Carcinoma in situ of oral cavity and pharynx

CD2_INSITU_OROPHARYNX

No definition available.

Endpoint definition

↥

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions not C3_OROPHARYNX	519681
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D00.01&, D00.02&, D00.03&, D00.04&, D00.05&, D00.06&, D00.07& Cause of death: ICD-10 — D00.01&, D00.02&, D00.03&, D00.04&, D00.05&, D00.06&, D00.07& Cancer registry: Topography ICD-O-3 — C09\|C10 Cancer registry: Morphology ICD-O-3 — ANY Cancer registry: Behaviour codes — 2 3 out of 7 registries used, show all original rules.	53
4. Check minimum number of events None	53
5. Include endpoints None	53
6. Filter based on genotype QC (FinnGen only)	53

Control definitions (FinnGen only)

Controls for this endpoint are individuals that are not cases.

Extra metadata

Level in the ICD hierarchy: 3
First used in FinnGen datafreeze: DF9
Parent code in ICD-10: D00

NAME	CD2_INSITU_OROPHARYNX
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS	!C3_OROPHARYNX
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D000[1-7]
HD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
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	D000[1-7]
COD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
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	C09\|C10
CANC_TOPO_EXCL
CANC_MORPH	ANY
CANC_MORPH_EXCL
CANC_BEHAV	2

Similar endpoints

↥

List of similar endpoints to Carcinoma in situ of oral cavity and pharynx based on the number of shared cases.

Similar with more cases:

Similar with less cases:

Carcinoma in situ of oropharynx, excluding all cancers

Case counts by codes

↥

FinnGen case counts by registry codes:

Upset plot

Full data table

Summary Statistics

↥

-FinRegistry-

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

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	53	18	35
Unadjusted period prevalence (%)	0.01	0.01	0.02
Median age at first event (years)	64.41	70.73	61.15

-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

cases

controls

unit

-log₁₀(p)

N cases

N controls

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

3.85

5.28

3.0

2.4

—

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

174

3.66

4.94

5.0

3.8

—

(3044640) Blood type and Crossmatch panel - Blood

121

3.25

4.25

3.0

2.5

—

(3002256) Pathology report gross observation

4.21

4.22

1.6

1.2

—

(40758558) Short blood count panel - Blood

3.25

3.96

10.7

7.0

—

(40768804) Tissue Pathology biopsy report

148

2.89

3.51

3.7

2.1

—

(4035726)

3.79

3.46

1.7

1.3

—

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

3.94

3.41

2.0

1.4

—

(3001604) Monocytes [#/volume] in Blood

194

2.86

3.34

7.9

6.2

0.6

e9/l

0.43

166

(3006315) Basophils [#/volume] in Blood

195

2.83

3.29

7.9

6.3

0.0

e9/l

0.28

169

(3019198) Lymphocytes [#/volume] in Blood

197

2.79

3.20

8.0

6.3

1.8

1.7

e9/l

0.12

172

(3013115) Eosinophils [#/volume] in Blood

201

2.70

3.01

8.0

6.4

0.2

e9/l

0.50

174

(3000991) Gas panel - Venous blood

3.59

3.01

8.9

9.3

—

(1761868) Lipid panel - Serum or Plasma

170

0.27

2.84

3.5

3.0

—

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

9.03

2.81

1.4

1.5

—

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

211

2.49

2.59

9.6

5.5

11.2

10.4

umol/l

0.17

199

(3023368) Bacteria identified in Blood by Culture

125

2.48

2.56

4.9

4.6

—

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

159

2.42

2.52

2.2

1.9

95.7

95.0

pmol/l

0.03

(42870588) Differential panel, method unspecified - Blood

127

2.43

2.46

6.4

5.9

—

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

2.76

2.39

1.2

1.7

—

(3030306) Epithelial cells.non-squamous [#/volume] in Urine by Automated count

2.64

2.31

2.1

2.3

0.3

0.8

e6/l

—

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

2.87

2.30

1.2

1.7

—

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

2.59

2.24

2.1

1.8

—

(4010399)

