Risteys · CD2_INSITU

Endpoint definition steps	FinnGen
Phenotype data	557745
1. Apply sex-specific rule None	557745
2. Check conditions not C3_LARYNX	557064
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D02.0& Hospital discharge: ICD-9 — 2310 Cause of death: ICD-10 — D02.0& Cause of death: ICD-9 — 2310 Cancer registry: Topography ICD-O-3 — C32 Cancer registry: Morphology ICD-O-3 — ANY Cancer registry: Behaviour codes — 2 3 out of 7 registries used, show all original rules.	62
4. Check minimum number of events None	62
5. Include endpoints None	62
6. Filter based on genotype QC (FinnGen only)	54

Summary Statistics

↥

-FinRegistry-

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

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	54	12	42
Unadjusted period prevalence (%)	0.02	0.00	0.02
Median age at first event (years)	65.68	47.82	70.79

-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

↥

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.

Matched cohort

Matched cases
55: Matched controls
550

Code

Vocabulary

Description

Odds Ratio

-log₁₀(p)

N matched cases

N matched controls

DQB10

NOMESCO Finland

Endoscopic excision of lesion of larynx

295.7

31.2

UDQ12

NOMESCO Finland

Flexible laryngoscopy

33.0

22.3

D14.1

ICD-10 Finland

Benign neoplasm: Larynx

152.8

20.1

D02.0

ICD-10 Finland

Carcinoma in situ: Larynx

+∞

20.0

C32.0

ICD-10 Finland

Malignant neoplasm: Glottis

130.3

17.8

DQA10

NOMESCO Finland

Biopsy of larynx

239.9

17.6

C320, 8077, 2

ICD-O-3

+∞

16.5

J38.3

ICD-10 Finland

Other diseases of vocal cords

47.9

14.5

D38.0

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Larynx

183.5

14.2

8070/2-C32.0

ICD-O-3

Squamous cell carcinoma in situ, NOS, of glottis

+∞

13.0

UDQ22

NOMESCO Finland

Microlaryngoscopy

61.2

12.6

ZXC10

NOMESCO Finland

Use of laser

30.5

10.9

J37.0

ICD-10 Finland

Chronic laryngitis

20.0

10.2

EP1AE

NOMESCO Finland

Neck ultrasound examination

16.8

10.2

WX734

NOMESCO Finland

JET-ventilation

+∞

8.5

WX404

NOMESCO Finland

Intravenous generell anesthesy

5.5

7.8

C32.9

ICD-10 Finland

Malignant neoplasm: Larynx, unspecified

+∞

7.4

2310A

ICD-9 Finland

Carcinoma in situ of respiratory system, Larynx

+∞

7.4

8070/2-C32.9

ICD-O-3

Squamous cell carcinoma in situ, NOS, of larynx, NOS

+∞

6.4

LabWAS

↥

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(40768804) Tissue Pathology biopsy report

159

3.42

4.77

3.8

2.1

—

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

232

2.82

3.22

5.5

9.2

1.22

1.20

mmol/l

1.19

202

(3013512) EKG study

162

2.67

3.15

7.3

4.7

—

(40761536) Microorganisms panel - Urine sediment

3.26

2.35

4.4

4.3

—

(40761511) CBC panel - Blood by Automated count

408

3.47

2.33

26.6

17.9

—

(3022096) Basophils/Leukocytes in Blood

190

2.27

2.28

8.2

6.2

0.40

0.57

1.03

173

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

260

2.29

2.14

7.1

7.5

12.63

11.80

umol/l

0.13

252

(40765161) Human bocavirus DNA [Presence] in Specimen by NAA with probe detection

