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Late syphilis

EFO Endpoint Browser PheWeb

AB1_LATE_SYPHILIS

Endpoint definition

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Endpoint definition steps

FinnGen

Phenotype data

473681

1. Apply sex-specific rule

None

473681

2. Check conditions

None

473681

3. Check pre-conditions, main-only, mode, registry filters

Registry filters:

  • Hospital discharge: ICD-10 — A52
  • Hospital discharge: ICD-9 — 09[2-6]
  • Hospital discharge: ICD-8 — 09[2-6]
  • Cause of death: ICD-10 — A52
  • Cause of death: ICD-9 — 09[2-6]
  • Cause of death: ICD-8 — 09[2-6]

2 out of 7 registries used, show all original rules.

411

4. Check minimum number of events

None

411

5. Include endpoints

None

411

6. Filter based on genotype QC (FinnGen only)

386

Control definitions (FinnGen only)

Control exclude AB1_SEXUAL_TRANSMISSION

Extra metadata

Level in the ICD hierarchy 4
First used in FinnGen datafreeze DF5

Case counts by codes

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FinnGen case counts by registry codes:

generic upset plot

Upset plot

Full data table

Summary Statistics

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-FinRegistry-

Key figures

All Female Male
Number of individuals
Whole population 3066 1237 1781
Only index persons 2556 1053 1503
Unadjusted period prevalence (%)
Whole population 0.04 0.04 0.05
Only index persons 0.05 0.04 0.06
Median age at first event (years)
Whole population 56.97 58.06 56.39
Only index persons 56.43 56.95 56.07

-FinnGen-

Key figures

All Female Male
Number of individuals 386 152 234
Unadjusted period prevalence (%) 0.09 0.06 0.12
Median age at first event (years) 55.58 54.82 56.08

-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

Mortality – FinRegistry

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Association

Association between endpoint AB1_LATE_SYPHILIS and mortality.

Females

Parameter HR [95% CI] p-value
AB1_LATE_SYPHILIS 3.108 [2.42, 4.0] < 0.001
Birth year 0.998 [0.99, 1.01] 0.642

During the follow-up period (1.1.1998 — 31.12.2019), 263 out of 865 females with AB1_LATE_SYPHILIS died.

Males

Parameter HR [95% CI] p-value
AB1_LATE_SYPHILIS 3.24 [2.65, 3.97] < 0.001
Birth year 0.985 [0.97, 1.0] 0.004

During the follow-up period (1.1.1998 — 31.12.2019), 430 out of 1274 males with AB1_LATE_SYPHILIS died.

Mortality risk

Mortality risk for people of age

years, who have AB1_LATE_SYPHILIS.

N-year risk Females Males
1 0.383% 0.582%
5 1.782% 3.208%
10 4.899% 7.828%
15 9.863% 14.955%
20 16.506% 24.491%

Relationships between endpoints

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Index endpoint: AB1_LATE_SYPHILIS – Late syphilis

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
FinnGen
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