Polygenic Score (PGS) ID: PGS002222

Predicted Trait
Reported Trait Ever contemplated self-harm / Recent thoughts of suicide or self-harm
Mapped Trait(s) Self-injurious behavior (HP_0100716)
Additional Trait Information psychiatric disorders
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_self_harm_thoughts
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 761,279
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: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
PPM012622 PSS009488|
European Ancestry|
6,459 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever contemplated self-harm / Recent thoughts of suicide or self-harm — — Partial Correlation (partial-r): 0.0516 [0.0272, 0.076] sex, age, birth date, deprivation index, 16 PCs —
PPM012623 PSS009262|
European Ancestry|
1,242 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever contemplated self-harm / Recent thoughts of suicide or self-harm — — Partial Correlation (partial-r): 0.0807 [0.0247, 0.1362] sex, age, birth date, deprivation index, 16 PCs —
PPM012624 PSS008816|
European Ancestry|
2,261 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever contemplated self-harm / Recent thoughts of suicide or self-harm — — Partial Correlation (partial-r): 0.108 [0.0669, 0.1488] sex, age, birth date, deprivation index, 16 PCs —
PPM012626 PSS008368|
South Asian Ancestry|
818 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever contemplated self-harm / Recent thoughts of suicide or self-harm — — Partial Correlation (partial-r): 0.0771 [0.0077, 0.1457] sex, age, birth date, deprivation index, 16 PCs —
PPM012627 PSS008144|
East Asian Ancestry|
428 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever contemplated self-harm / Recent thoughts of suicide or self-harm — — Partial Correlation (partial-r): 0.063 [-0.0343, 0.1591] sex, age, birth date, deprivation index, 16 PCs —
PPM012628 PSS007932|
African Ancestry|
374 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever contemplated self-harm / Recent thoughts of suicide or self-harm — — Partial Correlation (partial-r): 0.0884 [-0.0159, 0.1909] sex, age, birth date, deprivation index, 16 PCs —
PPM012629 PSS009036|
African Ancestry|
512 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever contemplated self-harm / Recent thoughts of suicide or self-harm — — Partial Correlation (partial-r): -0.0688 [-0.1562, 0.0198] sex, age, birth date, deprivation index, 16 PCs —
PPM012625 PSS008590|
Greater Middle Eastern Ancestry|
203 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever contemplated self-harm / Recent thoughts of suicide or self-harm — — Partial Correlation (partial-r): 0.1064 [-0.0392, 0.2477] 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
PSS009036 — — 512 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009262 — — 1,242 individuals — European Poland (NE Europe) UKB —
PSS008590 — — 203 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008816 — — 2,261 individuals — European Italy (South Europe) UKB —
PSS008368 — — 818 individuals — South Asian India (South Asia) UKB —
PSS009488 — — 6,459 individuals — European UK (+ Ireland) UKB —
PSS008144 — — 428 individuals — East Asian China (East Asia) UKB —
PSS007932 — — 374 individuals — African American or Afro-Caribbean Carribean UKB —