Risteys · Q17_REDUCT_DEFECTS_UNSPE

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 — Q73 Cause of death: ICD-10 — Q73 2 out of 7 registries used, show all original rules.	23
4. Check minimum number of events None	23
5. Include endpoints None	23
6. Filter based on genotype QC (FinnGen only)	23

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	209	98	111
Only index persons	181	88	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	-	16.91	10.80
Only index persons	15.65	18.37	13.08

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	23	10	13
Unadjusted period prevalence (%)	0.00	0.00	0.01
Median age at first event (years)	52.53	50.00	54.48

-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

4.49

2.97

2.0

3.7

—

(40768804) Tissue Pathology biopsy report

3.45

2.12

1.6

1.8

—

(43054903) Holo-transcobalamin II [Moles/volume] in Serum

3.10

1.79

1.9

1.6

pmol/l

105.1

100.5

—

(3015736) pH of Urine

3.03

1.74

2.1

4.4

—

(3012544) pH of Venous blood

3.68

1.71

3.3

7.9

—

(3033658) Prothrombin time (PT) actual/Normal

3.08

1.69

5.4

4.7

96.8

92.4

—

(3018095) Leukocytes [#/volume] in Urine

2.71

1.43

4.1

3.6

e6/l

43.9

32.5

—

(3026008) Bacteria identified in Urine by Culture

2.68

1.36

1.8

3.9

—

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

137

2.44

0.94

3.6

3.2

—

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

2.14

0.90

2.5

4.5

—

0.0

—

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

2.18

0.89

1.8

2.1

—

(42870588) Differential panel, method unspecified - Blood

1.99

0.87

10.6

8.8

—

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

2.05

0.81

6.9

5.1

mmol/l

1.2

1.01

(3037522) Nuclear Ab [Titer] in Serum

2.37

0.80

1.4

1.5

—

514.3

—

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

2.02

0.79

4.5

7.0

—

0.0

—

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

1.99

0.75

2.4

4.5

—

0.0

—

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

2.00

0.74

3.1

2.7

—

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

2.08

0.73

2.0

1.9

—

(1761868) Lipid panel - Serum or Plasma

0.49

0.60

4.8

2.6

—

(3044889) 12 lead EKG panel

122

1.66

0.55

3.3

2.9

—

(3013512) EKG study

1.70

0.54

2.4

4.8

—

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

1.54

0.48

3.5

2.8

umol/l

372.5

348.4

—

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

1.78

0.47

2.4

1.5

—

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

0.59

0.45

2.4

4.4

—

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

0.00

0.43

0.0

1.5

—

(3019225) pH of Specimen

0.00

0.43

0.0

2.1

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.58

0.40

6.2

4.8

—

(36304419) Bacteria [Presence] in Urine

1.53

0.36

4.0

2.6

—

(3044640) Blood type and Crossmatch panel - Blood

1.49

0.36

1.9

—

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

176

0.70

0.35

4.5

3.8

mmol/l

1.4

0.04

164

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

1.50

0.31

2.7

1.8

ug/l

96.1

95.3

—

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

131

1.42

0.29

3.3

3.5

pmol/l

14.5

14.3

0.06

122

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

130

0.71

0.25

4.0

2.8

u/l

35.9

40.0

0.22

125

(3023368) Bacteria identified in Blood by Culture

1.28

0.24

7.4

5.8

—

(40758558) Short blood count panel - Blood

1.30

0.22

8.5

6.0

—

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

0.00

0.22

0.0

1.5

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.22

0.0

1.1

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.22

0.0

1.5

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.22

0.0

1.6

—

(3002173) Hemoglobin [Mass/volume] in Arterial blood

0.00

0.22

0.0

5.4

—

126.1

—

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

0.00

0.22

0.0

1.7

—

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

0.00

0.22

0.0

1.5

—

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

0.00

0.22

0.0

1.2

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.22

0.0

1.5

—

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

0.00

0.22

0.0

1.5

—

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

0.00

0.22

0.0

1.5

—

(3008898) HLA-B27 [Presence]

0.00

0.22

0.0

1.0

—

(4010399)

