Risteys · D3

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 — D81.1 Cause of death: ICD-10 — D81.1 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	167	91	73
Only index persons	139	84	55
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	46.10	43.74	48.74
Only index persons	41.88	43.65	39.17

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	19	15	-
Unadjusted period prevalence (%)	0.00	0.01	-
Median age at first event (years)	45.41	40.30	-

-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

(3043849) Epstein Barr virus DNA [Units/volume] (viral load) in Serum or Plasma by NAA with probe detection

+∞

6.60

1.2

0.0

—

(3007853) Bacteria identified in Skin by Aerobe culture

10.28

4.47

5.0

1.7

—

(3003458) Phosphate [Moles/volume] in Serum or Plasma

7.94

4.06

14.0

3.5

mmol/l

1.0

—

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

6.17

3.54

5.8

3.7

—

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

5.81

3.33

6.6

4.1

e6/l

0.7

0.5

0.36

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

6.14

3.20

5.3

4.0

umol/l

3.3

11.7

—

(3052851) Hemolysis interference index of Serum or Plasma

12.85

3.16

9.0

1.2

—

(3002582) Erythrocytes [#/volume] in Urine

5.27

3.05

6.6

4.2

e6/l

31.7

1711.9

0.48

(3012544) pH of Venous blood

6.25

2.78

21.7

2.1

—

(3018677) aPTT in Platelet poor plasma by Coagulation assay

6.25

2.78

2.4

3.4

28.1

33.9

—

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

7.38

2.78

4.0

1.3

—

(36304419) Bacteria [Presence] in Urine

4.71

2.68

7.2

4.2

—

(3043924) Respiratory syncytial virus RNA [Identifier] in Specimen by NAA with probe detection

5.50

2.54

2.1

1.5

—

(3042936) Bacteria identified in Isolate by Culture

4.90

2.32

5.4

2.9

—

(3024561) Albumin [Mass/volume] in Serum or Plasma

4.04

2.25

19.9

4.3

g/l

32.5

35.9

1.08

(40758558) Short blood count panel - Blood

3.93

2.21

37.2

6.3

—

(3000991) Gas panel - Venous blood

5.73

2.08

32.0

6.5

—

(3015399) Transferrin receptor.soluble [Mass/volume] in Serum or Plasma

3.88

2.03

9.3

1.9

mg/l

2.4

3.1

—

(3038288) Influenza virus B RNA [Presence] in Specimen by NAA with probe detection

