Risteys · CD2_INSITU_LIVER_GALLBLADDER_BILE

Endpoint definition steps	FinnGen
Phenotype data
1. Apply sex-specific rule None	-
2. Check conditions not C3_LIVER_INTRAHEPATIC_BILE_DUCTS or not C3_GALLBLADDER or not C3_BILIARY_TRACT	-
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D01.5& Hospital discharge: ICD-9 — 2308 Cause of death: ICD-10 — D01.5& Cause of death: ICD-9 — 2308 Cancer registry: Topography ICD-O-3 — C2[2-4] 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	25	16	9
Unadjusted period prevalence (%)	0.00	0.01	0.00
Median age at first event (years)	60.23	56.85	66.25

-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

unit

cases

controls

-log₁₀(p)

N cases

N controls

(3033658) Prothrombin time (PT) actual/Normal

7.43

5.85

11.4

3.5

85.8

92.1

0.40

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

6.49

5.08

6.4

2.0

—

(3044640) Blood type and Crossmatch panel - Blood

6.40

4.67

6.0

1.9

—

(3002256) Pathology report gross observation

10.08

4.65

1.3

1.1

—

(40768797) Stomach Pathology biopsy report

6.28

4.35

1.4

1.2

—

(3042936) Bacteria identified in Isolate by Culture

6.00

4.16

2.9

2.6

—

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

4.49

3.18

8.2

3.4

—

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

5.25

3.04

8.2

2.3

u/l

35.4

33.9

—

(36031861) Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection

7.47

2.88

1.8

1.6

—

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

3.71

2.53

10.0

6.0

mmol/l

1.2

0.17

(3023368) Bacteria identified in Blood by Culture

3.78

2.50

5.4

4.1

—

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

7.45

2.49

2.4

3.3

—

(3016431) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Serum or Plasma

3.76

2.48

11.5

7.5

mmol/l

1.2

0.34

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

3.86

2.17

1.6

—

(3018418) pH of Serum or Plasma

3.39

2.14

2.5

3.9

—

7.4

—

(40768804) Tissue Pathology biopsy report

3.22

2.06

3.7

1.6

—

(3022250) Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma by Lactate to pyruvate reaction

3.81

1.78

1.8

2.8

u/l

196.3

244.2

—

(3044889) 12 lead EKG panel

137

3.29

1.73

4.9

3.3

—

(3022217) INR in Platelet poor plasma by Coagulation assay

3.07

1.59

4.4

22.5

—

1.3

—

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

2.73

1.57

2.7

1.8

pmol/l

112.7

93.0

—

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

2.74

1.56

9.1

1.9

u/l

59.4

57.4

0.09

(3019150) Specific gravity of Urine by Refractometry

2.81

1.53

2.1

4.5

—

1.0

—

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

2.63

1.47

2.2

2.6

nmol/l

62.5

73.5

0.91

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

2.30

1.15

2.7

4.4

—

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

2.71

1.15

1.2

1.7

—

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

2.71

1.15

1.2

1.6

—

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

2.58

1.08

2.0

1.7

—

(42870588) Differential panel, method unspecified - Blood

2.16

0.93

10.1

5.5

—

(40758558) Short blood count panel - Blood

2.03

0.92

2.8

5.6

—

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

2.08

0.91

2.2

4.3

—

0.0

—

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

2.13

0.90

1.4

—

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

121

1.89

0.83

13.6

2.6

u/l

80.9

42.5

0.70

112

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

1.97

0.81

3.1

5.3

—

0.0

—

(3015736) pH of Urine

1.94

0.75

2.2

4.1

—

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

100

1.91

0.74

2.4

4.1

—

0.0

—

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

1.98

0.70

2.2

1.7

—

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

1.78

0.65

1.7

3.1

ng/l

1825.8

1837.2

—

(3021960) Folate [Moles/volume] in Serum or Plasma

1.82

0.56

1.7

1.6

nmol/l

28.7

18.3

—

(3026008) Bacteria identified in Urine by Culture

1.59

0.49

2.3

3.6

—

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

1.53

0.45

5.0

3.2

—

(40761536) Microorganisms panel - Urine sediment

0.00

0.43

0.0

2.5

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

0.00

0.42

0.0

1.7

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.42

0.0

1.2

—

(36304419) Bacteria [Presence] in Urine

1.48

0.35

2.7

—

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

1.50

0.33

2.1

4.2

—

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

120

1.38

0.24

2.4

2.5

—

(3004529) Oxygen [Partial pressure] adjusted to patient's actual temperature in Venous blood

