Carcinoma in situ of oropharynx, excluding all cancers

CD2_INSITU_OROPHARYNX_EXALLC

No definition available.

Endpoint definition

↥

Endpoint definition steps	FinnGen
Phenotype data
1. Apply sex-specific rule None	-
2. Check conditions not C3_OROPHARYNX	-
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.	-
4. Check minimum number of events None	-
5. Include endpoints None	-
6. Filter based on genotype QC (FinnGen only) None	-

Control definitions (FinnGen only)

Control exclude: C3_CANCER, C3_CANCER_WIDE

Extra metadata

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

NAME	CD2_INSITU_OROPHARYNX_EXALLC
CONTROL_EXCLUDE	C3_CANCER\|C3_CANCER_WIDE
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 oropharynx, excluding all cancers based on the number of shared cases.

Similar with more cases:

Similar with less cases:

Carcinoma in situ of oral cavity and pharynx

Case counts by codes

↥

FinnGen case counts by registry codes:

No upset plot: script not run.

No upset table: script not run.

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	53	18	35
Unadjusted period prevalence (%)	0.01	0.01	0.02
Median age at first event (years)	64.41	70.73	61.15

-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

No data

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

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

10.87

14.67

3.0

2.2

0.2

g/l

0.48

(4035726)

11.64

10.27

1.7

1.2

—

(3002256) Pathology report gross observation

7.50

7.80

1.6

1.1

—

(40768804) Tissue Pathology biopsy report

4.88

7.59

3.7

1.6

—

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

4.44

6.40

3.0

1.8

—

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

160

4.14

5.91

5.0

3.1

—

(3044640) Blood type and Crossmatch panel - Blood

106

3.85

5.47

3.0

1.9

—

(40758558) Short blood count panel - Blood

3.69

4.78

10.7

5.8

—

(3000991) Gas panel - Venous blood

5.08

4.61

8.9

8.1

—

(3023368) Bacteria identified in Blood by Culture

103

3.18

3.96

4.9

3.9

—

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

3.68

3.53

12.5

9.7

—

(3020779) Urea [Moles/volume] in Serum or Plasma

3.94

3.41

2.5

10.8

9.9

mmol/l

0.00

(3001604) Monocytes [#/volume] in Blood

193

2.88

3.39

7.9

5.3

0.6

e9/l

0.51

162

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

194

2.86

3.34

9.6

3.5

11.2

11.3

umol/l

0.02

178

(3006315) Basophils [#/volume] in Blood

194

2.86

3.34

7.9

5.3

0.0

e9/l

0.03

165

(3019198) Lymphocytes [#/volume] in Blood

195

2.83

3.29

8.0

5.4

1.8

e9/l

0.03

167

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

3.82

3.27

2.0

1.3

—

(3013115) Eosinophils [#/volume] in Blood

199

2.74

3.11

8.0

5.3

0.2

e9/l

1.24

168

(1761868) Lipid panel - Serum or Plasma

171

0.27

3.03

3.5

3.3

—

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

3.09

3.02

2.1

1.5

—

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

3.16

2.99

1.2

1.7

—

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

3.40

2.98

1.2

1.7

—

(42870588) Differential panel, method unspecified - Blood

119

2.65

2.89

6.4

5.7

—

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

2.98

2.85

2.1

2.8

0.3

0.9

e6/l

—

(4010399)

