Risteys · D3_COMBIMMUDEFNAS

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 — D81.9 Hospital discharge: ICD-9 — 2792A Cause of death: ICD-10 — D81.9 Cause of death: ICD-9 — 2792A 2 out of 7 registries used, show all original rules.	38
4. Check minimum number of events None	38
5. Include endpoints None	38
6. Filter based on genotype QC (FinnGen only)	38

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	281	156	122
Only index persons	229	132	97
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	53.68	51.43	56.82
Only index persons	53.66	50.02	58.61

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	38	27	11
Unadjusted period prevalence (%)	0.01	0.01	0.00
Median age at first event (years)	51.31	50.12	54.24

-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

(3007164) IgA [Mass/volume] in Serum or Plasma

5.20

5.96

4.6

1.3

2.1

2.2

g/l

0.13

(3042936) Bacteria identified in Isolate by Culture

5.66

5.41

4.9

1.7

—

(3040853) Adenovirus DNA [Identifier] in Specimen by NAA with probe detection

16.66

4.77

4.1

1.2

—

(3042194) Human metapneumovirus RNA [Presence] in Specimen by NAA with probe detection

13.87

4.47

4.1

1.2

—

(42870588) Differential panel, method unspecified - Blood

4.07

4.33

15.3

4.5

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

8.27

3.53

2.7

—

(3019069) Monocytes/100 leukocytes in Blood

141

3.67

3.47

16.4

5.1

8.2

0.01

134

(3012095) Magnesium [Moles/volume] in Serum or Plasma

4.04

3.44

10.3

4.2

0.8

mmol/l

0.06

(3018010) Neutrophils/100 leukocytes in Blood

142

3.63

3.41

14.2

5.0

56.6

54.3

0.41

135

(3018418) pH of Serum or Plasma

3.48

3.41

8.6

4.0

7.4

—

(3023368) Bacteria identified in Blood by Culture

3.52

3.41

7.9

2.8

—

(3000494) Fungus identified in Specimen by Culture

4.32

3.30

3.0

1.3

—

(3002030) Lymphocytes/100 leukocytes in Blood

146

3.47

3.19

15.4

5.0

29.5

31.8

0.45

137

(36305247) Microscopic observation [Identifier] in Isolate by Gram stain

8.63

3.18

2.3

1.4

—

(3022145) Colonoscopy Study observation

4.17

3.16

1.1

1.3

—

(3022096) Basophils/100 leukocytes in Blood

138

3.37

3.14

15.0

4.8

0.6

0.7

0.49

130

(3010421) pH of Blood

11.22

3.06

13.8

3.0

7.4

7.5

—

(3027315) Oxygen [Partial pressure] in Blood

11.22

3.06

13.8

3.0

8.1

9.9

kpa

—

(3013290) Carbon dioxide [Partial pressure] in Blood

11.22

3.06

13.8

3.0

5.4

4.7

kpa

—

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

3.28

2.92

3.6

2.3

2.7

2.5

mg/l

0.18

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

3.52

2.86

5.3

1.6

—

(3016293) Bicarbonate [Moles/volume] in Serum or Plasma

5.03

2.86

10.5

13.2

25.6

25.2

mmol/l

—

(40761536) Microorganisms panel - Urine sediment

5.45

2.74

9.9

3.0

—

(40760892) CBC W Ordered Manual Differential panel - Blood

3.10

2.67

9.8

5.3

—

(4035726)

