Malignant neoplasm of other and ill-defined sites in the lip, oral cavity and pharynx

C3_LIP_ORAL_PHARYNX_NAS

hypopharynx cancer: A primary or metastatic malignant neoplasm that affects the hypopharynx.

Endpoint definition

↥

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions None	520210
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Cause of death: ICD-10 — C14 Cause of death: ICD-9 — 149 Cause of death: ICD-8 — 149 Cancer registry: Topography ICD-O-3 — C14 Cancer registry: Morphology ICD-O-3 — ANY Cancer registry: Behaviour codes — 3 2 out of 7 registries used, show all original rules.	33
4. Check minimum number of events None	33
5. Include endpoints None	33
6. Filter based on genotype QC (FinnGen only)	33

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

NAME	C3_LIP_ORAL_PHARYNX_NAS
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10
HD_ICD_9
HD_ICD_8
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	C14
COD_ICD_9	149
COD_ICD_8	149
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	C14
CANC_TOPO_EXCL
CANC_MORPH	ANY
CANC_MORPH_EXCL
CANC_BEHAV	3

Similar endpoints

↥

List of similar endpoints to Malignant neoplasm of other and ill-defined sites in the lip, oral cavity and pharynx based on the number of shared cases.

Similar with more cases:

Similar with less cases:

None

Case counts by codes

↥

FinnGen case counts by registry codes:

Not enough data for 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	33	5	28
Unadjusted period prevalence (%)	0.01	0.00	0.01
Median age at first event (years)	68.71	71.45	68.22

-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

(4035726)

