Severe combined immunodeficiency [SCID] with reticular dysgenesis

D3_SCIDA

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 — D81.0 Cause of death: ICD-10 — D81.0 2 out of 7 registries used, show all original rules.	109
4. Check minimum number of events None	109
5. Include endpoints None	109
6. Filter based on genotype QC (FinnGen only)	109

Control definitions (FinnGen only)

Control exclude: D3_IMMUNEMECHANISM

Extra metadata

Level in the ICD hierarchy: 4
First used in FinnGen datafreeze: DF2
Parent code in ICD-10: D81
Name in latin: Deficientia immunalis mixta gravis cum dysgenesia reticulari

NAME	D3_SCIDA
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	D810
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	D810
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 Severe combined immunodeficiency [SCID] with reticular dysgenesis 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	872	485	380
Only index persons	752	436	316
Unadjusted period prevalence (%)
Whole population	0.01	0.01	0.01
Only index persons	0.01	0.02	0.01
Median age at first event (years)
Whole population	54.06	50.10	58.88
Only index persons	51.47	48.96	54.94

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	109	63	46
Unadjusted period prevalence (%)	0.02	0.02	0.02
Median age at first event (years)	52.67	46.37	61.31

-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

No data

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.

Matched cohort

Matched cases
98: Matched controls
979

Code

Vocabulary

Description

Odds Ratio

-log₁₀(p)

N matched cases

N matched controls

D81.0

ICD-10 Finland

Severe combined immunodeficiency [SCID] with reticular dysgenesis

+∞

141.2

T81.0

ICD-10 Finland

Haemorrhage and haematoma complicating a procedure, not elsewhere classified

18.2

22.5

Y83

ICD-10 Finland

Surgical operation and other surgical procedures as the cause of abnormal reaction of the patient, or of later complication, without mention of misadventure at the time of the procedure

8.4

11.5

D80.1

ICD-10 Finland

Nonfamilial hypogammaglobulinaemia

+∞

9.5

120

Kela drug reimbursment

Hypogammaglobulinaemia

+∞

8.4

M05BA04

ATC

alendronic acid; oral

8.2

UJD10

NOMESCO Finland

Esophagoscopy, gastroscopy and duodenoscopy

3.5

7.3

179

JN3AE

NOMESCO Finland

Abdominal ultrasound examination

4.6

6.3

D80.9

ICD-10 Finland

Immunodeficiency with predominantly antibody defects, unspecified

+∞

6.3

LabWAS

↥

(ID) Name

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

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

195

3.11

7.36

3.4

1.9

3.3

3.2

mg/l

0.11

178

(3007853) Bacteria identified in Skin by Aerobe culture

100

3.42

6.61

3.3

1.6

—

(3022948) Iron [Moles/volume] in Serum or Plasma

128

3.12

6.26

4.6

2.6

12.6

14.7

umol/l

0.60

114

(3032080) INR in Blood by Coagulation assay

348

2.61

5.69

11.6

7.5

1.0

1.2

inr

2.79

105

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

396

2.59

5.51

15.5

7.2

1.2

mmol/l

0.69

338

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

367

2.50

5.22

14.1

6.1

1.2

mmol/l

0.31

333

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

3.98

4.96

1.5

1.3

—

(3042936) Bacteria identified in Isolate by Culture

123

2.72

4.52

3.4

1.8

—

(3008909) Norovirus RNA [Presence] in Stool by NAA with probe detection

4.42

4.27

2.4

1.3

—

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

3.29

4.23

2.2

1.4

—

(3044640) Blood type and Crossmatch panel - Blood

271

2.29

4.20

3.8

2.3

—

(3001604) Monocytes [#/volume] in Blood

420

2.27

4.18

12.9

6.1

0.6

e9/l

0.95

369

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

375

2.25

4.16

4.3

2.6

200.8

103.7

ug/l

1.20

344

(3006315) Basophils [#/volume] in Blood

421

2.26

4.15

13.0

6.2

0.0

e9/l

0.09

369

(3018418) pH of Serum or Plasma

249

2.29

4.09

9.6

4.4

7.4

0.23

(46236952) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (MDRD)