5.37

2.11

2.2

1.4

—

(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma

215

2.17

2.03

6.5

4.8

49.43

38.61

ng/l

0.19

174

(3002030) Lymphocytes/Leukocytes in Blood

200

2.10

1.91

8.6

6.2

25.33

24.31

0.18

185

(3037467) Urinalysis macro (dipstick) panel - Urine

290

2.19

1.83

4.0

4.9

—

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

3.81

1.65

1.6

—

(3023368) Bacteria identified in Blood by Culture

163

1.98

1.63

5.1

4.7

—

(3021440) Promyelocytes/Leukocytes in Blood

2.43

1.50

1.9

4.2

0.00

0.14

—

(3040853) Adenovirus DNA [Identifier] in Specimen by NAA with probe detection

3.33

1.47

2.2

1.4

—

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

2.42

1.45

1.2

1.5

—

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

2.20

1.40

7.9

3.7

—

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

3.13

1.39

2.0

1.4

—

(3042936) Bacteria identified in Isolate by Culture

2.12

1.38

1.8

2.1

—

(3026493) Urate [Moles/volume] in Serum or Plasma

120

1.89

1.31

2.7

3.8

402.46

352.66

umol/l

0.72

103

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

201

1.80

1.29

3.0

2.8

—

estimate

—

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

201

1.80

1.29

2.1

2.3

—

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

2.36

1.28

5.5

6.1

1.19

1.22

mmol/l

—

(3041096) Erythrocytes [Presence] in Urine by Automated

122

1.85

1.24

3.5

3.8

0.00

estimate

—

(3020682) Albumin/Creatinine [Ratio] in Urine

166

1.79

1.24

4.5

4.1

4.43

12.05

mg/mmol

1.40

109

(3027945) Reticulocytes/Erythrocytes in Blood

2.05

1.20

2.7

2.9

1.66

1.83

0.27

(3017181) Myelocytes/Leukocytes in Blood

2.17

1.20

1.9

4.0

0.40

1.16

—

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

2.08

1.01

1.0

1.5

—

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

1.80

1.00

2.1

2.0

—

(3023520) Reticulocytes [#/volume] in Blood

1.91

1.00

2.4

2.6

70.97

66.32

e9/l

—

(3000067) Parathyrin.intact [Mass/volume] in Serum or Plasma

0.00

1.00

0.0

6.2

—

96.74

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.82

0.99

3.9

7.5

—

(3012516) Albumin [Mass/volume] in Urine

158

1.65

0.95

3.2

3.3

64.62

78.29

mg/l

0.09

109

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

244

1.62

0.93

3.0

4.5

0.00

27.07

estimate

0.49

(3044640) Blood type and Crossmatch panel - Blood

150

1.65

0.92

2.4

2.6

—

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

150

1.65

0.92

3.3

4.4

0.00

0.04

estimate

—

(4035726) Immunohistochemistry procedure

2.00

0.92

1.6

1.2

—

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

2.00

0.92

2.1

4.9

67.95

66.48

g/l

—

(42870588) Differential panel, method unspecified - Blood

145

1.60

0.82

9.2

5.6

—

(3002032) Base excess in Venous blood by calculation

1.72

0.77

2.7

4.3

2.69

2.49

mmol/l

—

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

203

1.53

0.76

2.5

2.4

97.04

84.82

pmol/l

0.86

117

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

242

1.53

0.76

3.0

4.5

0.00

estimate

-0.00

(3007853) Bacteria identified in Skin by Aerobe culture

1.66

0.74

1.7

1.8

—

(3004588) Protein electrophoresis panel - Serum or Plasma

1.76

0.71

2.1

3.4

—

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

390

1.64

0.69

4.8

5.5

1.40

1.38

mmol/l

0.08

345

(3017446) Testosterone [Moles/volume] in Serum or Plasma

1.70

0.65

1.9

2.1

5.93

13.45

nmol/l

—

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

248

1.46

0.64

3.0

4.5

0.00

estimate

-0.00

(3026782) Osmolality of Urine

108

1.53

0.61

2.5

3.4

591.50

539.16

mosm/kgh2o

—

(3020961) Endomysium IgA Ab [Titer] in Serum

0.00

0.61

0.0

1.0

—

(3000492) Spirometry study

1.86

0.61

2.3

1.8

—

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

184

1.43

0.56

3.2

4.7

0.00

0.06

estimate

—

(3013707) Erythrocyte sedimentation rate [Velocity] in Red Blood Cells by Westergren method

