PGS Publication: PGP000175

Publication Information (EuropePMC)
Title Transethnic Genome-Wide Association Study Provides Insights in the Genetic Architecture and Heritability of Long QT Syndrome.
PubMed ID 32429735(Europe PMC)
doi 10.1161/circulationaha.120.045956
Publication Date May 20, 2020
Journal Circulation
Author(s) Lahrouchi N, Tadros R, Crotti L, Mizusawa Y, Postema PG, Beekman L, Walsh R, Hasegawa K, Barc J, Ernsting M, Turkowski KL, Mazzanti A, Beckmann BM, Shimamoto K, Diamant UB, Wijeyeratne YD, Kucho Y, Robyns T, Ishikawa T, Arbelo E, Christiansen M, Winbo A, Jabbari R, Lubitz SA, Steinfurt J, Rudic B, Loeys B, Shoemaker MB, Weeke PE, Pfeiffer R, Davies B, Andorin A, Hofman N, Dagradi F, Pedrazzini M, Tester DJ, Bos JM, Sarquella-Brugada G, Campuzano Ó, Platonov PG, Stallmeyer B, Zumhagen S, Nannenberg EA, Veldink JH, van den Berg LH, Al-Chalabi A, Shaw CE, Shaw PJ, Morrison KE, Andersen PM, Müller-Nurasyid M, Cusi D, Barlassina C, Galan P, Lathrop M, Munter M, Werge T, Ribasés M, Aung T, Khor CC, Ozaki M, Lichtner P, Meitinger T, van Tintelen JP, Hoedemaekers Y, Denjoy I, Leenhardt A, Napolitano C, Shimizu W, Schott JJ, Gourraud JB, Makiyama T, Ohno S, Itoh H, Krahn AD, Antzelevitch C, Roden DM, Saenen J, Borggrefe M, Odening KE, Ellinor PT, Tfelt-Hansen J, Skinner JR, van den Berg MP, Olesen MS, Brugada J, Brugada R, Makita N, Breckpot J, Yoshinaga M, Behr ER, Rydberg A, Aiba T, Kääb S, Priori SG, Guicheney P, Tan HL, Newton-Cheh C, Ackerman MJ, Schwartz PJ, Schulze-Bahr E, Probst V, Horie M, Wilde AA, Tanck MWT, Bezzina CR.
Released in PGS Catalog: May 28, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000768
(PRS_QT)
 PGP000175 |
Lahrouchi N et al. Circulation (2020)
 QT-interval QT interval 68
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000768/ScoringFiles/PGS000768.txt.gz

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) 		Evaluated Score 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 PGS000768
(PRS_QT)
 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 PGS000768
(PRS_QT)
 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 PGS000768
(PRS_QT)
 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 PGS000768
(PRS_QT)
 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 PGS000768
(PRS_QT)
 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 PGS000768
(PRS_QT)
 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 PGS000768
(PRS_QT)
 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 PGS000768
(PRS_QT)
 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 PGS000768
(PRS_QT)
 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 —