3.17

4.00

2.1

2.7

58.8

65.0

ml/min/173m2

—

(3013115) Eosinophils [#/volume] in Blood

438

2.20

3.88

13.2

6.4

0.2

e9/l

0.25

389

(3019198) Lymphocytes [#/volume] in Blood

430

2.18

3.83

13.0

6.2

1.7

1.8

e9/l

0.39

385

(3023368) Bacteria identified in Blood by Culture

219

2.22

3.63

5.6

4.0

—

(3032035) Polymorphonuclear cells/100 leukocytes in Blood

6.07

3.41

5.6

3.6

57.0

59.1

—

(3030905) Polymorphonuclear cells [#/volume] in Blood

6.07

3.41

5.5

2.4

4.0

4.3

e9/l

—

(3021440) Promyelocytes/100 leukocytes in Blood

2.90

3.31

5.3

5.8

0.4

0.1

—

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

2.59

3.24

4.2

3.1

—

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

129

2.33

3.20

2.3

1.7

—

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

153

2.22

3.09

1.8

1263.5

1280.8

nmol/l

0.03

120

(3037522) Nuclear Ab [Titer] in Serum

117

2.35

3.06

1.8

1.4

354.3

516.4

titre

—

(3052649) Adenosine deaminase [Enzymatic activity/volume] in Serum or Plasma

10.39

3.01

2.4

1.4

16.6

15.2

u/l

—

(3017181) Myelocytes/100 leukocytes in Blood

2.67

2.86

5.5

5.6

2.4

0.7

—

(3009508) Creatinine [Moles/volume] in Urine

255

1.97

2.81

4.2

2.8

6.2

7.9

mmol/l

1.88

218

(3007847) Interleukin 2 Receptor Soluble [Units/volume] in Serum or Plasma

8.65

2.77

5.8

1.3

801.2

929.3

u/ml

—

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

343

1.91

2.77

3.5

2.4

78.8

76.2

nmol/l

0.26

295

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

503

1.94

2.77

13.3

10.2

4.5

4.1

e9/l

0.66

444

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

248

1.97

2.76

3.6

3.0

0.2

0.4

e6/l

0.91

184

(3034770) Mitochondria Ab [Titer] in Serum

4.46

2.73

1.1

1.3

—

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

192

2.03

2.71

5.3

2.2

—

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

3.83

2.64

2.4

3.0

—

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

313

1.88

2.60

2.3

2.0

96.6

94.2

pmol/l

0.13

151

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

133

2.14

2.58

2.2

1.7

—

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

398

1.84

2.49

7.7

3.9

—

(3000494) Fungus identified in Specimen by Culture

100

2.22

2.39

1.5

1.4

—

(3025941) Bacteria identified in Stool by Culture

2.75

2.36

1.4

1.2

—

(3030306) Epithelial cells.non-squamous [#/volume] in Urine by Automated count

138

2.05

2.34

2.4

2.7

0.9

0.8

e6/l

0.09

(36304419) Bacteria [Presence] in Urine

244

1.86

2.31

3.7

2.8

—

(40769539) Bacteria identified based on 16S rRNA gene [Identifier] in Specimen by Sequencing

4.81

2.30

1.5

1.2

—

(3016650) Hepatitis A virus Ab [Presence] in Serum

4.81

2.30

1.0

—

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

314

1.80

2.29

5.4

3.2

—

(42870588) Differential panel, method unspecified - Blood

279

1.82

2.28

12.9

5.5

—

(3021589) Normoblasts [#/volume] in Blood

378

1.78

2.28

16.0

9.5

0.0

e9/l

0.47

305

(40768804) Tissue Pathology biopsy report

353

1.77

2.21

2.8

1.9

—

(3028167) CD3+CD4+ (T4 helper) cells [#/volume] in Blood

5.18

2.09

1.2

1.6

—

653.0

—

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

4.17

2.07

2.3

1.2

—

(1616796) Gas panel - Central venous blood

4.71

1.96

3.2

3.3

—

(3021901) Oxygen saturation in Capillary blood

4.71

1.96

1.4

2.8

—

(3013327) Hepatitis A virus IgM Ab [Presence] in Serum

4.71

1.96

1.0

—

(3034780) Angiotensin converting enzyme [Enzymatic activity/volume] in Serum or Plasma

