Yaws

AB1_YAWNS

No definition available.

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: Hospital discharge: ICD-10 — A66 Cause of death: ICD-10 — A66 2 out of 7 registries used, show all original rules.	46
4. Check minimum number of events None	46
5. Include endpoints None	46
6. Filter based on genotype QC (FinnGen only)	46

Control definitions (FinnGen only)

Control exclude: AB1_OTHER_SPIROCHAETAL

Extra metadata

Level in the ICD hierarchy: 3
First used in FinnGen datafreeze: DF5

NAME	AB1_YAWNS
CONTROL_EXCLUDE	AB1_OTHER_SPIROCHAETAL
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	A66
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	A66
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
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

Similar endpoints

↥

List of similar endpoints to Yaws 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:

Upset plot

Full data table

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	432	212	219
Only index persons	412	200	212
Unadjusted period prevalence (%)
Whole population	0.01	0.01	0.01
Only index persons	0.01	0.01	0.01
Median age at first event (years)
Whole population	33.17	36.75	29.72
Only index persons	33.39	36.30	30.65

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	46	23	23
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	52.53	45.06	60.00

-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

cases

controls

unit

-log₁₀(p)

N cases

N controls

(40768804) Tissue Pathology biopsy report

137

4.02

5.00

2.3

1.9

—

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

3.36

3.40

2.9

2.4

—

(3037467) Urinalysis macro (dipstick) panel - Urine

234

3.48

3.16

3.7

3.8

—

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

7.83

2.61

1.0

1.1

—

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

6.84

2.43

1.2

2.0

—

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

124

2.28

1.91

3.7

2.4

65.6

73.7

nmol/l

0.71

111

(4035726)

3.12

1.89

1.5

1.3

—

(3000494) Fungus identified in Specimen by Culture

2.72

1.63

1.3

1.4

—

(3042936) Bacteria identified in Isolate by Culture

2.42

1.44

2.0

1.9

—

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

262

2.14

1.41

3.3

3.1

—

(3026008) Bacteria identified in Urine by Culture

2.07

1.36

4.0

2.4

—

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

2.15

1.15

17.4

3.4

14.4

10.2

umol/l

—

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

2.15

1.15

1.9

1.8

—

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

1.99

1.04

2.6

1.6

—

(3013707) Erythrocyte sedimentation rate by Westergren method

256

1.82

1.01

4.9

3.8

13.0

10.8

mm/h

0.60

236

(3007853) Bacteria identified in Skin by Aerobe culture

2.07

0.88

1.8

1.2

—

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

185

1.62

0.80

13.6

6.2

15.0

10.6

umol/l

0.41

173

(3026493) Urate [Moles/volume] in Serum or Plasma

1.71

0.76

4.5

2.4

358.9

344.2

umol/l

0.19

(3023368) Bacteria identified in Blood by Culture

1.71

0.76

5.3

4.3

—

(40763571) Iron/Transferrin [Ratio] in Serum or Plasma

1.83

0.74

1.7

2.2

30.3

27.0

—

(3019225) pH of Specimen

1.88

0.68

1.4

4.0

—

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

144

1.54

0.65

6.8

4.1

—

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

1.75

0.63

1.2

1.6

—

(1761868) Lipid panel - Serum or Plasma

144

0.61

0.62

3.7

2.9

—

(3046870) Tissue transglutaminase IgG Ab [Units/volume] in Serum

0.00

0.61

0.0

1.0

—

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

1.69

0.61

2.9

3.5

—

(3020059) Calcium [Moles/volume] corrected for albumin in Serum or Plasma

1.58

0.61

1.8

2.5

mmol/l

—

(40758558) Short blood count panel - Blood

1.58

0.59

12.5

7.7

—

(3044640) Blood type and Crossmatch panel - Blood

1.58

0.59

3.5

2.7

—

(3009035) Cobalamin (Vitamin B12) [Moles/volume] in Serum or Plasma

1.66

0.58

2.2

1.6

382.2

451.2

pmol/l

—

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

1.66

0.57

1.5

2.5

11.9

14.6

nmol/l

—

(3002256) Pathology report gross observation

1.57

0.54

1.7

1.2

—

(3048689) Calprotectin [Mass/mass] in Stool

1.65

0.52

2.6

1.8

183.9

125.5

ug/g

—

(3019309) Folate [Moles/volume] in Red Blood Cells

1.58

0.50

1.6

1.7

1863.7

1215.8

nmol/l

—

(40768797) Stomach Pathology biopsy report

1.50

0.48

1.3

1.4

—

(3019902) Methicillin resistant Staphylococcus aureus [Presence] in Specimen by Organism specific culture