4.53

2.63

1.9

1.4

—

(3048816) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Blood

4.32

2.53

7.0

5.2

1.2

mmol/l

—

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

133

2.85

2.46

3.5

2.8

127.8

77.4

ug/l

1.13

121

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

108

2.80

2.43

2.3

2.0

107.2

97.3

pmol/l

0.25

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

131

2.61

2.13

17.7

7.0

1.2

mmol/l

0.33

113

(3004588) Protein electrophoresis panel - Serum or Plasma

4.53

2.13

9.5

1.2

—

(3018677) aPTT in Platelet poor plasma by Coagulation assay

3.12

2.12

1.9

3.9

30.0

30.3

—

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

227

2.98

2.08

18.2

7.1

90.7

78.4

u/l

0.67

211

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

2.56

1.98

1.6

1.3

2.5

2.7

u/ml

—

(3013707) Erythrocyte sedimentation rate by Westergren method

229

2.91

1.88

8.7

3.7

17.5

10.4

mm/h

1.13

211

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

102

2.45

1.88

3.9

3.6

—

(3000492) Spirometry study

3.19

1.74

3.1

1.4

—

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

3.55

1.74

9.3

4.7

—

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

2.89

1.71

5.9

1.5

—

(3026782) Osmolality of Urine

2.63

1.70

4.5

2.7

492.9

576.7

mosm/kgh2o

0.71

(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma

2.34

1.66

4.6

3.4

43.7

18.6

ng/l

—

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

2.79

1.65

5.9

1.5

—

(3051714) Fibrin D-dimer FEU [Mass/volume] in Platelet poor plasma

2.43

1.62

2.2

2.4

1.3

1.2

mg/l

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.94

1.60

3.3

1.6

—

(3012516) Albumin [Mass/volume] in Urine

2.34

1.51

7.2

3.2

10055.5

96.0

mg/l

—

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

3.43

1.49

3.2

1.5

1.1

g/l

—

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

3.43

1.49

3.6

1.5

0.1

0.2

g/l

—

(3000850) Epithelial cells [#/volume] in Urine

2.41

1.45

4.5

2.7

4.9

5.6

e6/l

0.13

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

2.77

1.36

1.0

—

(3032080) INR in Blood by Coagulation assay

2.09

1.30

23.3

5.7

1.1

1.2

inr

—

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

2.65

1.30

1.7

1.5

—

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

2.30

1.15

1.7

1.4

—

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

2.58

1.12

8.6

5.1

7.2

5.5

mmol/l

—

(40768804) Tissue Pathology biopsy report

115

1.87

1.00

1.9

—

(40758558) Short blood count panel - Blood

1.97

1.00

15.7

6.3

—

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

183

1.85

0.95

12.3

4.3

6.4

6.5

mmol/l

0.06

160

(3033658) Prothrombin time (PT) actual/Normal

1.91

0.92

5.3

5.0

97.7

94.3

0.26

(3013512) EKG study

1.88

0.88

5.1

3.7

—

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

1.85

0.84

4.8

4.0

0.1

0.3

e6/l

0.58

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

1.87

0.78

1.9

1.7

—

(36304419) Bacteria [Presence] in Urine

1.79

0.77

4.8

3.9

—

(3021447) Carbon dioxide [Partial pressure] in Venous blood

2.06

0.73

8.8

6.8

6.1

5.9

kpa

—

(3012544) pH of Venous blood

2.06

0.73

8.8

6.7

—

(40768797) Stomach Pathology biopsy report

1.77

0.71

1.7

1.3

—

(3020682) Albumin/Creatinine [Ratio] in Urine

1.74

0.68

5.0

3.6

23.3

7.4

mg/mmol

—

(3044889) 12 lead EKG panel

195

1.63

0.66

5.2

3.2

—

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

1.90

0.62

6.0

8.6

105.7

103.7

mmol/l

—

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

1.68

0.62

1.7

1.9

—

(3041096) Erythrocytes [Presence] in Urine by Automated

1.65

0.61

8.0

3.1

—

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

229

1.62

0.59

5.3

3.6

—

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

1.63

0.58

8.4

3.2

0.0

estimate

—

(3015736) pH of Urine

122

1.54

0.55

2.9

3.2

—

(3026008) Bacteria identified in Urine by Culture

1.56

0.53

4.2

2.7

—

(3002582) Erythrocytes [#/volume] in Urine

1.58

0.53

4.7

3.8

30.8

12.9

e6/l

0.33

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

154

1.47

0.47

6.2

3.4

0.0

estimate

—

(3037467) Urinalysis macro (dipstick) panel - Urine

205

1.46

0.44

7.6

4.0

—

(3029187) Natriuretic peptide.B prohormone N-Terminal [Mass/volume] in Serum or Plasma