2.79

1.91

1.0

1.2

37.9

32.4

u/l

—

(3020891) Body temperature

2.79

1.91

6.4

5.1

—

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

3.33

1.91

1.0

1.6

—

(3002582) Erythrocytes [#/volume] in Urine

275

1.72

1.88

4.1

3.2

24.4

45.7

e6/l

0.59

211

(3005702) Mycobacterium sp identified in Specimen by Organism specific culture

3.67

1.86

1.7

1.4

—

(3026389) Candida sp identified in Specimen by Organism specific culture

4.31

1.84

1.0

1.3

—

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

3.18

1.83

2.3

3.2

184.9

192.1

—

(40761535) Cells panel - Urine sediment

2.21

1.79

6.4

4.1

—

(3013290) Carbon dioxide [Partial pressure] in Blood

3.98

1.73

2.6

2.5

5.4

4.9

kpa

—

(3027315) Oxygen [Partial pressure] in Blood

3.98

1.73

2.4

2.5

9.0

kpa

—

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

3.98

1.73

1.2

—

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

153

1.82

1.73

2.3

1.8

—

(3018095) Leukocytes [#/volume] in Urine

327

1.64

1.69

5.0

3.8

495.3

35.2

e6/l

0.54

230

(3029879) Epithelial cells.squamous [#/volume] in Urine by Automated count

131

1.85

1.65

3.0

2.9

3.8

2.7

e6/l

0.20

(3022313) Gas panel - Capillary blood

2.62

1.63

16.4

3.6

—

(3000991) Gas panel - Venous blood

2.08

1.57

16.7

8.9

—

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

2.96

1.53

2.0

1.2

—

(3002256) Pathology report gross observation

103

1.90

1.52

1.6

1.2

—

(40761536) Microorganisms panel - Urine sediment

2.10

1.50

3.6

3.5

—

(3012516) Albumin [Mass/volume] in Urine

245

1.63

1.50

4.5

3.0

75.0

331.3

mg/l

0.48

157

(3004588) Protein electrophoresis panel - Serum or Plasma

2.16

1.50

1.1

2.5

—

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

177

1.70

1.48

3.1

1.5

2.3

2.8

g/l

0.51

110

(3002032) Base excess in Venous blood by calculation

1.99

1.42

9.9

4.6

3.1

2.4

mmol/l

—

(3013707) Erythrocyte sedimentation rate by Westergren method

665

1.61

1.40

7.9

4.1

16.5

11.6

mm/h

1.93

608

(3012544) pH of Venous blood

1.97

1.37

9.9

4.5

—

(3021337) Troponin I.cardiac [Mass/volume] in Serum or Plasma

164

1.68

1.36

3.3

3.0

56.5

133.2

ng/l

0.61

120

(3020630) Protein [Mass/volume] in Serum or Plasma

2.00

1.35

1.2

3.1

64.1

66.6

g/l

0.57

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

1.84

1.29

1.9

1.6

—

(3013512) EKG study

246

1.56

1.25

4.7

3.8

—

(40768797) Stomach Pathology biopsy report

118

1.74

1.25

1.8

1.2

—

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

452

1.49

1.24

4.3

3.8

0.0

estimate

0.00

(36032419) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Immunoassay

0.00

1.17

0.0

1.9

—

(3045414) Leukocytes [Presence] in Urine

2.42

1.14

1.4

1.5

—

(3020682) Albumin/Creatinine [Ratio] in Urine

260

1.51

1.14

5.5

3.6

21.1

10.5

mg/mmol

0.31

155

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

2.27

1.10

2.4

1.5

—

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

2.44

1.10

1.4

1.3

—

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

460

1.45

1.09

4.4

3.8

0.0

estimate

0.49

(3052851) Hemolysis interference index of Serum or Plasma

2.20

1.07

3.7

2.6

—

(40768443) Skin Pathology biopsy report

2.20

1.07

1.7

1.2

—

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

183

1.55

1.07

2.3

1.8

1.6

1.0

mg/l

0.61

148

(36031861) Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection

2.00

1.05

2.2

1.6

—

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

454

1.43

1.02

5.9

5.2

0.0

estimate

0.00

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

101

1.68

1.00

2.8

1.6

—

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

0.00

0.99

0.0

1.4

—

(3048689) Calprotectin [Mass/mass] in Stool

110

1.65

0.98

2.4

1.8

106.0

82.3

ug/g

0.16

(3043723) Beta 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

1.95

0.96

1.0

2.4

—

(3015736) pH of Urine

362

1.41

0.95

4.6

3.6

—

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

2.29

0.95

1.3

1.7

—

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

113

1.60

0.88

17.5

8.7

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

1.88

0.88

1.0

1.2

—

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

1.62

0.84

2.1

1.7

—

(3008898) HLA-B27 [Presence]

