Risteys · AB1_LEISHMANIASIS

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 — B55 Hospital discharge: ICD-9 — 08[5] Hospital discharge: ICD-8 — 08[5] Cause of death: ICD-10 — B55 Cause of death: ICD-9 — 08[5] Cause of death: ICD-8 — 08[5] 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	214	93	111
Only index persons	182	89	93
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	43.74	44.10	44.49
Only index persons	43.01	44.05	42.01

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	24	11	13
Unadjusted period prevalence (%)	0.00	0.00	0.01
Median age at first event (years)	41.45	41.57	41.34

-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

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(ID) Name

N Cases

N Controls

-log₁₀(p)

cases

controls

unit

cases

controls

-log₁₀(p)

N cases

N controls

(3022096) Basophils/100 leukocytes in Blood

3.50

2.14

9.9

4.9

0.8

0.7

0.14

(3006504) Eosinophils/100 leukocytes in Blood

3.38

2.12

9.8

4.8

3.2

3.0

0.09

(3019069) Monocytes/100 leukocytes in Blood

3.38

2.12

9.9

5.5

8.8

8.7

0.03

(3018010) Neutrophils/100 leukocytes in Blood

3.38

2.12

9.6

4.7

55.3

57.4

0.29

(3002030) Lymphocytes/100 leukocytes in Blood

3.26

2.08

9.8

4.9

30.1

27.0

0.53

(3013115) Eosinophils [#/volume] in Blood

3.20

2.05

10.3

5.8

e9/l

0.2

0.19

(3042936) Bacteria identified in Isolate by Culture

3.52

1.81

1.9

3.9

—

(3001604) Monocytes [#/volume] in Blood

2.87

1.79

10.5

4.8

e9/l

0.6

0.03

(3001308) Cholesterol in LDL [Moles/volume] in Serum or Plasma

202

0.32

1.69

4.1

4.8

mmol/l

3.0

2.8

0.26

195

(3019900) Cholesterol [Moles/volume] in Serum or Plasma

201

0.33

1.66

3.9

4.7

mmol/l

4.8

4.7

0.31

194

(3023602) Cholesterol in HDL [Moles/volume] in Serum or Plasma

199

0.35

1.59

3.9

4.6

mmol/l

1.4

0.14

192

(3006315) Basophils [#/volume] in Blood

2.82

1.58

10.7

4.8

e9/l

0.0

0.40

(3000494) Fungus identified in Specimen by Culture

3.28

1.54

1.7

2.4

—

(3037467) Urinalysis macro (dipstick) panel - Urine

132

3.10

1.53

3.8

4.3

—

(3037522) Nuclear Ab [Titer] in Serum

2.98

1.53

1.1

1.5

—

576.0

—

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

102

2.25

1.08

13.7

8.3

e9/l

4.6

3.9

0.28

(40760892) CBC W Ordered Manual Differential panel - Blood

2.42

1.03

4.0

3.9

—

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

101

0.46

0.89

2.5

5.9

—

(3002256) Pathology report gross observation

0.00

0.84

0.0

1.2

—

(3027238) Thyroperoxidase Ab [Units/volume] in Serum or Plasma

0.00

0.61

0.0

1.2

—

166.0

—

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

1.84

0.47

1.8

3.1

umol/l

5.4

17.0

—

(40761511) CBC panel - Blood by Automated count

208

0.59

0.45

13.1

13.9

—

(4035726)

0.00

0.43

0.0

1.4

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

0.00

0.42

0.0

1.1

—

(3013707) Erythrocyte sedimentation rate by Westergren method

142

1.67

0.42

4.1

mm/h

9.1

12.5

0.44

128

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

0.00

0.41

0.0

6.8

—

(3015736) pH of Urine

1.57

0.38

3.1

3.5

—

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

140

0.71

0.25

2.9

3.5

—

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

1.33

0.22

1.3

1.4

—

(3008898) HLA-B27 [Presence]

