Polygenic Score (PGS) ID: PGS000768

Predicted Trait
Reported Trait QT-interval
Mapped Trait(s) QT interval (EFO_0004682)
Released in PGS Catalog: May 28, 2021
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Score Details

Score Construction
PGS Name PRS_QT
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 68
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000175
Citation (link to publication) Lahrouchi N et al. Circulation (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
71,061 individuals (100%)
PGS Evaluation
East Asian: 33.3%
European: 33.3%
Multi-ancestry (including European): 33.3%
  • European
  • East Asian
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002500
Europe PMC: 24952745
 71,061 individuals European
(Italy,Germany)		 28 cohorts
  • AGES
  • ,ARIC
  • ,BLSA
  • ,BRIGHT
  • ,CHS
  • ,CROATIA-KORCULA
  • ,CROATIA-SPLIT
  • ,DCCT
  • ,EDIC
  • ,ERF
  • ,FHS
  • ,Health2000
  • ,HealthABC
  • ,INGI-Carlantino
  • ,INGI-FVG
  • ,KORA
  • ,LifeLines
  • ,MICROS
  • ,ORCADES
  • ,POPGEN
  • ,PREVEND
  • ,RS
  • ,SHIP
  • ,SardiNIA
  • ,TwinsUK
  • ,YFS
  • ,deCODE
  • ,eMERGE

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
PPM001976 PSS000987|
European Ancestry|
9,457 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome β: 0.322 (0.03) — Odds Ratio (OR, top 25% vs. bottom 25%): 2.27 [1.9, 2.7] PCs (1-10) —
PPM001977 PSS000987|
European Ancestry|
9,457 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome in individuals with a single rare variant in a major LQTS gene β: 0.277 (0.032) — Odds Ratio (OR, top 25% vs. bottom 25%): 2.09 [1.74, 2.51] PCs (1-10) —
PPM001978 PSS000987|
European Ancestry|
9,457 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome in individuals without a single rare variant in a major LQTS gene β: 0.733 (0.09) — Odds Ratio (OR, top 25% vs. bottom 25%): 5.0 [2.73, 9.17] PCs (1-10) —
PPM001979 PSS000988|
East Asian Ancestry|
2,089 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome β: 0.412 (0.055) — Odds Ratio (OR, top 25% vs. bottom 25%): 2.9 [2.09, 4.04] PCs (1-10) Only 60 of the 68 SNP PRS were utilised. rs17457880, rs17460657, rs4656345, rs10040989, rs9920, rs1296720, rs17763769, rs1805128 were not included due to INFO < 0.3 and rs12300631 was used as a proxy for rs3026445.
PPM001980 PSS000988|
East Asian Ancestry|
2,089 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome in individuals with a single rare variant in a major LQTS gene β: 0.384 (0.058) — Odds Ratio (OR, top 25% vs. bottom 25%): 2.41 [1.71, 3.4] PCs (1-10) Only 60 of the 68 SNP PRS were utilised. rs17457880, rs17460657, rs4656345, rs10040989, rs9920, rs1296720, rs17763769, rs1805128 were not included due to INFO < 0.3 and rs12300631 was used as a proxy for rs3026445.
PPM001981 PSS000988|
East Asian Ancestry|
2,089 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome in individuals without a single rare variant in a major LQTS gene β: 0.74 (0.129) — Odds Ratio (OR, top 25% vs. bottom 25%): 12.6 [3.28, 41.67] PCs (1-10) Only 60 of the 68 SNP PRS were utilised. rs17457880, rs17460657, rs4656345, rs10040989, rs9920, rs1296720, rs17763769, rs1805128 were not included due to INFO < 0.3 and rs12300631 was used as a proxy for rs3026445.
PPM001982 PSS000989|
Multi-ancestry (including European)|
11,546 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome β: 0.343 (0.0263) — Odds Ratio (OR, top 25% vs. bottom 25%): 2.52 [2.16, 2.94] PCs (1-10) For Japanese individuals only 60 of the 68 SNP PRS were utilised. rs17457880, rs17460657, rs4656345, rs10040989, rs9920, rs1296720, rs17763769, rs1805128 were not included due to INFO < 0.3 and rs12300631 was used as a proxy for rs3026445.
PPM001983 PSS000989|
Multi-ancestry (including European)|
11,546 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome in individuals with a single rare variant in a major LQTS gene β: 0.294 (0.028) — Odds Ratio (OR, top 25% vs. bottom 25%): 2.23 [1.9, 2.62] PCs (1-10) For Japanese individuals only 60 of the 68 SNP PRS were utilised. rs17457880, rs17460657, rs4656345, rs10040989, rs9920, rs1296720, rs17763769, rs1805128 were not included due to INFO < 0.3 and rs12300631 was used as a proxy for rs3026445.
PPM001984 PSS000989|
Multi-ancestry (including European)|
11,546 individuals
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 Reported Trait: Long QT syndrome in individuals without a single rare variant in a major LQTS gene β: 0.735 (0.0738) — Odds Ratio (OR, top 25% vs. bottom 25%): 6.13 [3.57, 10.52] PCs (1-10) For Japanese individuals only 60 of the 68 SNP PRS were utilised. rs17457880, rs17460657, rs4656345, rs10040989, rs9920, rs1296720, rs17763769, rs1805128 were not included due to INFO < 0.3 and rs12300631 was used as a proxy for rs3026445.