1.92

0.83

1.3

1.0

—

(3019060) Gas panel - Arterial blood

1.80

0.83

5.5

4.7

—

(40758558) Short blood count panel - Blood

221

1.43

0.81

12.1

7.5

—

(40760892) CBC W Ordered Manual Differential panel - Blood

194

1.45

0.81

10.0

5.5

—

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

1.72

0.80

7.3

6.3

26.5

24.6

mmol/l

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.80

0.0

1.5

—

(40766189) Gliadin peptide IgG Ab [Units/volume] in Serum by Immunoassay

0.00

0.80

0.0

1.2

—

20.5

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.80

0.0

1.5

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.80

0.0

1.6

—

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

0.00

0.80

0.0

1.6

—

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

0.00

0.80

0.0

1.6

—

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

0.00

0.80

0.0

1.6

—

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

0.00

0.80

0.0

1.6

—

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

0.00

0.79

0.0

1.7

—

(4034850)

0.00

0.79

0.0

16.5

—

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

895

0.70

0.79

5.5

4.9

2.5

2.8

mmol/l

1.80

822

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

195

1.44

0.79

1.3

0.4

2.0

u/ml

—

(3019225) pH of Specimen

1.71

0.78

14.3

4.5

—

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

215

1.41

0.75

4.6

3.8

—

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

1.63

0.72

1.7

1.9

—

(3000330) Specific gravity of Urine by Test strip

1.75

0.71

2.4

3.8

—

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

1.89

0.69

2.2

1.6

—

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

340

1.33

0.69

5.8

3.9

32.8

32.2

ng/l

0.03

235

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

1.82

0.67

1.0

2.7

0.0

g/l

—

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

669

1.33

0.66

5.3

3.8

14.6

14.8

pmol/l

0.23

611

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

879

0.73

0.66

5.1

4.4

4.3

4.7

mmol/l

2.26

811

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

184

1.39

0.65

2.0

1.8

428.1

443.0

pmol/l

0.09

158

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

1.76

0.64

2.8

1.9

—

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

570

1.30

0.62

2.8

3.1

—

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

877

0.74

0.62

5.1

4.4

1.4

1.5

mmol/l

0.63

803

(3037467) Urinalysis macro (dipstick) panel - Urine

603

1.29

0.59

8.2

4.3

—

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

0.53

0.58

1.8

—

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

1.48

0.57

3.6

2.5

5.1

9.3

umol/l

1.37

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

1.53

0.52

1.2

1.1

—

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

242

1.27

0.45

5.1

4.1

0.0

estimate

0.00

(4035726)

1.43

0.44

1.2

1.3

—

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

1.59

0.43

1.2

1.3

—

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

1.59

0.43

1.0

1.2

—

(3014702) Chromogranin A [Moles/volume] in Serum or Plasma

0.00

0.41

0.0

3.6

—

2.7

—

(40766183) Gliadin peptide IgA Ab [Units/volume] in Serum by Immunoassay

0.00

0.41

0.0

1.2

—

4.0

—

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

0.00

0.41

0.0

3.4

—

56.6

—

(3026008) Bacteria identified in Urine by Culture

265

1.24

0.39

3.1

2.9

—

(4010399)

1.35

0.39

1.7

1.3

—

(1761868) Lipid panel - Serum or Plasma

326

0.81

0.38

3.7

2.7

—

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

356

1.20

0.34

4.7

3.9

—

(3021614) Rheumatoid factor [Units/volume] in Serum or Plasma

165

1.26

0.34

1.8

1.2

20.0

35.6

iu/ml

0.69

(3044889) 12 lead EKG panel

615

1.19

0.33

5.4

3.6

—

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

148

1.26

0.32

2.1

1.3

—

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

1.27

0.28

2.1

1.5

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

1.25

0.26

1.9

1.4

—

(21494755) Public health laboratory ask at order entry panel

0.69

0.25

1.2

1.4

—

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

1.37

0.24

1.6

1.9

—

(3020460) C reactive protein [Mass/volume] in Serum or Plasma

872

1.18

0.22

32.4

13.6

21.8

22.5

mg/l

0.09

676

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

849

0.86

0.22

4.5

3.9

1.4

1.2

mmol/l

0.85

773

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

1.20

0.22

8.8

8.5

—

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

222

1.16

0.21

1.5

—

(21494670) JAK2 gene exon 14 targeted mutation analysis in Blood or Tissue by Molecular genetics method