12.26

11.16

1.5

1.2

—

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

118

3.59

3.00

5.0

4.1

—

(3013650) Neutrophils [#/volume] in Blood by Automated count

145

3.39

2.76

16.2

12.3

4.4

4.6

e9/l

0.20

126

(40768804) Tissue Pathology biopsy report

2.88

2.24

2.7

2.0

—

(3044640) Blood type and Crossmatch panel - Blood

2.71

2.00

2.7

2.3

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.50

1.16

1.3

1.8

—

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

2.39

0.97

8.3

13.1

—

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

2.04

0.97

1.3

—

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

0.00

0.83

0.0

1.5

—

(42870588) Differential panel, method unspecified - Blood

1.84

0.82

7.5

6.8

—

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

1.89

0.81

2.5

2.1

—

(3000494) Fungus identified in Specimen by Culture

2.17

0.76

1.0

1.3

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.88

0.70

6.1

7.7

—

(3042936) Bacteria identified in Isolate by Culture

1.79

0.68

1.0

1.7

—

(3012544) pH of Venous blood

1.85

0.66

1.4

2.4

—

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

1.66

0.56

1.2

1.8

—

(3019198) Lymphocytes [#/volume] in Blood

124

1.56

0.53

6.3

7.3

1.7

1.8

e9/l

0.09

107

(3023368) Bacteria identified in Blood by Culture

1.59

0.49

4.5

5.4

—

(3035995) Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma

196

1.57

0.48

15.0

8.7

66.5

77.9

u/l

2.51

187

(3037467) Urinalysis macro (dipstick) panel - Urine

173

0.67

0.44

4.6

3.4

—

(3002256) Pathology report gross observation

1.55

0.42

1.2

—

(36660697) Celiac disease serology panel - Serum

0.00

0.42

0.0

1.3

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.42

0.0

1.5

—

(3009508) Creatinine [Moles/volume] in Urine

0.61

0.42

2.8

3.1

5.8

7.4

mmol/l

—

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

1.56

0.39

1.2

2.0

—

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

104

0.70

0.36

4.3

3.4

—

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

1.44

0.34

1.6

2.0

—

(3041096) Erythrocytes [Presence] in Urine by Automated

0.66

0.30

3.6

2.3

—

(3013512) EKG study

1.34

0.22

2.6

3.7

—

(3043723) Beta 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.22

0.0

1.0

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

0.00

0.22

0.0

2.8

—

(1761482) Bacteria [#/volume] in Urine by Culture

0.00

0.21

0.0

3.2

—

(3004248) Sex hormone binding globulin [Moles/volume] in Serum or Plasma

0.00

0.21

0.0

1.8

—

38.8

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

0.00

0.20

0.0

1.1

—

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

1.26

0.20

1.7

1.8

24.1

21.5

nmol/l

—

(3033658) Prothrombin time (PT) actual/Normal

0.73

0.19

4.8

4.3

69.6

86.4

—

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

102

1.28

0.18

2.6

3.0

—

(40758558) Short blood count panel - Blood

1.19

0.18

10.8

7.9

—

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

118

0.78

0.18

1.8

3.0

—

(36304419) Bacteria [Presence] in Urine

1.19

0.17

2.6

2.8

—

(3008486) Thyroxine (T4) free [Moles/volume] in Serum or Plasma

166

1.19

0.11

5.7

3.6

14.2

15.3

pmol/l

1.00

151

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

267

0.88

0.09

32.6

19.4

76.4

82.5

umol/l

0.81

267

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

0.80

0.08

2.1

2.2

90.9

72.5

nmol/l

—

(3044889) 12 lead EKG panel

190

1.13

0.06

5.1

4.1

—

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

139

0.89

0.04

3.8

3.9

20.6

20.9

—

(3003338) MCHC [Mass/volume]

206

0.93

0.01

29.6

22.2

333.6

333.5

g/l

0.03

206

(3009542) Hematocrit [Volume Fraction] of Blood

208

1.03

0.00

22.4

19.0

40.3

39.9

0.11

149

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

0.96

0.00

3.0

4.0

—

(3035285) Chloride [Moles/volume] in Venous blood

0.00

0.0

1.8

—

106.6

—

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

0.00

0.0

1.2

—

(3025245) SCL-70 extractable nuclear Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.2

—

(36304997) Mycobacterium tuberculosis stimulated gamma interferon release by CD4+ and CD8+ T-cells [Units/volume] in Blood

0.00

0.0

1.0

—

(4094501)

0.00

0.0

1.0

—

(3004383) Neutrophil cytoplasmic Ab.classic [Titer] in Serum by Immunofluorescence

0.00

0.0

1.3

—

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

0.00

0.0

1.0

—

0.0

—

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

0.00

0.0

1.5

—

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

0.00

0.0

1.0

—

0.0

—

(3006999) Ribonucleoprotein extractable nuclear Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(3023183) Ammonium ion [Moles/volume] in Plasma

0.00

0.0

1.3

—

28.8

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.00

0.0

1.9

—

(3024928) Oxygen saturation in Venous blood

0.00

0.0

1.3

—

(3041354) Potassium [Moles/volume] in Venous blood

0.00

0.0

1.8

—

4.3

—

(3027450) Sjogrens syndrome-B extractable nuclear Ab [Units/volume] in Serum

0.00

0.0

1.2

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.0

—

0.0

—

(3033705) Calcium.ionized [Moles/volume] in Venous blood

0.00

0.0

1.8

—

(3051611) Lipemic interference index of Serum or Plasma

0.00

0.0

4.4

—

(44790048)

0.00

0.0

1.6

—

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

0.00

0.0

1.2

—

0.2

—

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

0.00

0.0

1.0

—

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

0.00

0.0

1.0

—

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

0.00

0.0

1.0

—

(3023150) Myeloperoxidase Ab [Units/volume] in Serum

0.00

0.0

2.6

—

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

0.00

0.0

1.6

—

(3023419) Bacteria identified in Sputum by Culture

0.00

0.0

5.8

—

(3026008) Bacteria identified in Urine by Culture

1.04

0.00

2.6

2.8

—

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

0.00

0.0

1.2

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.1

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.0

1.2

—

(44790049)

0.00

0.0

1.6

—

(1761868) Lipid panel - Serum or Plasma

0.89

0.00

2.4

3.0

—

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

0.00

0.0

1.1

—

(44806118)

0.00

0.0

1.6

—

(3049804) Myeloperoxidase IgG Ab [Units/volume] in Serum

0.00

0.0

1.0

—

(44790047)

0.00

0.0

1.6

—

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

0.00

0.0

1.8

—

(40761511) CBC panel - Blood by Automated count

258

1.04

0.00

25.4

14.5

—

(37019628) Gastrointestinal bacterial pathogens panel - Stool by NAA with probe detection

0.00

0.0

1.2

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.8

—

510.4

—

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

0.00

0.0

1.3

—

5.9

—

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

0.00

0.0

1.0

—

(3006257) Acetylcholine receptor Ab [Moles/volume] in Serum

0.00

0.0

1.0

—

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

0.00

0.0

1.2

—

1.2

—

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

0.00

0.0

3.7

—

Mortality – FinRegistry

↥

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

Relationships between endpoints

↥

Index endpoint: C3_LIP_ORAL_PHARYNX_NAS – Malignant neoplasm of other and ill-defined sites in the lip, 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

Malignant neoplasm of other and ill-defined sites in the lip, 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

Case counts by code for Malignant neoplasm of other and ill-defined sites in the lip, oral cavity and pharynx (C3_LIP_ORAL_PHARYNX_NAS)

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