3.28

2.19

1.6

1.3

—

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

2.70

2.18

12.5

10.8

—

(3003458) Phosphate [Moles/volume] in Serum or Plasma

2.57

2.11

4.1

5.9

0.9

1.0

mmol/l

0.91

(3000494) Fungus identified in Specimen by Culture

2.69

2.05

2.2

1.5

—

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

146

2.18

1.97

2.5

2.2

84.0

76.1

nmol/l

0.54

127

(3019832) Treponema pallidum Ab [Presence] in Serum

3.50

1.95

1.1

1.6

—

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

2.63

1.85

1.4

1.6

—

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

2.57

1.78

1.3

1.5

—

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

254

2.11

1.75

4.6

—

100.3

—

(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

3.07

1.71

1.9

1.7

—

(3042936) Bacteria identified in Isolate by Culture

2.21

1.49

2.4

1.7

—

(3041096) Erythrocytes [Presence] in Urine by Automated

117

0.37

1.49

2.6

3.8

—

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

2.43

1.46

2.1

3.2

5.3

5.8

umol/l

—

(36304419) Bacteria [Presence] in Urine

117

1.97

1.44

2.5

2.9

—

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

2.01

1.37

1.4

—

(3021879) Hepatitis B virus core Ab [Presence] in Serum

2.51

1.34

1.3

1.5

—

(3022313) Gas panel - Capillary blood

2.95

1.31

3.8

2.1

—

(3030467) Casts [#/volume] in Urine by Automated count

121

1.89

1.29

2.7

3.0

0.4

0.2

e6/l

0.20

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

2.23

1.26

1.4

1.7

—

(3036481) Cortisol [Moles/volume] in Serum or Plasma

2.15

1.04

2.7

2.1

369.6

360.8

nmol/l

—

(43054914) Glucose tolerance 2 hours panel - Serum or Plasma

2.15

1.04

1.1

1.5

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

2.37

0.97

2.0

2.7

2.2

1.4

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.01

0.92

2.4

2.0

—

(3051552) Clostridioides difficile toxin genes [Presence] in Stool by NAA with probe detection