0.00

0.21

0.0

1.1

—

(3014973) Borrelia burgdorferi IgM Ab [Units/volume] in Cerebral spinal fluid

0.00

0.21

0.0

1.2

—

(3016018) Differential panel - Cerebral spinal fluid

0.00

0.21

0.0

1.1

—

(3010380) Borrelia burgdorferi IgG Ab [Units/volume] in Cerebral spinal fluid

0.00

0.21

0.0

1.2

—

(3023410) Appearance of Cerebral spinal fluid

0.00

0.21

0.0

1.1

—

(40768795) Lymph node Pathology biopsy report

0.00

0.21

0.0

1.1

—

(3009201) Thyrotropin [Units/volume] in Serum or Plasma

811

1.16

0.21

6.2

4.6

2.5

1.9

mu/l

0.46

735

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

0.00

0.20

0.0

1.1

—

(3019150) Specific gravity of Urine by Refractometry

204

1.16

0.20

5.4

4.4

—

1.0

—

(3022145) Colonoscopy Study observation

100

1.22

0.19

1.0

1.3

—

(3009542) Hematocrit [Volume Fraction] of Blood

796

0.89

0.17

32.1

14.5

36.9

39.7

1.26

596

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

842

0.89

0.14

5.7

4.5

6.0

5.9

mmol/l

0.14

776

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

1.18

0.11

2.4

1.9

—

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

1.14

0.10

1.6

2.0

—

(3022621) pH of Urine by Test strip

1.08

0.09

2.2

2.6

—

(3041942) Cyclic citrullinated peptide Ab [Units/volume] in Serum

156

1.11

0.08

1.9

1.2

8.6

u/ml

—

(3004410) Hemoglobin A1c/Hemoglobin.total in Blood

816

0.93

0.08

6.8

5.7

41.0

40.0

mmol/mol

0.31

754

(3000492) Spirometry study

1.10

0.08

3.4

1.3

—

(3003510) Neisseria gonorrhoeae DNA [Presence] in Urine by NAA with probe detection

1.08

0.08

1.7

1.8

—

(36660697) Celiac disease serology panel - Serum

1.09

0.07

1.0

1.1

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.83

0.07

2.1

1.6

—

(40761511) CBC panel - Blood by Automated count

930

0.93

0.04

29.5

12.1

—

(3041096) Erythrocytes [Presence] in Urine by Automated

260

1.05

0.03

3.8

3.3

—

(40764999) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)

837

0.96

0.01

24.2

12.8

80.5

81.1

ml/min/173m2

0.07

679

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

154

1.05

0.00

1.5

—

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

228

1.01

0.00

1.7

1.8

1.7

1.4

mmol/l

0.72

195

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

215

0.97

0.00

5.4

4.4

22.6

22.1

0.04

104

(3011436) Histone Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(3024474) Albumin [Mass/volume] in Cerebral spinal fluid

0.00

0.0

1.0

—

245.8

—

(3020876) Protein [Mass/time] in 24 hour Urine

0.00

0.0

2.0

—

(3037875) Bordetella parapertussis DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.2

—

(36305771) Cryptosporidium sp DNA [Presence] in Stool by NAA with probe detection

0.00

0.0

1.0

—

(3051593) INR in Capillary blood by Coagulation assay

0.00

0.0

10.1

—

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

0.00

0.0

9.8

—

851.8

—

(3019497) Choriogonadotropin.beta subunit free [Moles/volume] in Serum or Plasma

0.00

0.0

1.2

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.0

1.0

—

32.7

—

(40759849) Smith extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.3

—

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

0.00

0.0

1.0

—

(40758897) Direct antiglobulin test.IgG specific reagent [Presence] on Red Blood Cells

0.00

0.0

3.0

—

(21491868) Cryoglobulin [Mass/volume] in Serum

0.00

0.0

1.0

—

(3028433) Virus identified in Specimen by Culture

0.00

0.0

1.8

—

(3032699) Streptococcus pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.4

—

(40759812) SCL-70 extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.3

—

(3042206) Streptococcus agalactiae Ag [Presence] in Vaginal fluid

0.00

0.0

1.2

—

(42529582) MDA5 Ab [Presence] in Serum by Line blot

0.00

0.0

1.0

—

(40759842) Ribonucleoprotein extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.3

—

(3033386) Bacteria [Presence] in Cerebral spinal fluid by Light microscopy

0.00

0.0

1.4

—

(42529598) SUMO-activating enzyme subunit 1 Ab [Presence] in Serum by Line blot

0.00

0.0

1.0

—

(3013637) Mi-2 Ab [Presence] in Serum

0.00

0.0

1.0

—

(3012447) Hantavirus puumala IgG Ab [Titer] in Serum

0.00

0.0

1.1

—

(40758895) Direct antiglobulin test.complement C3d specific reagent [Presence] on Red Blood Cells

