Polygenic Score (PGS) ID: PGS002034

Predicted Trait
Reported Trait Congenital deficiency of other clotting factors (including factor VII)
Mapped Trait(s) congenital vitamin K-dependent coagulation factors deficiency (MONDO_0015722)
Additional Trait Information hematopoietic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_286.12
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 32,552
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 75%
South Asian: 25%
4 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM011143 PSS009296|
European Ancestry|
19,864 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0563 [0.0424, 0.0702] sex, age, birth date, deprivation index, 16 PCs —
PPM011144 PSS009070|
European Ancestry|
4,108 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0533 [0.0227, 0.0838] sex, age, birth date, deprivation index, 16 PCs —
PPM011145 PSS008624|
European Ancestry|
6,613 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.046 [0.0219, 0.07] sex, age, birth date, deprivation index, 16 PCs —
PPM011146 PSS008178|
South Asian Ancestry|
6,272 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0358 [0.011, 0.0605] sex, age, birth date, deprivation index, 16 PCs —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS009070 — — 4,108 individuals — European Poland (NE Europe) UKB —
PSS008624 — — 6,613 individuals — European Italy (South Europe) UKB —
PSS009296 — — 19,864 individuals — European UK (+ Ireland) UKB —
PSS008178 — — 6,272 individuals — South Asian India (South Asia) UKB —