4.64

2.02

2.2

1.5

—

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

4.00

1.95

5.1

1.9

—

(3016431) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Serum or Plasma

3.77

1.93

16.8

4.5

mmol/l

1.2

0.31

(3022096) Basophils/100 leukocytes in Blood

3.61

1.89

46.8

5.0

0.5

0.7

0.70

(3006315) Basophils [#/volume] in Blood

3.45

1.84

46.8

5.8

e9/l

0.0

0.49

(3001604) Monocytes [#/volume] in Blood

3.45

1.84

46.8

5.7

e9/l

0.6

0.09

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

3.46

1.75

3.8

2.5

—

(42870588) Differential panel, method unspecified - Blood

3.27

1.74

37.6

4.4

—

(3023368) Bacteria identified in Blood by Culture

3.25

1.68

21.9

5.0

—

(3013115) Eosinophils [#/volume] in Blood

3.30

1.59

47.5

6.3

e9/l

0.1

0.2

1.02

(3002030) Lymphocytes/100 leukocytes in Blood

3.23

1.58

47.2

5.5

25.3

28.2

0.58

(3019198) Lymphocytes [#/volume] in Blood

3.23

1.58

46.9

5.9

e9/l

1.8

1.9

0.04

(3014576) Chloride [Moles/volume] in Serum or Plasma

3.85

1.54

18.8

7.1

mmol/l

105.4

106.1

—

(3044640) Blood type and Crossmatch panel - Blood

3.18

1.54

5.6

2.8

—

(3048689) Calprotectin [Mass/mass] in Stool

3.02

1.37

6.5

2.0

ug/g

143.8

82.8

—

(3026008) Bacteria identified in Urine by Culture

2.80

1.29

2.6

2.5

—

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

2.86

1.24

2.4

4.0

—

(3015736) pH of Urine

2.46

1.14

3.4

3.5

—

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

2.57

1.11

16.2

4.9

mmol/l

1.2

0.21

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

2.10

0.84

11.4

3.3

ug/l

446.0

71.5

0.92

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

2.10

0.84

5.3

3.9

—

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

2.06

0.72

2.2

1.3

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.64

0.0

1.3

—

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

1.67

0.47

11.2

4.2

mmol/l

10.0

6.2

0.47

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

0.00

0.43

0.0

1.5

—

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

0.00

0.43

0.0

1.4

—

(3021960) Folate [Moles/volume] in Serum or Plasma

1.67

0.41

3.8

1.5

nmol/l

30.3

19.2

—

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

1.62

0.41

1.7

1.8

mmol/l

1.3

1.5

—

(3041096) Erythrocytes [Presence] in Urine by Automated

1.57

0.40

3.8

3.0

—

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

139

0.63

0.38

4.3

3.6

mmol/l

1.6

1.3

0.55

126

(40768804) Tissue Pathology biopsy report

1.57

0.34

2.3

1.8

—

(3044889) 12 lead EKG panel

101

0.64

0.33

4.9

3.7

—

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

1.43

0.26

2.4

1.7

—

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

149

0.77

0.24

4.5

4.2

mmol/l

2.6

2.8

0.59

133

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

0.00

0.22

0.0

1.0

—

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

0.00

0.22

0.0

1.4

—

(3020891) Body temperature

0.00

0.22

0.0

2.2

—

(3008230) Borrelia burgdorferi IgM Ab [Units/volume] in Serum

0.00

0.22

0.0

2.4

—

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

0.00

0.22

0.0

1.6

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.22

0.0

1.2

—

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

0.00

0.22

0.0

1.5

—

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

122

0.77

0.21

5.3

5.0

pmol/l

13.7

14.5

0.61

115

(3002109) Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma

0.00

0.21

0.0

1.9

—

(40761535) Cells panel - Urine sediment

0.00

0.21

0.0

2.0

—

(3005785) Creatine kinase.MB [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

2.1

—

4.3

—

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

146

0.84

0.11

4.3

4.1

mmol/l

4.4

4.7

0.78

133

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

145

0.87

0.11

4.6

4.1

mmol/l

1.4

1.5

0.76

133

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

1.26

0.10

1.8

1.7

—

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

0.00

0.0

2.0

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

0.00

0.0

7.9

—

0.8

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

0.00

0.0

7.9

—

1.8

—

(3015816) F5 gene p.Arg506Gln [Presence] in Blood or Tissue by Molecular genetics method

0.00

0.0

1.4

—

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

0.00

0.0

2.2

—

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

1.02

0.00

4.2

3.4

—

(40768793) Breast Pathology biopsy report

0.00

0.0

1.3

—

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

0.00

0.0

1.6

—

0.5

—

(3016888) Borrelia burgdorferi IgG Ab [Units/volume] in Serum

0.00

0.0

1.1

—

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

0.00

0.0

1.4

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.0

1.5

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.0

1.4

—

(1002102) Choriogonadotropin.intact+Beta subunit [Mass/volume] in Serum or Plasma

0.00

0.0

1.4

—

(4034850)

0.00

0.0

9.0

—

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

0.00

0.0

1.8

—

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

0.00

0.0

1.4

—

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

0.00

0.0

1.7

—

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

0.00

0.0

1.4

—

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

113

0.94

0.00

4.0

3.4

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.0

1.4

—

(3009340) Metanephrine [Moles/volume] in Serum or Plasma

0.00

0.0

1.4

—

(3030408) 3-Methoxytyramine [Moles/volume] in Serum or Plasma

0.00

0.0

1.6

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.4

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.2

—

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

0.00

0.0

1.5

—

62.6

—

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

0.00

0.0

1.4

—

Mortality – FinRegistry

↥

Association

Association between endpoint D3_SCIDB and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have D3_SCIDB.

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: D3_SCIDB – Severe combined immunodeficiency [SCID] with low T- and B-cell numbers

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	D3_SCIDB
CONTROL_EXCLUDE	D3_IMMUNEMECHANISM
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D811
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	D811
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

Severe combined immunodeficiency [SCID] with low T- and B-cell numbers

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