Linear scleroderma

L12_LINEARSCLERODERMA

scleroderma: Scleroderma is a rare autoimmune connective tissue disorder characterized by abnormal hardening of the skin and, sometimes, other organs. It is classified into two main forms: localized scleroderma and systemic sclerosis (SSc), the latter comprising three subsets; diffuse cutaneous SSc (dcSSc), limited cutaneous SSc (lcSSc) and limited SSc (lSSc) (see these terms).

Suggest a new description

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 — L94.1 Cause of death: ICD-10 — L94.1 2 out of 7 registries used, show all original rules.	37
4. Check minimum number of events None	37
5. Include endpoints None	37
6. Filter based on genotype QC (FinnGen only)	37

Control definitions (FinnGen only)

Control exclude: L12_OTHERSKINSUBCUTIS

Extra metadata

Level in the ICD hierarchy: 4
First used in FinnGen datafreeze: DF2
Parent code in ICD-10: L94
Name in latin: Scleroderma lineare

NAME	L12_LINEARSCLERODERMA
CONTROL_EXCLUDE	L12_OTHERSKINSUBCUTIS
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	L941
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	L941
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 Linear scleroderma 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	272	202	69
Only index persons	260	193	67
Unadjusted period prevalence (%)
Whole population	0.00	0.01	0.00
Only index persons	0.01	0.01	0.00
Median age at first event (years)
Whole population	40.43	43.60	31.61
Only index persons	39.50	42.25	31.61

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	37	29	8
Unadjusted period prevalence (%)	0.01	0.01	0.00
Median age at first event (years)	40.52	39.79	43.18