0.00

0.22

0.0

1.2

—

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

179

0.81

0.21

4.8

4.2

mmol/l

4.4

4.7

0.77

169

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

179

0.81

0.21

4.6

4.1

mmol/l

1.3

1.4

0.61

168

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

0.00

0.21

0.0

2.9

—

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

1.25

0.19

3.0

3.1

—

(3019050) Tissue transglutaminase IgA Ab [Units/volume] in Serum

1.08

0.10

1.4

1.3

—

0.8

—

(3025839) Triglyceride [Moles/volume] in Serum or Plasma

1.08

0.10

1.4

1.9

mmol/l

2.6

1.5

—

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

104

1.11

0.01

4.2

mmol/l

6.6

7.2

0.33

(3037467) Urinalysis macro (dipstick) panel - Urine

124

0.93

0.00

4.4

4.7

—

(3017918) Cytomegalovirus IgG Ab [Titer] in Serum or Plasma

0.00

0.0

1.0

—

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

0.00

0.0

1.6

—

1.2

—

(3036489) Thrombin time

0.00

0.0

12.8

—

22.0

—

(3049717) Cytology report of Urine Cyto stain

0.00

0.0

1.3

—

(3013707) Erythrocyte sedimentation rate by Westergren method

147

1.06

0.00

4.3

4.0

mm/h

9.2

10.6

0.24

139

(3024928) Oxygen saturation in Venous blood

0.00

0.0

11.4

—

(3022914) Cancer Ag 19-9 [Units/volume] in Serum or Plasma

0.00

0.0

5.0

—

14.0

—

(3000515) Antithrombin actual/normal in Platelet poor plasma by Chromogenic method

0.00

0.0

13.2

—

75.8

—

(3039162) Centromere protein B Ab [Units/volume] in Serum

0.00

0.0

1.4

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.4

—

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

0.00

0.0

1.7

—

0.2

—

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

0.00

0.0

1.6

—

(3050238) Crystals [Presence] in Synovial fluid by Light microscopy

0.00

0.0

1.6

—

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

0.00

0.0

1.7

—

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

0.00

0.0

1.4

—

(3016881) Enterovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.2

—

(40761536) Microorganisms panel - Urine sediment

0.00

0.0

4.9

—

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

0.00

0.0

1.2

—

(3023081) Carboxyhemoglobin/Hemoglobin.total in Blood

0.00

0.0

4.5

—

1.8

—

(3014007) Fractional oxyhemoglobin in Arterial blood

0.00

0.0

4.6

—

88.6

—

(3023939) Sjogrens syndrome-A extractable nuclear Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(3019250) Coagulation factor VIII activity actual/normal in Platelet poor plasma by Coagulation assay

0.00

0.0

14.4

—

186.4

—

(3015635) Cytomegalovirus IgM Ab [Units/volume] in Serum or Plasma

0.00

0.0

1.0

—

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

0.00

0.0

1.3

—

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

0.00

0.0

3.0

—

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

0.00

0.0

1.0

—

(3014162) Mycobacterium tuberculosis DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.8

—

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

0.00

0.0

1.3

—

7.5

—

(3007930) Methemoglobin/Hemoglobin.total in Blood

0.00

0.0

4.5

—

0.8

—

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

0.00

0.0

1.1

—

(3020148) Glutamate decarboxylase 65 Ab [Units/volume] in Serum

0.00

0.0

1.0

—

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

0.00

0.0

1.3

—

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

0.00

0.0

7.3

—

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

0.00

0.0

1.4

—

(3045414) Leukocytes [Presence] in Urine

0.00

0.0

1.2

—

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

0.00

0.0

1.4

—

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

0.00

0.0

13.0

—

2.8

—

(3020891) Body temperature

0.00

0.0

2.2

—

(3020961) Endomysium IgA Ab [Titer] in Serum

0.00

0.0

1.3

—

Mortality – FinRegistry

↥

Association

Association between endpoint Q17_REDUCT_DEFECTS_UNSPE_LIMB and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have Q17_REDUCT_DEFECTS_UNSPE_LIMB.

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: Q17_REDUCT_DEFECTS_UNSPE_LIMB – Reduction defects of unspecified limb

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	Q17_REDUCT_DEFECTS_UNSPE_LIMB
CONTROL_EXCLUDE	Q17_CONGEN_MALFO_DEFORMAT_MUSCULOS_SYSTEM
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	Q73
HD_ICD_9
HD_ICD_8
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	Q73
COD_ICD_9
COD_ICD_8
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

Reduction defects of unspecified limb

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