0.00

0.22

0.0

4.4

—

59.4

—

(3004588) Protein electrophoresis panel - Serum or Plasma

0.00

0.20

0.0

1.6

—

(4010399)

0.00

0.20

0.0

1.3

—

(3037467) Urinalysis macro (dipstick) panel - Urine

135

1.28

0.15

5.3

4.2

—

(3019050) Tissue transglutaminase IgA Ab [Units/volume] in Serum

1.20

0.11

1.2

1.3

—

0.8

—

(3029937) Albumin [Presence] in Urine by Test strip

0.81

0.09

3.0

4.4

—

0.0

—

(3027273) Bicarbonate [Moles/volume] in Venous blood

0.00

0.0

3.9

—

26.3

—

(3021584) Pregnancy associated plasma protein A [Units/volume] in Serum or Plasma

0.00

0.0

1.6

—

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

0.00

0.0

1.4

—

(3020961) Endomysium IgA Ab [Titer] in Serum

0.00

0.0

1.0

—

(3021387) Prolactin [Units/volume] in Serum or Plasma

0.00

0.0

1.9

—

484.4

—

(46235831) Pregnancy associated plasma protein A [Multiple of the median] adjusted in Serum or Plasma

0.00

0.0

1.6

—

(3025130) Human papilloma virus identified in Specimen

0.00

0.0

1.8

—

(1001926) Buprenorphine [Presence] in Urine by Screen method

0.00

0.0

1.0

—

(3041096) Erythrocytes [Presence] in Urine by Automated

0.98

0.00

1.4

3.5

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.0

—

(3008714) Choriogonadotropin [Multiple of the median] adjusted in Serum or Plasma

0.00

0.0

1.6

—

(1761868) Lipid panel - Serum or Plasma

0.87

0.00

1.8

3.0

—

(36033641) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay

0.00

0.0

1.2

—

(3051611) Lipemic interference index of Serum or Plasma

0.00

0.0

3.0

—

(3027008) Opiates [Presence] in Urine

0.00

0.0

1.0

—

(36305247) Microscopic observation [Identifier] in Isolate by Gram stain

0.00

0.0

1.2

—

(3007778) Kappa light chains/Lambda light chains [Mass Ratio] in Serum

0.00

0.0

1.0

—

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

0.00

0.0

1.4

—

(3050129) First trimester maternal screen panel - Serum or Plasma

0.00

0.0

1.8

—

(3006093) Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.4

—

(3049207) Fetal Trisomy 21 risk [Likelihood] Based on maternal age

0.00

0.0

1.6

—

(3020321) Streptococcus agalactiae [Presence] in Vaginal fluid by Organism specific culture

0.00

0.0

1.0

—

(3052851) Hemolysis interference index of Serum or Plasma

0.00

0.0

5.9

—

(3011371) Neisseria gonorrhoeae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.4

—

(3000620) Complement C3 [Mass/volume] in Serum or Plasma

0.00

0.0

1.1

—

1.1

—

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

0.00

0.0

1.4

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.0

1.0

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.0

1.6

—

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

0.00

0.0

1.4

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.2

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.0

1.0

—

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

0.00

0.0

1.6

—

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

0.00

0.0

1.8

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.0

1.0

—

(3016879) Cocaine [Presence] in Urine

0.00

0.0

1.0

—

(40763531) Fetal Nuchal fold [Multiple of the median] Thickness adjusted for maternal weight

0.00

0.0

1.6

—

(3017766) Complement C4 [Mass/volume] in Serum or Plasma

0.00

0.0

1.1

—

0.3

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.2

—

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

0.00

0.0

1.3

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_INSITU_LIVER_GALLBLADDER_BILE_EXALLC and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have CD2_INSITU_LIVER_GALLBLADDER_BILE_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_LIVER_GALLBLADDER_BILE_EXALLC – Carcinoma in situ of liver, gallbladder and bile ducts

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

Extremity

rg [CI]

Extremity

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

NAME	CD2_INSITU_LIVER_GALLBLADDER_BILE_EXALLC
CONTROL_EXCLUDE	C3_CANCER\|C3_CANCER_WIDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS	!C3_LIVER_INTRAHEPATIC_BILE_DUCTS\|!C3_GALLBLADDER\|!C3_BILIARY_TRACT
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D015
HD_ICD_9	2308
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	D015
COD_ICD_9	2308
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	C2[2-4]
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 liver, gallbladder and bile ducts

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