Risteys · CD2_INSITU_URINARY_NOS

Endpoint definition steps	FinnGen
Phenotype data
1. Apply sex-specific rule None	-
2. Check conditions None
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D09.1& Hospital discharge: ICD-9 — 2339 Cause of death: ICD-10 — D09.1& Cause of death: ICD-9 — 2339 2 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-

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

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	19	9	10
Unadjusted period prevalence (%)	0.00	0.00	0.00
Median age at first event (years)	56.60	42.26	69.52

-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

(3026008) Bacteria identified in Urine by Culture

4.95

2.88

3.8

3.3

—

(36304419) Bacteria [Presence] in Urine

4.55

2.60

2.2

3.2

—

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

7.97

2.53

9.2

1.5

e6/l

0.0

0.1

—

(3041096) Erythrocytes [Presence] in Urine by Automated

3.95

2.18

2.4

3.6

—

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

3.82

2.16

6.8

2.9

—

(40768804) Tissue Pathology biopsy report

4.00

2.06

3.6

1.7

—

(3023368) Bacteria identified in Blood by Culture

3.43

1.80

4.9

3.9

—

(42870588) Differential panel, method unspecified - Blood

3.19

1.71

8.3

4.6

—

(3021589) Normoblasts [#/volume] in Blood

3.03

1.64

14.1

9.0

e9/l

0.0

0.00

(3013512) EKG study

3.01

1.51

3.2

4.0

—

(3022217) INR in Platelet poor plasma by Coagulation assay

3.32

1.51

32.7

16.5

—

(3022096) Basophils/100 leukocytes in Blood

2.63

1.32

10.9

4.9

0.5

0.7

0.83

(3003338) MCHC [Mass/volume]

116

0.37

1.29

37.4

16.8

g/l

323.1

331.8

—

116

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

2.51

1.20

4.7

3.6

—

(3016771) Amylase [Enzymatic activity/volume] in Serum or Plasma

2.44

1.17

1.8

1.5

u/l

42.9

58.9

—

(3015736) pH of Urine

2.46

1.14

3.8

3.0

—

(3006504) Eosinophils/100 leukocytes in Blood

2.51

1.10

10.9

5.0

2.9

0.03

(3019069) Monocytes/100 leukocytes in Blood

2.40

1.08

10.9

5.2

8.8

0.01

(3006315) Basophils [#/volume] in Blood

2.29

1.05

10.2

5.1

e9/l

0.0

0.31

(3002030) Lymphocytes/100 leukocytes in Blood

2.29

1.05

11.0

5.2

22.1

27.0

1.00

(3001604) Monocytes [#/volume] in Blood

2.29

1.05

10.2

5.1

e9/l

0.6

0.00

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

2.19

0.88

4.7

3.2

—

(3019198) Lymphocytes [#/volume] in Blood

2.15

0.85

10.3

5.1

e9/l

1.6

1.7

0.41

(3013115) Eosinophils [#/volume] in Blood

2.01

0.82

10.3

4.8

e9/l

0.2

0.06

(3032080) INR in Blood by Coagulation assay

1.99

0.67

3.2

10.2

inr

1.1

1.2

—

(3018010) Neutrophils/100 leukocytes in Blood

1.94

0.67

9.7

4.9

65.6

57.9

—

(40758558) Short blood count panel - Blood

1.97

0.64

5.8

4.3

—

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

1.88

0.64

17.0

6.3

e9/l

3.4

4.4

1.50

(3044889) 12 lead EKG panel

1.99

0.64

4.6

4.0

—

(3037467) Urinalysis macro (dipstick) panel - Urine

101

1.90

0.63

7.2

4.0

—

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

115

1.82

0.49

13.0

4.9

u/l

94.5

76.5

0.55

109

(3018006) Microscopic observation [Identifier] in Cervix by Cyto stain.thin prep

0.00

0.43

0.0

1.3

—

(3029187) Natriuretic peptide.B prohormone N-Terminal [Mass/volume] in Serum or Plasma

1.50

0.35

1.6

2.9

ng/l

829.7

792.8

—

(3044640) Blood type and Crossmatch panel - Blood

1.44

0.24

3.3

1.9

—

(43534045) MCM6 gene c.-13910C>T and -13915T>G [Identifier] in Blood or Tissue by Molecular genetics method Nominal

0.00

0.22

0.0

1.0

—

(36660697) Celiac disease serology panel - Serum

0.00

0.22

0.0

1.1

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.22

0.0

1.4

—

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

1.27

0.20

3.4

2.1

—

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

1.37

0.20

8.7

3.4

umol/l

9.8

12.9

—

(1761868) Lipid panel - Serum or Plasma

1.22

0.11

2.6

2.9

—

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

1.22

0.09

10.1

6.1

mmol/l

1.2

—

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

0.00

0.0

1.0

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.0

—

(3008152) Bicarbonate [Moles/volume] in Arterial blood

0.00

0.0

3.6

—

24.0

—

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

0.00

0.0

1.1

—

(3020891) Body temperature

0.00

0.0

3.0

—

(3004490) Bicarbonate [Moles/volume] standard in Capillary blood

0.00

0.0

2.4

—

24.0

—

(3036489) Thrombin time

0.00

0.0

2.2

—

21.3

—

(3052851) Hemolysis interference index of Serum or Plasma

0.00

0.0

2.8

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

0.00

0.0

2.9

—

(3023024) Carbon dioxide [Partial pressure] in Capillary blood

0.00

0.0

1.8

—

4.8

—

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

1.07

0.00

5.0

2.8

—

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

0.00

0.0

1.6

—

(3022313) Gas panel - Capillary blood

0.00

0.0

2.4

—

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

0.00

0.0

1.0

—

(3029338) Protein.monoclonal band 3 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

1.0

—

0.0

—

(3016407) Fibrinogen [Mass/volume] in Platelet poor plasma by Coagulation assay

0.00

0.0

2.3

—

2.7

—

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

0.00

0.0

12.2

—

(3004248) Sex hormone binding globulin [Moles/volume] in Serum or Plasma

0.00

0.0

1.6

—

43.4

—

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

0.00

0.0

1.8

—

(3029379) Protein.monoclonal band 4 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

1.0

—

0.0

—

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

0.00

0.0

1.5

—

(4034850)

0.00

0.0

12.2

—

(1616796) Gas panel - Central venous blood

0.00

0.0

3.4

—

(3037551) Cancer Ag 125 [Units/volume] in Serum or Plasma

0.00

0.0

1.2

—

26.4

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.0

—

(3000515) Antithrombin actual/normal in Platelet poor plasma by Chromogenic method

0.00

0.0

2.0

—

71.8

—

(3028626) Oxygen [Partial pressure] in Capillary blood

0.00

0.0

1.0

—

8.6

—

Mortality – FinRegistry

↥

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

Relationships between endpoints

↥

Index endpoint: CD2_INSITU_URINARY_NOS_EXALLC – Carcinoma in situ, other and unspecified urinary organs

GWS hits: -

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

NAME	CD2_INSITU_URINARY_NOS_EXALLC
CONTROL_EXCLUDE	C3_CANCER\|C3_CANCER_WIDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D091
HD_ICD_9	2339
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	D091
COD_ICD_9	2339
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 and unspecified urinary organs

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