4.12

2.72

1.6

1.2

—

(36304419) Bacteria [Presence] in Urine

2.66

2.69

2.5

2.8

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

3.95

2.62

11.9

5.0

0.6

0.7

—

(3000494) Fungus identified in Specimen by Culture

3.08

2.56

2.2

1.7

—

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

3.21

2.55

1.4

—

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

232

2.50

2.51

4.6

3.9

—

33.0

—

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

161

2.38

2.43

2.2

1.9

95.7

94.1

pmol/l

0.06

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

2.97

2.26

1.3

1.5

—

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

100

2.40

2.22

2.7

3.1

0.4

e6/l

0.01

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

3.30

2.03

12.6

4.9

1.3

1.8

—

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

2.85

1.97

1.4

1.5

—

(3019832) Treponema pallidum Ab [Presence] in Serum

3.50

1.95

1.1

1.5

—

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

2.89

1.91

2.1

2.3

5.3

5.5

umol/l

—

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

2.95

1.81

1.3

1.5

—

(3009445) Proteinase 3 Ab [Units/volume] in Serum

3.62

1.80

1.0

1.1

—

(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

1.3

—

(40761535) Cells panel - Urine sediment

3.07

1.71

4.7

3.0

—

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

3.25

1.63

1.5

1.4

—

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

158

1.95

1.51

2.5

2.4

83.9

75.5

nmol/l

0.59

139

(3022313) Gas panel - Capillary blood

3.34

1.47

3.8

4.4

—

(3042936) Bacteria identified in Isolate by Culture

2.14

1.39

2.4

1.6

—

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

2.95

1.31

14.6

8.0

—

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

1.93

1.25

1.4

1.3

—

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

131

1.85

1.24

3.3

3.0

—

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

2.47

1.22

12.7

4.8

24.3

24.8

mmol/l

—

(3020891) Body temperature

2.65

1.18

6.0

3.4

—

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

2.12

1.14

1.3

—

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

2.52

1.11

1.8

3.1

25.5

25.0

mmol/l

—

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

2.40

1.05

2.0

3.5

52.8

56.1

—

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

2.15

1.04

1.1

1.6

—

(3041096) Erythrocytes [Presence] in Urine by Automated

100

0.45

1.03

2.6

3.4

—

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

2.08

1.01

2.7

1.9

369.6

396.1

nmol/l

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

2.37

0.97

2.0

2.5

2.2

1.4

—

(3018095) Leukocytes [#/volume] in Urine

131

1.70

0.96

3.2

3.6

8.0

65.7

e6/l

1.06

(3021589) Normoblasts [#/volume] in Blood

177

1.65

0.95

10.0

8.6

0.0

e9/l

0.50

143

(3007853) Bacteria identified in Skin by Aerobe culture

1.91

0.89

2.4

2.1

—

(3019225) pH of Specimen

2.05

0.87

13.8

3.3

—

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

1.71

0.83

5.3

3.2

—

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

1.92

0.82

2.2

3.2

130.5

129.9

g/l

—

(3002032) Base excess in Venous blood by calculation

1.91

0.76

2.3

4.7

1.0

1.7

mmol/l

—

(3021447) Carbon dioxide [Partial pressure] in Venous blood

1.91

0.76

2.3

4.8

5.7

kpa

—

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

405

1.73

0.76

30.0

12.4

37.9

21.8

mg/l

2.01

312

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

1.94

0.70

1.2

1.7

—

(3013707) Erythrocyte sedimentation rate by Westergren method

297

1.53

0.68

6.3

4.1

15.9

12.1

mm/h

0.78

272

(3012544) pH of Venous blood

1.68

0.68

2.3

4.8

—

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

180

1.49

0.66

4.0

3.8

15.8

53.3

ng/l

1.55

137

(3019060) Gas panel - Arterial blood

1.80

0.65

9.2

4.3

—

(3024354) Oxygen [Partial pressure] in Venous blood

1.86

0.61

2.2

3.0

4.0

4.7

kpa

—

(3022145) Colonoscopy Study observation

1.70

0.58

1.5

1.2

—

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

236

1.40

0.51

2.9

2.7

—

(3037467) Urinalysis macro (dipstick) panel - Urine

259

1.36

0.45

4.3

4.4

—

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

135

1.38

0.42

3.9

2.7

37.4

29.4

u/l

0.44

123

(4094501)