0.00

0.0

3.0

—

(37020937) Giardia lamblia DNA [Presence] in Stool by NAA with probe detection

0.00

0.0

1.0

—

(1001509) Gas and Carbon monoxide and Electrolytes panel - Arterial blood

0.00

0.0

1.7

—

(40764127) Haemophilus influenzae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.2

—

(4027681)

0.00

0.0

1.1

—

(3010838) Calcium [Moles/time] in 24 hour Urine

0.00

0.0

1.4

—

(40764126) Parainfluenza virus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.1

—

(3049539) Genetic diseases [Identifier] in Blood or Tissue by FISH Nominal

0.00

0.0

1.0

—

(3029075) Extractable nuclear Ab panel - Serum

0.00

0.0

1.0

—

(3016436) Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma

0.00

0.0

1.5

—

218.3

—

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

0.00

0.0

1.0

—

(3026515) Parvovirus B19 IgM Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(40759844) Sjogrens syndrome-B extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.3

—

(40759883) Oligoclonal Bands IgG [Presence] in Cerebral spinal fluid by Isoelectric focusing

0.00

0.0

1.0

—

(3041145) Herpes simplex virus IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.0

—

(3011831) Apolipoprotein B/Apolipoprotein A-I [Percentile]

0.00

0.0

1.7

—

(3053028) Streptococcus sp identified in Specimen by Organism specific culture

0.00

0.0

1.0

—

(3016914) Bacteria identified in Cerebral spinal fluid by Culture

0.00

0.0

1.4

—

(3011166) Borrelia burgdorferi Ab [Presence] in Cerebral spinal fluid

0.00

0.0

1.2

—

(3030136) 5-Hydroxyindoleacetate [Moles/volume] in Serum or Plasma

0.00

0.0

3.7

—

61.8

—

(40759836) Histone Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.3

—

(40759843) Sjogrens syndrome-A extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.3

—

(3045788) Cell count panel - Pleural fluid

0.00

0.0

1.3

—

(3016244) Insulin [Units/volume] in Serum or Plasma

0.00

0.0

3.6

—

10.7

—

(42528593) TIF1-gamma Ab [Presence] in Serum by Line blot

0.00

0.0

1.0

—

(3008364) Apolipoprotein A-I [Mass/volume] in Serum or Plasma

0.00

0.0

1.7

—

(3009550) Parvovirus B19 IgG Ab [Titer] in Serum

0.00

0.0

1.2

—

(3004915) Chlamydophila pneumoniae IgA Ab [Units/volume] in Serum

0.00

0.0

1.0

—

(3035880) pH of Pleural fluid

0.00

0.0

1.2

—

(43055089) Myosin Ab [Presence] in Serum or Plasma by Immunoblot

0.00

0.0

1.1

—

(3000012) Reticulocyte production index

0.00

0.0

1.6

—

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

0.00

0.0

13.2

—

1318.5

—

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

0.00

0.0

1.8

—

(3028679) Herpes simplex virus Ab [Presence] in Serum

0.00

0.0

1.0

—

Mortality – FinRegistry

↥

Association

Association between endpoint D3_SCIDA and mortality.

Females

Parameter	HR [95% CI]	p-value
D3_SCIDA	1.58 [1.22, 2.05]	< 0.001
Birth year	0.998 [0.99, 1.01]	0.713

During the follow-up period (1.1.1998 — 31.12.2019), 107 out of 410 females with D3_SCIDA died.

Males

Parameter	HR [95% CI]	p-value
D3_SCIDA	2.004 [1.5, 2.67]	< 0.001
Birth year	0.989 [0.98, 1.0]	0.019

During the follow-up period (1.1.1998 — 31.12.2019), 131 out of 318 males with D3_SCIDA died.

Mortality risk

Mortality risk for people of age

years, who have D3_SCIDA.

N-year risk	Females	Males
1	0.107%	0.413%
5	0.81%	2.358%
10	2.497%	6.308%
15	4.631%	11.351%
20	8.111%	18.92%

Relationships between endpoints

↥

Index endpoint: D3_SCIDA – Severe combined immunodeficiency [SCID] with reticular dysgenesis

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

Severe combined immunodeficiency [SCID] with reticular dysgenesis

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)

Matched cohort

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints