Risteys · E4_LYSOPOSTTRANS

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 — E77.0 Cause of death: ICD-10 — E77.0 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	97	47	49
Only index persons	82	41	41
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	51.52	50.78	51.58
Only index persons	53.22	52.52	53.92

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	19	12	7
Unadjusted period prevalence (%)	0.00	0.00	0.00
Median age at first event (years)	55.64	53.51	59.30

-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

(3013512) EKG study

6.77

3.84

8.0

2.4

—

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

5.81

3.33

2.5

2.1

ng/l

598.9

338.0

0.35

(1761868) Lipid panel - Serum or Plasma

5.27

2.91

4.5

2.6

—

(3041096) Erythrocytes [Presence] in Urine by Automated

4.26

2.44

5.0

2.4

—

(3012544) pH of Venous blood

7.06

2.37

4.8

4.4

—

(3007853) Bacteria identified in Skin by Aerobe culture

5.23

1.95

3.2

1.9

—

(3019198) Lymphocytes [#/volume] in Blood

3.74

1.85

8.2

5.7

e9/l

2.2

3.2

0.38

(3021589) Normoblasts [#/volume] in Blood

3.45

1.84

6.2

7.9

e9/l

0.0

0.00

(40760892) CBC W Ordered Manual Differential panel - Blood

3.43

1.80

3.5

6.1

—

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

3.35

1.76

4.8

3.1

—

(36304419) Bacteria [Presence] in Urine

3.35

1.71

3.3

2.6

—

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

2.99

1.57

8.5

3.9

—

0.0

—

(3015736) pH of Urine

2.86

1.46

4.3

2.7

—

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

2.76

1.21

1.3

1.4

mg/l

0.6

1.1

—

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

2.46

1.09

4.1

3.1

—

0.0

—

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

2.40

1.08

4.5

3.1

—

0.0

—

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

2.32

0.95

3.7

2.9

—

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

166

+∞

0.86

24.8

12.3

mmol/l

140.0

0.01

161

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

2.25

0.84

3.6

4.4

—

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

1.98

0.74

1.1

1.5

—

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

1.98

0.69

1.2

1.4

—

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

1.99

0.67

2.6

1.9

nmol/l

81.8

83.5

—

(3013115) Eosinophils [#/volume] in Blood

1.93

0.65

8.1

5.9

e9/l

0.3

0.2

1.33

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

0.00

0.64

0.0

2.5

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.64

0.0

1.2

—

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

169

+∞

0.64

25.2

12.2

mmol/l

4.0

0.37

162

(3026008) Bacteria identified in Urine by Culture

1.93

0.59

1.4

2.7

—

(3016771) Amylase [Enzymatic activity/volume] in Serum or Plasma

1.82

0.57

3.1

2.3

u/l

60.0

63.4

—

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

1.61

0.48

5.0

2.5

ug/l

76.3

114.3

—

(3006315) Basophils [#/volume] in Blood

1.66

0.48

8.6

6.1

e9/l

0.1

0.0

—

(3037467) Urinalysis macro (dipstick) panel - Urine

103

1.83

0.48

3.6

3.8

—

(3001604) Monocytes [#/volume] in Blood

1.63

0.47

8.6

6.0

e9/l

0.5

0.6

—

(3023368) Bacteria identified in Blood by Culture

1.76

0.47

8.2

3.8

—

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

0.00

0.43

0.0

1.8

—

(4035726)

0.00

0.43

0.0

1.3

—

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

1.62

0.41

2.7

2.2

umol/l

301.5

345.8

—

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

1.44

0.24

9.7

5.3

ug/l

1.4

1.8

—

(40761535) Cells panel - Urine sediment

0.00

0.22

0.0

4.4

—

(36660697) Celiac disease serology panel - Serum

0.00

0.22

0.0

1.1

—

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

0.00

0.22

0.0

1.2

—

(4010399)

0.00

0.21

0.0

1.2

—

(40761536) Microorganisms panel - Urine sediment

0.00

0.21

0.0

2.4

—

(42870588) Differential panel, method unspecified - Blood

1.13

0.10

13.0

5.9

—

(3044889) 12 lead EKG panel

119

1.29

0.09

3.5

3.6

—

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

110

1.25

0.09

4.0

3.0

u/l

87.5

46.8

0.94

103

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

1.23

0.09

3.9

2.7

—

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

0.00

0.0

1.3

—

0.2

—

(3047181) Lactate [Moles/volume] in Blood

0.00

0.0

5.7

—

1.2

—

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

0.00

0.0

1.7

—

40.9

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.0

1.0

—

(3027008) Opiates [Presence] in Urine

0.00

0.0

1.0

—

(3016879) Cocaine [Presence] in Urine

0.00

0.0

1.0

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.0

1.0

—

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

0.00

0.0

1.4

—

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

0.00

0.0

1.3

—

1.1

—

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

0.00

0.0

1.3

—

(3029338) Protein.monoclonal band 3 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

1.5

—

0.0

—

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

0.00

0.0

1.0

—

(3044640) Blood type and Crossmatch panel - Blood

1.09

0.00

2.0

2.1

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.0

1.0

—

(42529406) Shigella sp [Presence] in Stool by Culture

0.00

0.0

1.6

—

(3039000) Anion gap in Blood

0.00

0.0

6.2

—

9.6

—

(3006418) Campylobacter sp identified in Tissue by Organism specific culture

0.00

0.0

1.6

—

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

0.00

0.0

1.0

—

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

0.00

0.0

1.2

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.0

1.2

—

(3042111) Morphology [Interpretation] in Bone marrow Narrative

0.00

0.0

2.5

—

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

0.00

0.0

1.4

—

(3012336) Haptoglobin [Mass/volume] in Serum or Plasma

0.00

0.0

6.4

—

1.0

—

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

1.10

0.00

11.4

3.9

g/l

37.7

36.1

—

(3013707) Erythrocyte sedimentation rate by Westergren method

125

1.13

0.00

9.3

4.2

mm/h

16.1

10.3

0.52

113

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

104

0.92

0.00

10.4

9.9

e9/l

4.0

3.6

—

(1002224) Polysomnography panel

0.00

0.0

1.3

—

(3013527) Hepatitis B virus core IgM Ab [Presence] in Serum

0.00

0.0

1.2

—

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

0.00

0.0

1.7

—

(3029379) Protein.monoclonal band 4 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

1.5

—

0.0

—

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

0.00

0.0

1.6

—

(3014765) Yersinia sp identified in Stool by Organism specific culture

0.00

0.0

1.6

—

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

0.00

0.0

1.0

—

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

0.00

0.0

1.4

—

(3018572) Chloride [Moles/volume] in Blood

0.00

0.0

6.2

—

106.4

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.5

—

0.0

—

Mortality – FinRegistry

↥

Association

Association between endpoint E4_LYSOPOSTTRANS and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have E4_LYSOPOSTTRANS.

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: E4_LYSOPOSTTRANS – Defects in post-translational modification of lysosomal enzymes

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	E4_LYSOPOSTTRANS
CONTROL_EXCLUDE	E4_METABOLIA
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	E770
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	E770
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

Defects in post-translational modification of lysosomal enzymes

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