.9

umol/l

103.1

85.2

0.77

190

(3004410) Hemoglobin A1c/Hemoglobin.total in Blood

168

1.25

0.08

9.3

6.7

mmol/mol

39.9

42.7

1.11

158

(3015736) pH of Urine

0.84

0.08

14.3

3.9

—

(3022096) Basophils/100 leukocytes in Blood

0.86

0.08

19.3

5.7

0.5

—

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

1.11

0.08

2.1

2.0

—

(3013115) Eosinophils [#/volume] in Blood

1.21

0.08

16.7

5.2

e9/l

0.2

—

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

142

1.14

0.03

6.3

5.5

—

643.7

—

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

109

1.02

0.00

3.6

2.7

u/l

46.0

44.2

0.06

(3016888) Borrelia burgdorferi IgG Ab [Units/volume] in Serum

0.00

0.0

1.0

—

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

0.00

0.0

1.6

—

(3018418) pH of Serum or Plasma

0.96

0.00

4.7

4.2

—

7.4

—

(3050238) Crystals [Presence] in Synovial fluid by Light microscopy

0.00

0.0

1.4

—

(3016650) Hepatitis A virus Ab [Presence] in Serum

0.00

0.0

1.0

—

(3006504) Eosinophils/100 leukocytes in Blood

1.02

0.00

18.6

5.7

3.2

2.1

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

0.00

0.0

1.2

—

(3019069) Monocytes/100 leukocytes in Blood

1.00

0.00

20.3

5.7

9.5

8.9

—

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

0.93

0.00

9.4

4.9

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

0.0

1.2

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

0.0

4.1

—

7.9

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

0.0

4.1

—

5.2

—

(3019198) Lymphocytes [#/volume] in Blood

1.02

0.00

15.9

5.1

e9/l

1.7

—

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

0.00

0.0

3.0

—

1.4

—

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

0.00

0.0

1.4

—

(3024928) Oxygen saturation in Venous blood

0.00

0.0

3.4

—

(42870588) Differential panel, method unspecified - Blood

0.91

0.00

15.2

4.3

—

(1616796) Gas panel - Central venous blood

0.00

0.0

2.3

—

(40761511) CBC panel - Blood by Automated count

179

1.02

0.00

23.1

16.4

—

(3003181) Sodium [Moles/volume] in Urine

0.00

0.0

1.2

—

55.6

—

(3018010) Neutrophils/100 leukocytes in Blood

1.00

0.00

17.5

5.3

61.5

59.8

—

(3002030) Lymphocytes/100 leukocytes in Blood

0.96

0.00

18.6

5.5

22.8

24.8

—

(4034850)

0.00

0.0

16.2

—

(3041096) Erythrocytes [Presence] in Urine by Automated

0.89

0.00

11.8

4.7

—

(40768800) Prostate Pathology biopsy report

0.00

0.0

1.5

—

(3032836) C peptide [Moles/volume] in Serum or Plasma --fasting

0.00

0.0

1.0

—

1.1

—

(3022806) Fractional oxyhemoglobin in Capillary blood

0.00

0.0

3.4

—

89.6

—

Mortality – FinRegistry

↥

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

Relationships between endpoints

↥

Index endpoint: CD2_INSITU_NOS – Carcinoma in situ, other/unspecified

GWS hits: -

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

NAME	CD2_INSITU_NOS
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D09[7\|9]
HD_ICD_9	234[8-9]
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	D09[7\|9]
COD_ICD_9	234[8-9]
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
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

≡ 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, other/unspecified

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, other/unspecified (CD2_INSITU_NOS)

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