-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

(3022096) Basophils/100 leukocytes in Blood

142

4.98

4.81

5.8

4.5

0.7

0.02

128

(3015171) Extractable nuclear Ab [Units/volume] in Serum

12.31

4.78

1.4

1.6

—

(3006504) Eosinophils/100 leukocytes in Blood

143

4.92

4.77

5.9

4.7

2.1

2.9

1.15

130

(3018010) Neutrophils/100 leukocytes in Blood

146

4.76

4.46

5.5

4.6

59.3

56.0

0.66

135

(3019069) Monocytes/100 leukocytes in Blood

147

4.70

4.44

6.0

4.8

8.0

7.9

0.08

134

(3002030) Lymphocytes/100 leukocytes in Blood

150

4.55

4.34

6.1

4.6

29.0

29.7

0.12

136

(42870588) Differential panel, method unspecified - Blood

4.13

4.29

5.3

4.1

—

(3021589) Normoblasts [#/volume] in Blood

131

3.80

3.60

9.5

8.4

0.0

e9/l

0.00

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

141

3.38

3.02

4.8

4.7

0.0

estimate

—

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

9.37

2.83

1.8

1.3

—

(3018095) Leukocytes [#/volume] in Urine

3.01

2.69

5.4

4.3

12.5

19.8

e6/l

0.29

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

6.26

2.65

3.3

2.0

—

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

140

3.03

2.60

3.5

3.3

0.0

estimate

—

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

140

3.03

2.60

3.5

3.2

0.0

estimate

—

(40768443) Skin Pathology biopsy report

7.00

2.45

1.4

1.3

—

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

7.00

2.45

2.6

1.6

—

(40758558) Short blood count panel - Blood

2.97

2.38

4.6

5.6

—

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

6.21

2.29

2.4

1.1

1.3

1.1

g/l

—

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

6.21

2.29

2.4

1.1

0.3

0.2

g/l

—

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

4.06

2.18

1.9

1.3

—

(3025159) Blasts/100 leukocytes in Blood

4.26

2.02

2.0

5.7

—

0.0

—

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

109

2.53

1.97

2.8

1.7

94.4

102.8

pmol/l

—

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

222

2.85

1.90

7.5

6.6

78.7

78.9

u/l

0.01

208

(36304419) Bacteria [Presence] in Urine

2.61

1.90

3.8

3.0

—

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

2.52

1.88

4.3

3.2

—

(3021440) Promyelocytes/100 leukocytes in Blood

3.77

1.83

2.0

5.2

—

0.0

—

(3017181) Myelocytes/100 leukocytes in Blood

3.77

1.83

2.0

5.2

—

0.3

—

(40761536) Microorganisms panel - Urine sediment

3.77

1.83

5.5

2.8

—

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

135

2.28

1.60

3.9

6.0

1.3

1.2

mmol/l

1.02

108

(3022250) Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma by Lactate to pyruvate reaction

3.05

1.50

1.2

3.5

344.7

222.7

u/l

—

(3015736) pH of Urine

111

2.21

1.49

2.3

3.2

—

(3002256) Pathology report gross observation

2.73

1.47

1.3

1.2

—

(3044889) 12 lead EKG panel

191

2.22

1.34

3.9

3.3

—

(3013721) Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma

2.15

1.34

4.4

2.8

25.9

32.0

u/l

1.05

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

2.21

1.27

2.3

3.0

—

(3041096) Erythrocytes [Presence] in Urine by Automated

2.17

1.27

4.1

3.0

—

(40760892) CBC W Ordered Manual Differential panel - Blood

2.06

1.14

2.8

4.5

—

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

2.59

1.13

1.0

1.5

—

(3026008) Bacteria identified in Urine by Culture

1.89

0.96

3.4

2.7

—

(3044640) Blood type and Crossmatch panel - Blood

1.90

0.94

2.5

2.1

—

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

1.87

0.90

2.0

2.2

51.6

54.9

u/l

0.17

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

2.11

0.89

3.3

2.1

—

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

103

1.77

0.82

4.0

3.1

—

(3004716) Salmonella sp identified in Stool by Organism specific culture

0.00

0.82

0.0

1.4

—

(3023368) Bacteria identified in Blood by Culture

1.84

0.74

4.1

3.7

—

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

1.90

0.69

2.4

1.3

—

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

205

1.68

0.67

4.2

2.7

36.9

41.8

u/l

0.22

196

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

1.83

0.66

2.4

1.3

—

(3032080) INR in Blood by Coagulation assay

100

1.64

0.64

3.1

5.7

1.1

inr

—

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

1.61

0.62

1.5

1.7

336.5

430.0

pmol/l

—

(4035726)

1.85

0.61

1.3

1.4

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.85

0.61

1.5

—

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

0.00

0.42

0.0

1.5

—

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

0.00

0.42

0.0

1.9

—

(40768804) Tissue Pathology biopsy report

131

0.68

0.40

2.0

1.7

—

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

120

1.42

0.38

5.0

3.8

36.0

36.1

g/l

0.02

112

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

1.51

0.38

2.8

1.3

—

(40768797) Stomach Pathology biopsy report

1.47

0.37

1.3

1.2

—

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

1.26

0.28

1.1

1.7

—

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

225

1.34

0.28

3.9

3.5

—

(3004789) Transferrin [Mass/volume] in Serum or Plasma

1.36

0.24

3.0

2.1

2.4

2.6

g/l

—

(3042936) Bacteria identified in Isolate by Culture

1.33

0.24

2.0

1.6

—

(3024889) Methemoglobin/Hemoglobin.total in Venous blood

0.00

0.22

0.0

3.1

—

0.5

—

(3027545) Mycoplasma pneumoniae Ab [Presence] in Serum by Immunoassay

0.00

0.22

0.0

1.5

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

0.00

0.22

0.0

3.1

—

0.9

—

(3004119) Hemoglobin [Mass/volume] in Venous blood

0.00

0.22

0.0

3.1

—

129.8

—

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

0.00

0.22

0.0

2.0

—

(3010521) Mycoplasma pneumoniae IgM Ab [Presence] in Serum by Immunoassay

0.00

0.22

0.0

1.1

—

(3008898) HLA-B27 [Presence]