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
PSS000987 Cases are individuals with a clinical diagnosis of long QT syndrome. Of the 1238 cases, 1115 were genotype positive meaning they carried a single rare variant in 1 of the 3 established major LQTS genes (KCNQ1 [LQT1], KCNH2 [LQT2] and SCN5A [LQT3]). 123 cases were genotype negative meaning no rare variant was identified in genes unequivocally associated with nonsyndromic LQTS (KCNQ1, KCNH2, SCN5A, CALM1-3, and TRDN). —
[
  • 1,238 cases
  • , 8,219 controls
]
 — European — NR —
PSS000988 Cases are individuals with a clinical diagnosis of long QT syndrome. Of the 418 cases, 356 were genotype positive meaning they carried a single rare variant in 1 of the 3 established major LQTS genes (KCNQ1 [LQT1], KCNH2 [LQT2] and SCN5A [LQT3]). 62 cases were genotype negative meaning no rare variant was identified in genes unequivocally associated with nonsyndromic LQTS (KCNQ1, KCNH2, SCN5A, CALM1-3, and TRDN). —
[
  • 418 cases
  • , 1,671 controls
]
 — East Asian
(Japanese)		 — NR —
PSS000989 Cases are individuals with a clinical diagnosis of long QT syndrome. Of the 1238 cases, 1115 were genotype positive meaning they carried a single rare variant in 1 of the 3 established major LQTS genes (KCNQ1 [LQT1], KCNH2 [LQT2] and SCN5A [LQT3]). 123 cases were genotype negative meaning no rare variant was identified in genes unequivocally associated with nonsyndromic LQTS (KCNQ1, KCNH2, SCN5A, CALM1-3, and TRDN). —
[
  • 1,238 cases
  • , 8,219 controls
]
 — European — NR —
PSS000989 Cases are individuals with a clinical diagnosis of long QT syndrome. Of the 418 cases, 356 were genotype positive meaning they carried a single rare variant in 1 of the 3 established major LQTS genes (KCNQ1 [LQT1], KCNH2 [LQT2] and SCN5A [LQT3]). 62 cases were genotype negative meaning no rare variant was identified in genes unequivocally associated with nonsyndromic LQTS (KCNQ1, KCNH2, SCN5A, CALM1-3, and TRDN). —
[
  • 418 cases
  • , 1,671 controls
]
 — East Asian
(Japanese)		 — NR —