323

1.44

0.56

5.7

4.3

14.03

13.22

mm/h

0.08

292

(3003338) MCHC [Entitic Mass/volume] in Red Blood Cells

317

0.71

0.55

27.3

27.1

333.19

331.47

g/l

0.74

317

(3012095) Magnesium [Moles/volume] in Serum or Plasma

1.53

0.52

4.3

4.1

0.78

0.79

mmol/l

0.09

(3022145) Colonoscopy Study observation

1.49

0.48

1.9

1.3

—

(40768797) Stomach Pathology biopsy report

1.50

0.45

1.5

1.2

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

1.62

0.43

2.4

3.2

1.86

1.07

—

(3024889) Methemoglobin/Hemoglobin.total in Venous blood

1.62

0.43

2.4

3.1

0.52

0.65

—

(1761868) Lipid panel - Serum or Plasma

116

1.40

0.43

4.8

3.9

—

(4034850) Laboratory test

0.00

0.40

0.0

18.9

—

(3014576) Chloride [Moles/volume] in Serum or Plasma

0.63

0.36

2.5

8.3

102.50

103.85

mmol/l

—

(3002256) Pathology report gross observation

1.31

0.31

1.4

1.3

—

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

1.32

0.28

1.7

—

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

0.75

0.25

3.3

3.0

11.36

11.80

umol/l

—

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

194

1.22

0.23

2.3

3.6

—

(3019060) Gas panel - Arterial blood

1.24

0.22

2.6

4.1

—

(3045716) Anion gap in Serum or Plasma by calculation

0.00

0.21

0.0

2.3

—

9.73

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.21

0.0

1.5

—

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

0.00

0.21

0.0

1.1

—

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

0.00

0.21

0.0

1.2

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.00

0.21

0.0

1.7

—

(3000991) Gas panel - Venous blood

1.25

0.21

2.3

12.7

—

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

0.00

0.20

0.0

1.1

—

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

1.21

0.17

2.0

1.9

—

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

0.76

0.16

3.0

2.28

2.22

g/l

—

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

210

1.16

0.15

6.7

5.1

21.21

21.58

0.04

118

(3007220) Creatine kinase [Enzymatic activity/volume] in Serum or Plasma

154

1.15

0.12

4.2

2.3

327.41

152.21

u/l

0.66

146

(40758558) Short blood count panel - Blood

135

0.86

0.11

9.8

7.1

—

(3024135) Streptococcus.beta-hemolytic [Presence] in Throat by Organism specific culture