1.50

0.43

3.9

3.1

4103.3

1034.8

ng/l

—

(36660697) Celiac disease serology panel - Serum

1.59

0.43

1.6

1.1

—

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

1.49

0.41

9.8

5.3

—

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

0.00

0.41

0.0

1.7

—

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

151

1.36

0.34

7.4

5.0

0.0

estimate

—

(40761511) CBC panel - Blood by Automated count

326

0.73

0.33

38.0

10.1

—

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

123

1.36

0.32

7.5

3.2

—

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

153

1.34

0.30

6.6

3.4

0.0

estimate

—

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

0.71

0.27

3.7

3.2

—

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

1.40

0.25

3.0

1.8

—

(3002256) Pathology report gross observation

1.36

0.24

1.2

—

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

0.00

0.22

0.0

1.9

—

0.0

—

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

0.00

0.22

0.0

5.5

—

33.5

—

(3008898) HLA-B27 [Presence]

0.00

0.22

0.0

1.1

—

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

0.00

0.22

0.0

1.3

—

(46237023) Hepatitis B virus core and surface Ab and surface Ag panel - Serum

0.00

0.22

0.0

1.2

—

(40768793) Breast Pathology biopsy report

0.00

0.21

0.0

1.0

—

(3023421) Hepatitis B virus surface Ab [Units/volume] in Serum

0.00

0.21

0.0

1.8

—

394.3

—

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

0.00

0.21

0.0

9.9

—

24.8

—

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

0.00

0.20

0.0

2.1

—

(3002385) Erythrocyte distribution width [Ratio]

261

1.28

0.19

46.9

14.6

14.0

13.4

1.37

256

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

0.70

0.18

2.4

2.0

—

(3009542) Hematocrit [Volume Fraction] of Blood

283

1.28

0.16

32.7

13.1

39.6

39.5

0.04

213

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

1.19

0.10

2.2

—

(3019832) Treponema pallidum Ab [Presence] in Serum

1.16

0.10

1.6

1.8

—

(3006923) Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma

320

1.24

0.09

25.0

9.6

30.3

25.0

u/l

0.91

308

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

0.83

0.08

1.0

1.5

—

(3044640) Blood type and Crossmatch panel - Blood

0.86

0.07

4.4

2.1

—

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

148

1.02

0.00

7.3

3.6

—

(3049506) Microalbumin [Mass/time] in Urine collected for unspecified duration

0.00

0.0

1.3

—

(3000924) Streptococcus pyogenes [Presence] in Throat by Organism specific culture

0.00

0.0

1.8

—

(3038177) Helicobacter pylori Ab [Presence] in Serum

0.00

0.0

1.0

—

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

0.00

0.0

4.0

—

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

0.00

0.0

1.1

—

(40762119) U1 small nuclear ribonucleoprotein 70kD Ab [Units/volume] in Serum

0.00

0.0

1.2

—

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

1.01

0.00

1.8

1.5

—

(21492711) Cytomegalovirus IgG Ab avidity [Presence] in Serum or Plasma by Immunoassay

0.00

0.0

1.8

—

(3047007) Chlamydophila sp Ab [Presence] in Serum

0.00

0.0

1.4

—

(4268621)

0.00

0.0

2.8

—

(3020629) Protein S Free Ag actual/normal in Platelet poor plasma by Immunoassay

0.00

0.0

1.2

—

91.0

—

(3018387) Mycoplasma pneumoniae IgG Ab [Units/volume] in Serum

0.00

0.0

1.0

—

(1761868) Lipid panel - Serum or Plasma

0.93

0.00

2.6

2.4

—

(3024666) Lithium, Blood [Moles/volume] in Serum or Plasma

0.00

0.0

7.2

—

0.7

—

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

0.00

0.0

2.4

—

1.3

—

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

0.95

0.00

1.7

1.4

—

(3002148) Methylenedioxymethamphetamine [Presence] in Urine by Screen method

0.00

0.0

1.2

—

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

0.00

0.0

2.4

—

7.4

—

(3023511) Choriogonadotropin [Units/volume] in Urine

0.00

0.0

1.2

—

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

0.00

0.0

1.3

—

(44816752) ERBB2 gene copy number/nucleus in Tissue by FISH

0.00

0.0

1.0

—

Mortality – FinRegistry

↥

Association

Association between endpoint D3_COMBIMMUDEFNAS and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have D3_COMBIMMUDEFNAS.

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_COMBIMMUDEFNAS – Combined immunodeficiency, unspecified

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	D3_COMBIMMUDEFNAS
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	D819
HD_ICD_9	2792A
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	D819
COD_ICD_9	2792A
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

Combined immunodeficiency, unspecified

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