2.12

0.90

1.5

1.3

—

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

2.05

0.87

12.7

5.7

24.3

25.2

mmol/l

—

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

1.82

0.85

1.3

—

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

2.29

0.78

14.6

7.7

—

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

2.29

0.78

1.2

1.8

—

(40761535) Cells panel - Urine sediment

1.97

0.77

4.7

3.1

—

(3020891) Body temperature

2.19

0.77

6.0

4.1

—

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

2.02

0.72

1.8

2.5

25.5

24.1

mmol/l

—

(3002032) Base excess in Venous blood by calculation

1.77

0.72

2.3

3.7

1.0

2.4

mmol/l

—

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

1.94

0.70

2.0

2.6

52.8

53.2

—

(3021589) Normoblasts [#/volume] in Blood

188

1.51

0.69

10.0

11.6

0.0

e9/l

0.00

155

(3009343) pH of Capillary blood

1.87

0.68

4.0

2.4

—

7.4

—

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

406

1.72

0.64

30.0

15.2

37.9

21.4

mg/l

2.11

334

(3004119) Hemoglobin [Mass/volume] in Venous blood

1.86

0.61

2.2

3.0

130.5

130.6

g/l

—

(3013707) Erythrocyte sedimentation rate by Westergren method

302

1.47

0.59

6.3

4.3

15.9

12.4

mm/h

0.69

273

(3019225) pH of Specimen

1.65

0.56

13.8

4.2

—

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

158

1.43

0.52

3.3

3.1

—

(3012544) pH of Venous blood

1.60

0.51

2.3

3.9

—

(3018095) Leukocytes [#/volume] in Urine

150

1.42

0.50

3.2

3.7

8.0

54.9

e6/l

1.70

106

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

104

1.47

0.49

5.3

3.5

—

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

239

1.36

0.46

2.9

2.8

—

(3019060) Gas panel - Arterial blood

1.67

0.44

9.2

3.9

—

(3013721) Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma

134

1.40

0.44

3.9

2.8

37.4

29.6

u/l

0.42

124

(3049717) Cytology report of Urine Cyto stain

0.00

0.42

0.0

2.8

—

(3009542) Hematocrit [Volume Fraction] of Blood

364

1.40

0.41

29.2

15.6

36.7

40.9

1.08

247

(3037121) Protein [Mass/volume] in Urine

0.00

0.41

0.0

3.3

—

0.1

—

(3044889) 12 lead EKG panel

292

1.34

0.41

5.5

4.1

—

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

165

0.72

0.40

5.0

4.1

—

(3013512) EKG study

143

0.71

0.38

5.5

4.4

—

(3022145) Colonoscopy Study observation

1.52

0.37

1.5

1.4

—

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

196

1.31

0.36

4.0

4.1

15.8

31.4

ng/l

2.25

153

(3026008) Bacteria identified in Urine by Culture

111

1.36

0.34

2.9

3.1

—

(40761511) CBC panel - Blood by Automated count

435

1.43

0.34

22.6

14.1

—

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

267

1.28

0.33

4.8

2.9

68.0

49.1

u/l

0.52

255

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

0.00

0.21

0.0

1.1

—

0.0

—

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

0.00

0.21

0.0

1.1

—

0.0

—

(3000570) Elastase.pancreatic [Mass/mass] in Stool

0.00

0.21

0.0

1.5

—

352.1

—

(40767503) Oxygen content in Capillary blood by calculation

0.00

0.21

0.0

3.5

—

16.1

—

(3012110) Lysozyme [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

1.6

—

11.4

—

(3037467) Urinalysis macro (dipstick) panel - Urine

276

1.20

0.20

4.3

4.7

—

(4094501)

0.00

0.20

0.0

1.1

—

(3035797) Protein.monoclonal band 2 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.20

0.0

1.1

—

0.0

—

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

172

0.82

0.19

3.0

3.5

13.6

21.7

—

(3041942) Cyclic citrullinated peptide Ab [Units/volume] in Serum

0.72

0.18

1.4

1.2

—

10.8

—

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

1.18

0.10

3.6

4.7

2.0

13.4

ug/l

—

(3002385) Erythrocyte distribution width [Ratio]

342

0.91

0.07

33.0

18.5

14.2

13.8

0.94

333

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

440

0.88

0.06

34.0

17.5

76.9

84.5

umol/l

1.13

440

(40760892) CBC W Ordered Manual Differential panel - Blood

1.14

0.06

7.3

6.2

—

(3015736) pH of Urine

169

0.92

0.04

4.8

3.7

—

(40764999) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)

384

1.06

0.01

22.1

15.1

80.3

77.6

ml/min/173m2

0.33

312

(40768806) Pleura Pathology biopsy report

0.00

0.0

1.0

—

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

0.00

0.0

2.3

—

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

0.00

0.0

1.5

—

(3021901) Oxygen saturation in Capillary blood

0.00

0.0

3.1

—

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

0.00

0.0

2.4

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.0

1.8

—

(3006588) Cancer Ag 15-3 [Units/volume] in Serum or Plasma

0.00

0.0

2.8

—

15.5

—

(21494670) JAK2 gene exon 14 targeted mutation analysis in Blood or Tissue by Molecular genetics method

0.00

0.0

1.1

—

(3021125) Hepatitis C virus RNA [Presence] in Serum or Plasma by NAA with probe detection

0.00

0.0

1.2

—

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

0.00

0.0

14.8

—

(3029511) Human papilloma virus DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.3

—

(3045424) Erythrocytes [Presence] in Urine

0.00

0.0

1.1

—

(40763082) Lactate dehydrogenase [Enzymatic activity/volume] in Pleural fluid by Lactate to pyruvate reaction

0.00

0.0

1.1

—

156.9

—

(3042631) Mycobacterium sp identified in Specimen

0.00

0.0

8.3

—

(40768795) Lymph node Pathology biopsy report

0.00

0.0

1.2

—

(3003434) Protein [Mass/volume] in Pleural fluid

0.00

0.0

1.1

—

31.9

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.0

1.8

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.4

—

(3027008) Opiates [Presence] in Urine

0.00

0.0

1.8

—

(3045788) Cell count panel - Pleural fluid

0.00

0.0

1.2

—

(3022806) Fractional oxyhemoglobin in Capillary blood

0.00

0.0

3.1

—

87.6

—

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

0.00

0.0

1.6

—

(40768797) Stomach Pathology biopsy report

0.83

0.00

1.0

1.2

—

(3044927) Protein electrophoresis panel - Urine

0.00

0.0

1.2

—

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

0.00

0.0

1.7

—

(3016879) Cocaine [Presence] in Urine

0.00

0.0

1.8

—

(3035880) pH of Pleural fluid

0.00

0.0

1.2

—

(3036782) Glucose [Moles/volume] in Pleural fluid

0.00

0.0

1.1

—

6.9

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.2

—

14.8

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.0

1.8

—

(21494815) CD4 cells/100 lymphocytes in Specimen

0.00

0.0

2.0

—

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

0.00

0.0

1.0

—

Mortality – FinRegistry

↥

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

Relationships between endpoints

↥

Index endpoint: CD2_INSITU_OROPHARYNX – Carcinoma in situ of oral cavity and pharynx

GWS hits: -

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

≡ 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 oral cavity and pharynx

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 oral cavity and pharynx (CD2_INSITU_OROPHARYNX)

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