1.12

0.10

1.0

1.4

—

(3000494) Fungus identified in Specimen by Culture

1.10

0.10

1.4

1.6

—

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

107

1.16

0.09

2.6

—

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

1.04

0.09

1.3

4.5

4.92

77.11

ug/l

—

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

1.11

0.08

3.0

10.5

—

(3019977) pH of Arterial blood

0.80

0.08

4.3

9.2

7.43

7.42

—

(3015736) pH of Urine

188

1.10

0.07

2.8

4.2

5.90

6.29

1.69

103

(3005013) Prostate Specific Ag Free [Mass/volume] in Serum or Plasma

151

1.08

0.04

3.6

3.5

0.86

0.75

ug/l

0.47

114

(3018095) Leukocytes [#/volume] in Urine

193

1.06

0.01

3.2

4.2

260.23

89.08

e6/l

0.37

149

(3026008) Bacteria identified in Urine by Culture

149

1.01

0.00

2.1

3.5

—

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

105

1.06

0.00

2.1

1.4

—

(3018418) pH of Serum or Plasma

136

1.04

0.00

6.8

5.9

7.39

7.40

0.34

(3003129) Base excess in Capillary blood by calculation

0.00

0.0

1.7

—

-0.27

—

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

0.00

0.0

1.3

—

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

0.00

0.0

2.0

—

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

0.00

0.0

8.2

—

432.83

—

(3000093) Morphology [Interpretation] in Blood Narrative

0.00

0.0

1.0

—

(21494434) Karyotype in Bone marrow

0.00

0.0

1.0

—

(4195642) Thrombophilia screening test

0.00

0.0

1.2

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

-0.00

0.0

1.6

—

(3015816) F5 gene p.Arg506Gln [Presence] in Blood or Tissue by Molecular genetics method

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.0

—

(21494890) Protein electrophoresis panel - 24 hour Urine

0.00

-0.00

0.0

6.1

—

(4268621) Lupus anticoagulant assay

0.00

-0.00

0.0

1.8

—

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

0.92

-0.00

1.0

2.5

5.48

5.00

ug/l

—

(3027008) Opiates [Presence] in Urine

0.00

-0.00

0.0

1.0

—

(3052649) Adenosine deaminase [Enzymatic activity/volume] in Serum or Plasma

0.00

-0.00

0.0

1.2

—

18.20

—

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

0.00

-0.00

0.0

1.2

—

(3027545) Mycoplasma pneumoniae Ab [Presence] in Serum by Immunoassay

0.00

-0.00

0.0

1.8

—

(3013527) Hepatitis B virus core IgM Ab [Presence] in Serum

0.00

-0.00

0.0

1.3

—

(3028369) Herpes simplex virus 1+2 DNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

1.6

—

(3014791) Apolipoprotein B [Mass/volume] in Serum or Plasma

0.00

-0.00

0.0

2.0

—

0.73

—

(3028300) Cannabinoids [Presence] in Urine

0.00

-0.00

0.0

1.0

—

(3016879) Cocaine [Presence] in Urine

0.00

-0.00

0.0

1.0

—

(40765096) Chromosome analysis panel by Banding

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

1.0

—

(3044941) Cell count panel - Synovial fluid

0.00

-0.00

0.0

1.3

—

(40760847) Basement membrane Ab [Titer] in Serum by Immunofluorescence

0.00

-0.00

0.0

1.4

—

(3012202) Varicella zoster virus DNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

1.4

—

(3043405) Microscopic observation [Identifier] in Specimen by Non-gynecological cytology method

0.00

-0.00

0.0

1.2

—

(3027944) Amphetamines [Presence] in Urine

0.00

-0.00

0.0

1.0

—

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

1.00

-0.00

1.2

1.7

—

(36032419) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Immunoassay

0.00

-0.00

0.0

1.3

—

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

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

1.1

—

216.00

—

(3032700) Glomerular basement membrane Ab [Units/volume] in Serum

0.00

-0.00

0.0

1.0

—

Mortality – FinRegistry

↥

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

Relationships between endpoints

↥

Index endpoint: CD2_INSITU_LARYNX – Carcinoma in situ of larynx

GWS hits: -

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

NAME	CD2_INSITU_LARYNX
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS	!C3_LARYNX
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D020
HD_ICD_9	2310
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	D020
COD_ICD_9	2310
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	C32
CANC_TOPO_EXCL
CANC_MORPH	ANY
CANC_MORPH_EXCL
CANC_BEHAV	2

≡ Risteys

R14

FinnGen R13 + FinRegistry

FinnGen R12 + FinRegistry

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 larynx

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 larynx (CD2_INSITU_LARYNX)

Summary Statistics

-FinRegistry-

-FinnGen-

Key figures

-FinnGen-

Age distribution of first events

-FinnGen-

Year distribution of first events

-FinnGen-

Cumulative Incidence Function

CodeWAS

Matched cohort

LabWAS

Mortality – FinRegistry

Relationships between endpoints