Risteys · AB1_COCCIDIOIDOMYCOSIS

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: Hospital discharge: ICD-10 — B38 Hospital discharge: ICD-9 — 114 Hospital discharge: ICD-8 — 114 Cause of death: ICD-10 — B38 Cause of death: ICD-9 — 114 Cause of death: ICD-8 — 114 2 out of 7 registries used, show all original rules.	24
4. Check minimum number of events None	24
5. Include endpoints None	24
6. Filter based on genotype QC (FinnGen only)	24

Summary Statistics

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-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	203	89	108
Only index persons	137	63	74
Unadjusted period prevalence (%)
Whole population	0.00	0.00	0.00
Only index persons	0.00	0.00	0.00
Median age at first event (years)
Whole population	59.92	54.98	63.29
Only index persons	52.29	50.34	53.96

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	24	8	16
Unadjusted period prevalence (%)	0.01	0.00	0.01
Median age at first event (years)	55.28	34.89	65.47

-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)

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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

(3002582) Erythrocytes [#/volume] in Urine

2.52

1.24

3.0

3.4

e6/l

15.0

35.5

—

(36304419) Bacteria [Presence] in Urine

2.22

0.99

2.6

3.6

—

(3018095) Leukocytes [#/volume] in Urine

2.24

0.98

3.2

4.0

e6/l

3.4

48.4

—

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

2.10

0.95

2.8

3.5

e6/l

0.7

0.2

—

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

1.76

0.64

4.3

3.7

—

(3002032) Base excess in Venous blood by calculation

0.00

0.63

0.0

3.5

—

2.4

—

(3017732) Neutrophils [#/volume] in Blood

0.00

0.63

0.0

2.0

—

3.4

—

(4010399)

