Risteys · AB1_SPOTTED

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 — A77 Hospital discharge: ICD-9 — 0820A Hospital discharge: ICD-8 — 08[1] Cause of death: ICD-10 — A77 Cause of death: ICD-9 — 0820A Cause of death: ICD-8 — 08[1] 2 out of 7 registries used, show all original rules.	19
4. Check minimum number of events None	19
5. Include endpoints None	19
6. Filter based on genotype QC (FinnGen only)	19

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	175	77	98
Only index persons	147	63	84
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	-	42.10	37.42
Only index persons	35.31	35.77	34.96

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	19	8	11
Unadjusted period prevalence (%)	0.00	0.00	0.00
Median age at first event (years)	42.17	28.92	51.81

-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)

↥

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

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

4.54

2.35

2.1

4.4

—

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

4.80

1.84

1.4

1.5

—

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

2.93

1.48

2.8

2.9

—

(40768804) Tissue Pathology biopsy report

2.52

1.15

1.7

2.0

—

(3015736) pH of Urine

2.40

1.12

2.1

3.1

—

(40758558) Short blood count panel - Blood

2.47

1.05

8.1

8.6

—

(36304419) Bacteria [Presence] in Urine

2.18

0.83

3.0

2.4

—

(42870588) Differential panel, method unspecified - Blood

2.14

0.77

9.5

6.9

—

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

2.15

0.74

1.4

1.3

—

(3013603) Prostate specific Ag [Mass/volume] in Serum or Plasma

2.04

0.71

5.7

4.4

ug/l

2.3

1.6

—

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

0.00

0.64

0.0

1.2

—

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

1.97

0.64

1.5

1.7

—

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

102

1.86

0.62

2.4

3.8

—

(3021589) Normoblasts [#/volume] in Blood

1.77

0.51

14.3

8.0

e9/l

0.0

—

(3037467) Urinalysis macro (dipstick) panel - Urine

107

1.68

0.47

3.7

—

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

1.69

0.45

1.4

1.7

—

(3003031) Transferrin.carbohydrate deficient.disialo/Transferrin.total in Serum or Plasma

0.00

0.43

0.0

1.4

—

1.8

—

(3022096) Basophils/100 leukocytes in Blood

1.54

0.34

12.4

8.7

0.7

0.6

—

(3006504) Eosinophils/100 leukocytes in Blood

1.51

0.34

12.4

8.2

2.7

2.0

—

(3023368) Bacteria identified in Blood by Culture

1.30

0.24

3.4

4.4

—

(3000492) Spirometry study

0.00

0.22

0.0

1.5

—

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

0.00

0.22

0.0

1.5

—

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

0.00

0.22

0.0

5.6

—

8.7

—

(3002385) Erythrocyte distribution width [Ratio]

132

0.75

0.22

23.2

18.2

13.4

13.7

0.55

132

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

0.00

0.22

0.0

1.8

—

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

0.00

0.22

0.0

1.5

—

(3011960) Natriuretic peptide B [Mass/volume] in Serum or Plasma

0.00

0.22

0.0

1.9

—

134.6

—

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

1.29

0.21

1.9

3.3

—

(3012544) pH of Venous blood

0.00

0.21

0.0

3.9

—

(1761868) Lipid panel - Serum or Plasma

1.40

0.21

1.5

2.5

—

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

1.33

0.21

3.1

4.7

—

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

116

1.38

0.20

7.2

8.5

u/l

63.5

84.3

2.03

110

(3013707) Erythrocyte sedimentation rate by Westergren method

105

1.39

0.20

4.6

4.7

mm/h

5.3

10.5

2.86

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

1.15

0.11

1.6

—

(46235831) Pregnancy associated plasma protein A [Multiple of the median] adjusted in Serum or Plasma

0.00

0.0

1.6

—

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

0.00

0.0

2.9

—

50.5

—

(3020321) Streptococcus agalactiae [Presence] in Vaginal fluid by Organism specific culture

0.00

0.0

1.1

—

(40763531) Fetal Nuchal fold [Multiple of the median] Thickness adjusted for maternal weight