1.69

0.44

2.4

3.7

—

(3016879) Cocaine [Presence] in Urine

0.00

0.42

0.0

1.6

—

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

0.00

0.42

0.0

1.1

—

(3044889) 12 lead EKG panel

244

1.38

0.41

3.4

3.7

—

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

0.00

0.41

0.0

2.4

—

19.4

—

(3022250) Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma by Lactate to pyruvate reaction

1.44

0.39

17.0

4.9

273.2

237.9

u/l

—

(3021347) Calcium.ionized [Moles/volume] in Serum or Plasma

138

1.37

0.38

11.4

5.6

1.2

mmol/l

0.42

127

(3019550) Sodium [Moles/volume] in Serum or Plasma

374

1.53

0.37

23.1

13.2

139.2

139.7

mmol/l

0.80

363

(3023103) Potassium [Moles/volume] in Serum or Plasma

375

1.51

0.37

23.6

13.2

4.0

mmol/l

0.21

364

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

1.39

0.34

1.7

1.6

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

1.41

0.33

1.3

1.7

—

(3035350) Ketones [Presence] in Urine by Test strip

162

1.29

0.29

2.6

3.4

—

0.0

—

(3019150) Specific gravity of Urine by Refractometry

1.33

0.28

2.1

3.7

—

1.0

—

(3009261) Glucose [Presence] in Urine by Test strip

164

1.27

0.26

2.7

3.5

—

0.0

—

(3021601) Nitrite [Presence] in Urine by Test strip

164

1.27

0.26

3.7

4.3

—

0.0

—

(3015736) pH of Urine

118

1.27

0.22

2.5

3.0

—

(3001122) Ferritin [Mass/volume] in Serum or Plasma

147

1.25

0.22

4.4

2.4

228.8

99.6

ug/l

0.70

135

(3018677) aPTT in Platelet poor plasma by Coagulation assay

1.21

0.22

6.8

2.7

33.3

30.2

—

(3046524) Influenza virus A Ag [Presence] in Nasopharynx by Immunoassay

0.00

0.21

0.0

1.0

—

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

0.00

0.21

0.0

2.0

—

(3043362) Influenza virus B Ag [Presence] in Nasopharynx by Immunoassay

0.00

0.21

0.0

1.0

—

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

0.00

0.21

0.0

2.3

—

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

0.00

0.21

0.0

1.7

—

48.2

—

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

0.00

0.21

0.0

1.0

—

(3003327) Ova and parasites identified in Stool by Light microscopy

0.00

0.21

0.0

1.4

—

(3014218) Bicarbonate [Moles/volume] standard in Arterial blood

0.00

0.21

0.0

8.8

—

24.2

—

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

0.00

0.21

0.0

1.5

—

(3018006) Microscopic observation [Identifier] in Cervix by Cyto stain.thin prep

1.29

0.21

1.7

1.5

—

(3015171) Extractable nuclear Ab [Units/volume] in Serum

0.00

0.21

0.0

1.0

—

(3002385) Erythrocyte distribution width [Ratio]

