Risteys · CD2_INSITU_OESOPHAGUS

Endpoint definition steps	FinnGen
Phenotype data
1. Apply sex-specific rule None	-
2. Check conditions not C3_OESOPHAGUS	-
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D00.1& Hospital discharge: ICD-9 — 2301A Cause of death: ICD-10 — D00.1& Cause of death: ICD-9 — 2301A Cancer registry: Topography ICD-O-3 — C15 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	41	8	33
Unadjusted period prevalence (%)	0.01	0.00	0.01
Median age at first event (years)	69.25	70.95	68.83

-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

(40768797) Stomach Pathology biopsy report

12.16

14.98

3.7

1.2

—

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

131

7.54

7.84

8.3

3.9

—

(3044640) Blood type and Crossmatch panel - Blood

100

5.98

7.29

4.0

2.2

—

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

5.71

7.17

4.0

2.3

—

(40768804) Tissue Pathology biopsy report

5.32

6.58

3.7

1.5

—

(3013742) Prealbumin [Mass/volume] in Serum or Plasma

7.15

6.18

3.0

1.5

g/l

0.2

0.33

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

4.54

4.53

11.6

9.5

—

(4035726)

9.08

3.72

1.3

1.2

—

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

3.96

3.63

5.7

5.0

31.0

30.8

—

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

155

3.54

2.4

1.9

pmol/l

98.2

88.9

0.44

(3002256) Pathology report gross observation

4.09

3.14

1.4

1.0

—

(3022313) Gas panel - Capillary blood

5.57

3.10

5.6

3.0

—

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

4.50

2.88

5.8

6.3

mmol/l

23.3

24.9

—

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

197

3.35

2.86

7.2

3.8

mmol/l

7.1

7.0

0.14

185

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

7.92

2.62

1.4

1.0

—

(3016502) Oxygen saturation in Arterial blood

3.30

2.51

6.5

5.4

97.8

93.5

1.55

(3019225) pH of Specimen

3.46

2.51

3.2

2.9

—

(3019060) Gas panel - Arterial blood

3.82

2.49

4.0

3.4

—

(36660697) Celiac disease serology panel - Serum

4.21

2.26

1.9

1.1

—

(3020961) Endomysium IgA Ab [Titer] in Serum

5.52

2.13

1.0

1.1

—

(42870588) Differential panel, method unspecified - Blood

105

2.51

2.10

6.9

4.9

—

(3022145) Colonoscopy Study observation

3.80

2.07

1.7

1.2

—

(3020891) Body temperature

3.94

1.91

5.8

3.4

—

(40761535) Cells panel - Urine sediment

3.06

1.84

2.5

3.5

—

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

3.72

1.82

7.2

7.1

—

(3012516) Albumin [Mass/volume] in Urine

112

2.30

1.76

3.1

3.6

mg/l

2932.6

114.8

0.45

(3023368) Bacteria identified in Blood by Culture

104

2.30

1.74

3.1

3.9

—

(3043409) Potassium [Moles/volume] in Arterial blood

3.91

1.66

3.4

3.3

mmol/l

4.0

3.9

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

3.03

1.66

7.3

6.1

1.4

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

3.03

1.66

7.3

6.0

0.9

0.6

—

(3000330) Specific gravity of Urine by Test strip

3.64

1.57

1.6

5.2

—

(586526) SARS-CoV-2 (COVID-19) RNA [Presence] in Nasopharynx by NAA with probe detection

2.80

1.53

1.3

1.5

—

(3020682) Albumin/Creatinine [Ratio] in Urine

120

2.09

1.43

3.4

4.5

mg/mmol

2.1

15.0

1.63

(3009201) Thyrotropin [Units/volume] in Serum or Plasma

280

2.25

1.13

5.0

4.3

mu/l

1.9

2.1

0.68

249

(3037467) Urinalysis macro (dipstick) panel - Urine

205

1.93

1.12

5.1

4.1

—

(3042936) Bacteria identified in Isolate by Culture

2.10

1.11

2.2

1.6

—

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

1.98

1.03

1.9

—

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

0.00

1.02

0.0

2.6

—

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

0.00

1.00

0.0

3.4

—

(3020630) Protein [Mass/volume] in Serum or Plasma

2.25

0.94

1.0

1.2

g/l

64.3

66.7

—

(3009542) Hematocrit [Volume Fraction] of Blood

267

1.90

0.93

24.7

14.4

34.3

40.7

0.85

174

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

2.17

0.91

1.5

1.8

—

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

2.09

0.88

1.5

1.9

—

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

119

1.73

0.85

2.6

3.4

—

(3000991) Gas panel - Venous blood

1.95

0.82

8.7

—

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

316

2.14

0.79

28.8

13.7

mg/l

27.3

26.8

0.03

247

(40758558) Short blood count panel - Blood

1.81

0.73

7.2

4.1

—

(3002582) Erythrocytes [#/volume] in Urine

113

0.54

0.71

2.7

2.9

e6/l

19.4

54.6

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.75

0.71

2.7

2.4

—

(3026008) Bacteria identified in Urine by Culture

1.65

0.68

3.3

3.1

—

(4010399)