0.00

0.21

0.0

1.0

—

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

0.00

0.21

0.0

1.5

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.21

0.0

1.5

—

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

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.2

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.21

0.0

1.5

—

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

0.00

0.21

0.0

1.5

—

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

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.5

—

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

0.00

0.21

0.0

1.5

—

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

0.00

0.21

0.0

1.2

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.20

0.0

1.8

—

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

140

1.25

0.19

3.0

3.8

—

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

0.75

0.17

1.8

1.3

—

(1761868) Lipid panel - Serum or Plasma

112

1.25

0.17

2.8

2.7

—

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

1.24

0.15

3.4

3.3

12.5

48.1

ng/l

—

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

1.16

0.09

1.6

2.1

—

(3013512) EKG study

1.08

0.08

5.9

3.9

—

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

0.83

0.08

1.7

1.8

—

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

1.08

0.08

1.2

1.6

—

(3010726) Horse dander IgE Ab [Units/volume] in Serum

0.00

0.0

1.0

—

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

0.00

0.0

1.2

—

(4306422)

0.00

0.0

1.0

—

(3003740) Influenza virus B Ag [Presence] in Specimen

0.00

0.0

1.3

—

(3027273) Bicarbonate [Moles/volume] in Venous blood

0.00

0.0

2.4

—

22.9

—

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

0.00

0.0

1.8

—

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

0.00

0.0

1.0

—

(3024928) Oxygen saturation in Venous blood

0.00

0.0

5.2

—

(3032155) Metanephrine Free [Moles/volume] in Serum or Plasma

0.00

0.0

1.6

—

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

0.00

0.0

2.0

—

(3025018) Bordetella pertussis Ab [Titer] in Serum

0.00

0.0

1.2

—

(3005136) Cladosporium herbarum IgE Ab [Units/volume] in Serum

0.00

0.0

1.0

—

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

0.00

0.0

1.7

—

(42529200) Cancer Ag 15-3 [Units/volume] in Serum or Plasma by Immunoassay

0.00

0.0

4.3

—

141.6

—

(3020287) Protein C actual/normal in Platelet poor plasma by Coagulation assay

0.00

0.0

1.0

—

114.3

—

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

0.98

0.00

1.4

2.3

—

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

0.00

0.0

9.2

—

727.2

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.9

—

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

0.00

0.0

1.5

—

(3025130) Human papilloma virus identified in Specimen

0.00

0.0

2.8

—

(3020891) Body temperature

0.00

0.0

3.3

—

(3002523) Influenza virus A Ag [Presence] in Specimen

0.00

0.0

1.3

—

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

0.00

0.0

1.2

—

(3005082) Progesterone [Moles/volume] in Serum or Plasma

0.00

0.0

1.0

—

24.5

—

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

0.00

0.0

3.2

—

(3020059) Calcium [Moles/volume] corrected for albumin in Serum or Plasma

0.96

0.00

1.8

3.1

2.3

2.4

mmol/l

—

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

0.00

0.0

15.0

—

1388.0

—

(3028626) Oxygen [Partial pressure] in Capillary blood

0.00

0.0

2.0

—

9.1

—

(3012413) Glucose [Moles/volume] in Serum or Plasma --2 hours post meal

0.00

0.0

1.6

—

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

0.94

0.00

1.2

1.7

—

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

0.00

-0.00

0.0

1.6

—

0.5

—

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

0.00

-0.00

0.0

2.9

—

10.6

—

(3018405) Lactate [Moles/volume] in Arterial blood

0.00

-0.00

0.0

9.4

—

1.2

—

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

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

2.1

—

48.9

—

Mortality – FinRegistry

↥

Association

Association between endpoint L12_LINEARSCLERODERMA and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have L12_LINEARSCLERODERMA.

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: L12_LINEARSCLERODERMA – Linear scleroderma

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

Linear scleroderma

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