0.00

0.22

0.0

1.1

—

(40761535) Cells panel - Urine sediment

0.00

0.22

0.0

2.1

—

(3028026) IgM [Mass/volume] in Serum or Plasma

0.00

0.22

0.0

1.6

—

1.2

—

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

0.00

0.22

0.0

2.6

—

(3041096) Erythrocytes [Presence] in Urine by Automated

1.29

0.21

5.7

3.5

—

(40768804) Tissue Pathology biopsy report

0.72

0.20

1.4

1.9

—

(42870588) Differential panel, method unspecified - Blood

1.29

0.20

8.4

4.8

—

(3003338) MCHC [Mass/volume]

172

0.79

0.19

25.7

18.5

g/l

332.3

0.00

172

(1761868) Lipid panel - Serum or Plasma

0.75

0.18

2.6

3.0

—

(3009508) Creatinine [Moles/volume] in Urine

1.18

0.10

2.5

2.9

mmol/l

8.6

8.5

—

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

1.12

0.10

1.7

3.1

—

21.9

—

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

0.76

0.09

6.8

2.9

—

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

0.81

0.09

5.7

3.5

—

(3021589) Normoblasts [#/volume] in Blood

1.13

0.08

22.8

8.6

e9/l

0.0

—

(3044889) 12 lead EKG panel

146

0.90

0.01

4.5

3.5

—

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

0.00

0.0

2.5

—

(3014051) Protein [Presence] in Urine by Test strip

0.00

0.0

1.3

—

(3026179) Normetanephrine [Moles/volume] in Serum or Plasma

0.00

0.0

2.2

—

0.5

—

(3032155) Metanephrine Free [Moles/volume] in Serum or Plasma

0.00

0.0

2.2

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.3

—

(4034850)

0.00

0.0

12.5

—

(3034770) Mitochondria Ab [Titer] in Serum

0.00

0.0

1.7

—

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

0.00

0.0

1.8

—

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

0.00

0.0

1.5

—

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

0.00

0.0

1.3

—

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

0.90

0.00

1.7

1.6

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.0

1.7

—

(40768793) Breast Pathology biopsy report

0.00

0.0

1.3

—

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

0.00

0.0

1.6

—

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

0.00

0.0

1.0

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.0

1.6

—

(3023368) Bacteria identified in Blood by Culture

0.98

0.00

14.0

6.7

—

(3028286) Albumin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

1.2

—

37.3

—

(3023465) Gamma globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

1.2

—

12.0

—

(3026008) Bacteria identified in Urine by Culture

1.03

0.00

1.6

2.4

—

(3030981) Hyaline casts [#/volume] in Urine by Automated count

0.00

0.0

2.2

—

0.2

—

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

0.00

0.0

1.6

—

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

0.00

0.0

1.3

—

(3024928) Oxygen saturation in Venous blood

0.00

0.0

7.6

—

(3045414) Leukocytes [Presence] in Urine

0.00

0.0

1.3

—

(3029713) Protein.monoclonal band 1 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

1.2

—

0.0

—

(3024891) Influenza virus A+B Ag [Presence] in Specimen

0.00

0.0

1.0

—

(3013512) EKG study

0.95

0.00

2.0

3.7

—

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

0.00

0.0

1.6

—

(3020891) Body temperature

0.00

0.0

2.6

—

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

0.00

0.0

2.0

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.0

1.6

—

(1002224) Polysomnography panel

0.00

0.0

1.0

—

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

0.00

0.0

1.6

—

(3048821) Cortisol [Moles/volume] in Serum or Plasma --post 1 mg dexamethasone PO overnight

0.00

0.0

1.4

—

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

0.00

0.0

1.6

—

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

0.00

0.0

1.2

—

0.0

—

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

0.00

0.0

1.6

—

(3049717) Cytology report of Urine Cyto stain

0.00

0.0

1.6

—

Mortality – FinRegistry

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Association

Association between endpoint AB1_LEISHMANIASIS and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have AB1_LEISHMANIASIS.

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_LEISHMANIASIS – Leishmaniasis

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

Extremity

rg [CI]

Extremity

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

NAME	AB1_LEISHMANIASIS
CONTROL_EXCLUDE	AB1_PROTOZOAL
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	B55
HD_ICD_9	08[5]
HD_ICD_8	08[5]
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	B55
COD_ICD_9	08[5]
COD_ICD_8	08[5]
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

Leishmaniasis

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