1.82

0.66

2.2

1.2

—

(3013512) EKG study

108

1.61

0.65

7.4

4.5

—

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

155

1.57

0.64

2.2

2.9

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.60

0.62

5.9

7.2

—

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

1.66

0.61

3.8

4.0

—

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

110

1.57

0.60

3.6

4.7

—

(40761536) Microorganisms panel - Urine sediment

0.00

0.60

0.0

4.0

—

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

0.00

0.60

0.0

2.3

—

(3004410) Hemoglobin A1c/Hemoglobin.total in Blood

301

1.76

0.59

8.7

7.2

mmol/mol

43.4

41.3

0.53

282

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

1.52

0.56

1.0

1.3

—

(3018095) Leukocytes [#/volume] in Urine

119

0.59

0.56

3.0

3.6

e6/l

185.2

41.1

—

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

142

1.48

0.51

3.9

6.1

—

0.0

—

(36304419) Bacteria [Presence] in Urine

0.59

0.49

3.7

3.0

—

(46235355) HIV 1 and 2 tests - Meaningful Use set

1.64

0.44

1.6

1.8

—

(3022217) INR in Platelet poor plasma by Coagulation assay

1.49

0.43

38.2

22.6

—

1.3

—

(3027238) Thyroperoxidase Ab [Units/volume] in Serum or Plasma

0.00

0.42

0.0

1.0

—

121.7

—

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

0.00

0.42

0.0

1.8

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.42

0.0

1.6

—

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

1.49

0.41

2.4

1.8

mmol/l

1.2

1.4

0.21

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

0.00

0.41

0.0

1.9

—

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

0.00

0.41

0.0

1.6

—

(3012544) pH of Venous blood

1.46

0.37

2.3

5.0

—

(3015736) pH of Urine

115

1.33

0.28

3.6

4.4

—

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

330

1.41

0.27

5.9

5.7

mmol/l

2.3

2.6

0.58

301

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

321

1.35

0.26

5.7

5.0

mmol/l

4.2

4.4

0.33

293

(3000494) Fungus identified in Specimen by Culture

1.40

0.24

1.2

1.7

—

(4094501)

0.00

0.21

0.0

1.2

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.00

0.21

0.0

1.8

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.20

0.0

1.6

—

(3018251) Fasting glucose [Moles/volume] in Serum or Plasma

323

1.31

0.16

6.3

4.9

mmol/l

6.1

6.2

0.13

290

(3020059) Calcium [Moles/volume] corrected for albumin in Serum or Plasma

0.81

0.09

2.0

mmol/l

2.5

2.4

—

(3018418) pH of Serum or Plasma

1.12

0.08

2.4

4.5

—

7.4

—

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

320

1.16

0.07

5.8

5.0

mmol/l

1.3

1.4

0.64

290

(3001784) Prostate Specific Ag Free/Prostate specific Ag.total in Serum or Plasma

168

1.13

0.07

4.3

3.7

18.8

25.0

—

(3044889) 12 lead EKG panel

232

0.89

0.07

5.6

4.2

—

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

311

0.99

0.00

5.0

4.5

mmol/l

1.3

0.06

284

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

0.00

0.0

1.3

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

0.0

3.7

—

5.0

—

(1002224) Polysomnography panel

0.00

0.0

1.1

—

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

0.00

0.0

1.3

—

244.3

—

(3020044) Glucose [Moles/volume] in Cerebral spinal fluid

0.00

0.0

1.3

—

3.6

—

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

0.00

0.0

1.0

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

0.0

3.7

—

7.3

—

(3027544) Mycobacterium sp identified in Sputum by Organism specific culture

0.00

0.0

4.8

—

(40762485) Glomerular basement membrane Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.0

—

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

0.00

0.0

3.0

—

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

0.89

0.00

2.6

3.6

ng/l

375.6

119.1

—

(3012447) Hantavirus puumala IgG Ab [Titer] in Serum

0.00

0.0

1.2

—

(3024928) Oxygen saturation in Venous blood

0.00

0.0

3.7

—

(3018301) Testosterone Free [Moles/volume] in Serum or Plasma

0.00

0.0

1.2

—

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

0.00

0.0

1.0

—

(3004915) Chlamydophila pneumoniae IgA Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(3041096) Erythrocytes [Presence] in Urine by Automated

0.98

0.00

2.1

4.3

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.2

—

4.1

—

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

0.00

0.0

3.8

—

(42868544) Hantavirus puumala IgM Ab [Presence] in Serum or Plasma by Immunofluorescence

0.00

0.0

1.2

—

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

0.00

0.0

1.6

—

2.0

—

(3026179) Normetanephrine [Moles/volume] in Serum or Plasma

0.00

0.0

2.4

—

0.5

—

(3019230) Fractional oxyhemoglobin in Venous blood

0.00

0.0

3.1

—

68.6

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.0

1.4

—

33.2

—

(3021788) Differential panel - Synovial fluid

0.00

0.0

1.0

—

(3044242) Glucose [Moles/volume] in Arterial blood

0.00

0.0

1.4

—

(3032155) Metanephrine Free [Moles/volume] in Serum or Plasma

0.00

0.0

2.4

—

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

0.00

0.0

5.6

—

(3019250) Coagulation factor VIII activity actual/normal in Platelet poor plasma by Coagulation assay

0.00

0.0

1.2

—

197.0

—

(3000093) Morphology [Interpretation] in Blood Narrative

0.00

0.0

1.0

—

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

0.00

0.0

1.2

—

672.2

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_INSITU_OESOPHAGUS_EXALLC and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have CD2_INSITU_OESOPHAGUS_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_OESOPHAGUS_EXALLC – Carcinoma in situ of oesophagus

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_OESOPHAGUS_EXALLC
CONTROL_EXCLUDE	C3_CANCER\|C3_CANCER_WIDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS	!C3_OESOPHAGUS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D001
HD_ICD_9	2301A
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	D001
COD_ICD_9	2301A
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	C15
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 oesophagus

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