312

0.81

0.21

24.5

16.4

13.8

13.6

0.35

307

(3050380) Cytology report of Cervical or vaginal smear or scraping Cyto stain

0.00

0.20

0.0

1.4

—

(3004410) Hemoglobin A1c/Hemoglobin.total in Blood

340

1.27

0.19

6.2

5.1

40.2

39.7

mmol/mol

0.12

318

(42870588) Differential panel, method unspecified - Blood

120

1.24

0.19

9.2

4.8

—

(40761511) CBC panel - Blood by Automated count

389

0.87

0.17

13.2

12.1

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.14

0.16

2.9

4.0

—

(36304419) Bacteria [Presence] in Urine

0.78

0.15

4.5

2.4

—

(3041096) Erythrocytes [Presence] in Urine by Automated

105

0.82

0.15

2.2

2.8

—

(3009508) Creatinine [Moles/volume] in Urine

104

1.21

0.14

3.4

8.1

7.9

mmol/l

0.05

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

1.18

0.10

1.8

2.3

—

(3022145) Colonoscopy Study observation

1.10

0.10

1.2

—

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

1.07

0.10

1.6

—

(21494755) Public health laboratory ask at order entry panel

1.05

0.09

1.2

1.4

—

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

133

0.87

0.09

5.1

4.7

1.4

2.2

ug/l

0.80

123

(3009542) Hematocrit [Volume Fraction] of Blood

348

1.16

0.08

19.8

12.9

38.9

40.8

0.56

274

(3018251) Fasting glucose [Moles/volume] in Serum or Plasma

348

1.16

0.08

6.1

4.1

6.3

5.8

mmol/l

1.21

320

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

122

0.87

0.08

4.4

2.8

—

(3029937) Albumin [Presence] in Urine by Test strip

0.83

0.07

2.4

3.8

—

0.0

—

(3013512) EKG study

1.11

0.03

3.2

3.8

—

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

129

1.01

0.00

2.6

3.5

—

(3048773) Triglyceride [Moles/volume] in Serum or Plasma --fasting

345

1.06

0.00

4.7

3.8

1.6

1.3

mmol/l

1.08

318

(3028707) Methadone [Presence] in Urine by Screen method

0.00

0.0

2.3

—

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

0.00

0.0

1.6

—

10.0

—

(40768800) Prostate Pathology biopsy report

0.00

0.0

1.1

—

(4094501)

0.00

0.0

1.0

—

(40768793) Breast Pathology biopsy report

0.00

0.0

1.1

—

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

1.00

0.00

1.8

1.5

—

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

1.00

0.00

1.6

1.8

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

0.0

3.9

—

8.2

—

(3035637) Corticotropin [Mass/volume] in Plasma

0.00

0.0

1.6

—

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

0.00

0.0

2.0

—

(3000855) Microscopic observation [Identifier] in Vaginal fluid by Gram stain

0.00

0.0

2.6

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.9

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

0.0

3.9

—

4.8

—

(3008757) Leukocyte morphology finding [Identifier] in Blood

0.00

0.0

2.2

—

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

0.00

0.0

1.4

—

(3042631) Mycobacterium sp identified in Specimen

0.00

0.0

5.3

—

(3005988) Vibrio sp identified in Specimen by Organism specific culture

0.00

0.0

1.4

—

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

0.00

0.0

1.0

—

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

0.00

0.0

1.2

—

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

0.89

0.00

2.0

1.7

—

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

0.00

0.0

1.8

—

(3000081) cloZAPine [Moles/volume] in Serum or Plasma

0.00

0.0

13.7

—

1594.3

—

(3008832) Norclozapine [Moles/volume] in Serum or Plasma

0.00

0.0

12.2

—

928.7

—

(21493466) Plesiomonas shigelloides DNA [Presence] in Stool by NAA with non-probe detection

0.00

0.0

1.4

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.0

1.1

—

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

0.00

0.0

1.3

—

(3006588) Cancer Ag 15-3 [Units/volume] in Serum or Plasma

0.00

0.0

4.6

—

21.6

—

(44816844) Macroprolactin [Units/volume] in Serum or Plasma

0.00

0.0

1.2

—

(1616796) Gas panel - Central venous blood

0.00

0.0

4.5

—

(3019539) Treponema pallidum Ab [Titer] in Serum by Hemagglutination

0.00

0.0

1.7

—

(3045424) Erythrocytes [Presence] in Urine

0.00

0.0

1.1

—

(40762485) Glomerular basement membrane Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.0

—

(3014791) Apolipoprotein B [Mass/volume] in Serum or Plasma

0.00

0.0

1.4

—

0.9

—

(3000093) Morphology [Interpretation] in Blood Narrative

0.00

0.0

1.0

—

Mortality – FinRegistry

↥

Association

Association between endpoint AB1_YAWNS and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have AB1_YAWNS.

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_YAWNS – Yaws

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

Yaws

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