0.00

0.63

0.0

1.6

—

(3012544) pH of Venous blood

0.00

0.63

0.0

3.5

—

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

0.00

0.63

0.0

4.6

—

32.1

—

(3041096) Erythrocytes [Presence] in Urine by Automated

1.64

0.53

2.3

2.5

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.77

0.46

4.8

10.5

—

(3000991) Gas panel - Venous blood

0.00

0.43

0.0

12.9

—

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

0.00

0.43

0.0

1.9

—

12.7

—

(3022145) Colonoscopy Study observation

0.00

0.41

0.0

1.3

—

(3023368) Bacteria identified in Blood by Culture

1.52

0.39

3.0

4.9

—

(1761868) Lipid panel - Serum or Plasma

1.48

0.38

2.8

3.3

—

(3021589) Normoblasts [#/volume] in Blood

0.64

0.32

11.8

8.5

e9/l

0.0

—

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

1.37

0.31

3.3

3.2

—

(36660697) Celiac disease serology panel - Serum

0.00

0.22

0.0

1.4

—

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

0.00

0.22

0.0

2.5

—

125.1

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

0.00

0.22

0.0

1.2

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

0.00

0.22

0.0

2.7

—

1.0

—

(3022621) pH of Urine by Test strip

0.00

0.22

0.0

2.2

—

(3024889) Methemoglobin/Hemoglobin.total in Venous blood

0.00

0.22

0.0

2.7

—

0.7

—

(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

0.00

0.22

0.0

1.5

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.00

0.22

0.0

1.6

—

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

0.00

0.21

0.0

1.9

—

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

0.00

0.21

0.0

2.3

—

24.3

—

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

0.00

0.20

0.0

7.6

—

12.1

—

(40761511) CBC panel - Blood by Automated count

172

1.50

0.20

12.0

12.4

—

(3013115) Eosinophils [#/volume] in Blood

1.20

0.18

3.6

8.6

e9/l

0.2

—

(3013512) EKG study

1.08

0.10

4.0

3.7

—

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

0.86

0.08

1.2

3.1

u/l

38.1

40.4

—

(3044889) 12 lead EKG panel

110

1.18

0.07

4.4

4.3

—

(3037467) Urinalysis macro (dipstick) panel - Urine

119

0.86

0.05

2.9

4.0

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.0

1.2

—

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

0.00

0.0

1.5

—

(3027008) Opiates [Presence] in Urine

0.00

0.0

1.2

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.0

1.3

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.0

1.2

—

(42870588) Differential panel, method unspecified - Blood

0.87

0.00

2.4

6.2

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.5

—

(3016407) Fibrinogen [Mass/volume] in Platelet poor plasma by Coagulation assay

0.00

0.0

1.2

—

4.3

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.3

—

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

0.00

0.0

1.2

—

(3016879) Cocaine [Presence] in Urine

0.00

0.0

1.2

—

(3020961) Endomysium IgA Ab [Titer] in Serum

0.00

0.0

1.0

—

(21494434) Karyotype in Bone marrow

0.00

0.0

1.0

—

(3024403) Complement+Immunoglobulin [Units/volume] in Red Blood Cells

0.00

0.0

3.0

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.0

1.0

—

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

1.00

0.00

2.9

3.8

—

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

0.00

0.0

2.1

—

38.4

—

(3015736) pH of Urine

0.89

0.00

3.0

—

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

0.00

0.0

1.6

—

(3023024) Carbon dioxide [Partial pressure] in Capillary blood

0.00

0.0

3.4

—

5.3

—

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

0.00

0.0

1.8

—

8.9

—

(3021584) Pregnancy associated plasma protein A [Units/volume] in Serum or Plasma

0.00

0.0

1.2

—

(36032269) Testosterone Free [Moles/volume] in Serum or Plasma by calculation

0.00

0.0

1.6

—

216.0

—

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

0.00

0.0

1.2

—

(3013201) Beta-2-Microglobulin [Mass/volume] in Serum or Plasma

0.00

0.0

2.4

—

3.7

—

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

0.00

0.0

7.8

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.0

—

(3000330) Specific gravity of Urine by Test strip

0.00

0.0

2.1

—

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

0.00

0.0

1.2

—

(3037551) Cancer Ag 125 [Units/volume] in Serum or Plasma

0.00

0.0

1.7

—

121.8

—

(3001604) Monocytes [#/volume] in Blood

1.06

0.00

3.5

8.0

e9/l

0.7

0.6

—

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

0.00

0.0

1.1

—

(40768804) Tissue Pathology biopsy report

0.92

0.00

2.1

2.0

—

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

0.00

0.0

2.6

—

(3042111) Morphology [Interpretation] in Bone marrow Narrative

0.00

0.0

2.4

—

(3026008) Bacteria identified in Urine by Culture

1.03

0.00

1.8

2.8

—

(21494890) Protein electrophoresis panel - 24 hour Urine

0.00

0.0

6.0

—

(46235759) Influenza virus B RNA [Presence] in Nasopharynx by NAA with probe detection

0.00

0.0

1.3

—

(3045414) Leukocytes [Presence] in Urine

0.00

0.0

1.8

—

(40758310) Human epididymis protein 4 [Moles/volume] in Serum or Plasma

0.00

0.0

2.2

—

93.4

—

(3022313) Gas panel - Capillary blood

0.00

0.0

4.4

—

(3004490) Bicarbonate [Moles/volume] standard in Capillary blood

0.00

0.0

4.4

—

24.9

—

(43534045) MCM6 gene c.-13910C>T and -13915T>G [Identifier] in Blood or Tissue by Molecular genetics method Nominal

0.00

0.0

1.0

—

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

0.00

0.0

9.3

—

(21492888) Glucose tolerance 2 hours gestational panel - Serum or Plasma

0.00

0.0

1.6

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

0.0

1.0

—

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

172

0.96

0.00

13.6

18.6

umol/l

76.0

84.0

1.01

172

(3052851) Hemolysis interference index of Serum or Plasma

0.00

0.0

2.1

—

Mortality – FinRegistry

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Association

Association between endpoint AB1_COCCIDIOIDOMYCOSIS and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have AB1_COCCIDIOIDOMYCOSIS.

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: AB1_COCCIDIOIDOMYCOSIS – Coccidioidomycosis

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

NAME	AB1_COCCIDIOIDOMYCOSIS
CONTROL_EXCLUDE	AB1_MYCOSES
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	B38
HD_ICD_9	114
HD_ICD_8	114
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	B38
COD_ICD_9	114
COD_ICD_8	114
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
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

Coccidioidomycosis

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)

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