0.00

0.0

1.6

—

(3008714) Choriogonadotropin [Multiple of the median] adjusted in Serum or Plasma

0.00

0.0

1.6

—

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

0.00

0.0

2.7

—

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

0.00

0.0

1.1

—

(3049207) Fetal Trisomy 21 risk [Likelihood] Based on maternal age

0.00

0.0

1.6

—

(3019145) Choriogonadotropin.beta subunit free [Mass/volume] in Serum or Plasma

0.00

0.0

1.7

—

(3025941) Bacteria identified in Stool by Culture

0.00

0.0

1.1

—

(3019060) Gas panel - Arterial blood

0.00

0.0

5.6

—

(40768793) Breast Pathology biopsy report

0.00

0.0

1.0

—

(3005895) Myoglobin [Mass/volume] in Serum or Plasma

0.00

0.0

1.8

—

593.2

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.0

2.1

—

(3024889) Methemoglobin/Hemoglobin.total in Venous blood

0.00

0.0

2.3

—

0.8

—

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

0.00

0.0

2.7

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.0

1.3

—

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

0.00

0.0

2.2

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.0

1.3

—

(3008037) Lactate [Moles/volume] in Venous blood

0.00

0.0

2.6

—

1.1

—

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

0.00

0.0

1.4

—

(3044254) Respiratory syncytial virus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

3.2

—

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

0.00

0.0

2.1

—

126.9

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.0

1.3

—

(3008152) Bicarbonate [Moles/volume] in Arterial blood

0.00

0.0

9.4

—

22.5

—

(3013826) Glucose [Moles/volume] in Serum or Plasma

1.00

0.00

6.3

4.3

mmol/l

6.9

6.5

—

(3016879) Cocaine [Presence] in Urine

0.00

0.0

2.1

—

(3038515) Glucose [Moles/volume] in Venous blood

0.00

0.0

2.6

—

8.0

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

0.00

0.0

2.3

—

1.2

—

(3022621) pH of Urine by Test strip

0.00

0.0

1.4

—

(3009466) Valproate [Moles/volume] in Serum or Plasma

0.00

0.0

5.2

—

241.8

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.0

2.1

—

(3047007) Chlamydophila sp Ab [Presence] in Serum

0.00

0.0

1.2

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.0

2.1

—

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

0.00

0.0

1.2

—

(3012336) Haptoglobin [Mass/volume] in Serum or Plasma

0.00

0.0

5.3

—

1.6

—

(3027008) Opiates [Presence] in Urine

0.00

0.0

2.1

—

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

0.00

0.0

1.4

—

(3018010) Neutrophils/100 leukocytes in Blood

1.09

0.00

13.5

7.7

52.6

60.1

—

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

0.00

0.0

2.3

—

24.2

—

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

0.00

0.0

3.7

—

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

102

0.96

0.00

1.7

3.3

u/l

29.4

63.8

—

(3000330) Specific gravity of Urine by Test strip

0.00

0.0

3.3

—

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

0.00

0.0

3.5

—

(1175715) Chlamydophila pneumoniae IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.2

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.0

2.2

—

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

0.00

0.0

1.8

—

(3050129) First trimester maternal screen panel - Serum or Plasma

0.00

0.0

1.8

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.2

—

(3044889) 12 lead EKG panel

104

0.92

0.00

4.1

3.4

—

(3017044) Thyrotropin receptor Ab [Units/volume] in Serum

0.00

0.0

1.2

—

Mortality – FinRegistry

↥

Association

Association between endpoint AB1_SPOTTED_FEVER and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have AB1_SPOTTED_FEVER.

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_SPOTTED_FEVER – Spotted fever [tick-borne rickettsioses]

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_SPOTTED_FEVER
CONTROL_EXCLUDE	AB1_RICKETTSIOSES
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	A77
HD_ICD_9	0820A
HD_ICD_8	08[1]
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	A77
COD_ICD_9	0820A
COD_ICD_8	08[1]
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

Spotted fever [tick-borne rickettsioses]

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