0.00

0.42

0.0

1.0

—

(3026008) Bacteria identified in Urine by Culture

109

1.39

0.38

2.9

2.8

—

(3044889) 12 lead EKG panel

294

1.32

0.38

5.5

3.6

—

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

269

1.27

0.30

4.8

2.9

68.0

50.6

u/l

0.47

256

(40761511) CBC panel - Blood by Automated count

439

1.36

0.25

22.6

11.5

—

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

0.00

0.21

0.0

1.5

—

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

0.00

0.21

0.0

1.0

—

0.0

—

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

0.00

0.21

0.0

1.0

—

0.0

—

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

0.00

0.21

0.0

1.5

—

295.1

—

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

0.00

0.21

0.0

2.3

—

12.3

—

(3010156) C reactive protein [Mass/volume] in Serum or Plasma by High sensitivity method

0.00

0.21

0.0

1.5

—

2.2

—

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

0.00

0.20

0.0

1.0

—

0.0

—

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

172

0.82

0.19

3.0

2.8

13.6

24.5

—

(3009542) Hematocrit [Volume Fraction] of Blood

379

1.23

0.19

29.2

13.1

36.7

41.2

1.16

260

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

0.73

0.18

1.4

1.3

—

22.3

—

(3013512) EKG study

128

0.82

0.15

5.5

4.2

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.23

0.15

7.3

3.8

—

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

141

0.90

0.06

5.0

3.6

—

(3015736) pH of Urine

149

1.11

0.06

4.8

3.3

—

(3002385) Erythrocyte distribution width [Ratio]

341

0.91

0.06

33.0

15.2

14.2

13.6

1.54

331

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

381

1.09

0.04

22.1

11.7

80.3

77.9

ml/min/173m2

0.29

312

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

438

0.90

0.03

34.0

14.4

76.9

83.9

umol/l

1.00

438

(3027944) Amphetamines [Presence] in Urine

0.00

0.0

1.6

—

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

0.00

0.0

1.3

—

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

0.00

0.0

2.2

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.0

1.8

—

31.8

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.4

—

(3007368) IgG [Mass/volume] in Cerebral spinal fluid

0.00

0.0

1.2

—

54.5

—

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

0.00

0.0

1.5

—

(40768797) Stomach Pathology biopsy report

0.85

0.00

1.0

1.1

—

(3024474) Albumin [Mass/volume] in Cerebral spinal fluid

0.00

0.0

1.2

—

295.2

—

(3011166) Borrelia burgdorferi Ab [Presence] in Cerebral spinal fluid

0.00

0.0

1.2

—

(40759883) Oligoclonal Bands IgG [Presence] in Cerebral spinal fluid by Isoelectric focusing

0.00

0.0

1.0

—

(3049717) Cytology report of Urine Cyto stain

0.00

0.0

2.0

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.0

1.7

—

(3027008) Opiates [Presence] in Urine

0.00

0.0

1.7

—

(3017569) Oxygen content in Arterial blood

0.00

0.0

1.0

—

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

0.00

0.0

2.1

—

(3016879) Cocaine [Presence] in Urine

0.00

0.0

1.7

—

(21494815) CD4 cells/100 lymphocytes in Specimen

0.00

0.0

2.2

—

(3009595) Pneumocystis jiroveci DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.3

—

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

0.00

0.0

1.6

—

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

0.00

0.0

1.1

—

(4027681)

0.00

0.0

1.2

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.0

1.7

—

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

0.00

0.0

1.0

—

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

0.00

0.0

1.2

—

(3045424) Erythrocytes [Presence] in Urine

0.00

0.0

1.0

—

(3021901) Oxygen saturation in Capillary blood

0.00

0.0

2.0

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_INSITU_OROPHARYNX_EXALLC and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have CD2_INSITU_OROPHARYNX_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_OROPHARYNX_EXALLC – Carcinoma in situ of oropharynx, excluding all cancers

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

rg [CI]

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

≡ 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 oropharynx, excluding all cancers

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