PGS Publication: PGP000088

Publication Information (EuropePMC)
Title Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses.
PubMed ID 32424353(Europe PMC)
doi 10.1038/s41588-020-0609-2
Publication Date May 18, 2020
Journal Nat Genet
Author(s) Zhang H, Ahearn TU, Lecarpentier J, Barnes D, Beesley J, Qi G, Jiang X, O'Mara TA, Zhao N, Bolla MK, Dunning AM, Dennis J, Wang Q, Ful ZA, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Arun BK, Auer PL, Azzollini J, Barrowdale D, Becher H, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bialkowska K, Blanco A, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Bondavalli D, Borg A, Brauch H, Brenner H, Briceno I, Broeks A, Brucker SY, Brüning T, Burwinkel B, Buys SS, Byers H, Caldés T, Caligo MA, Calvello M, Campa D, Castelao JE, Chang-Claude J, Chanock SJ, Christiaens M, Christiansen H, Chung WK, Claes KBM, Clarke CL, Cornelissen S, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Devilee P, Diez O, Domchek SM, Dörk T, Dwek M, Eccles DM, Ekici AB, Evans DG, Fasching PA, Figueroa J, Foretova L, Fostira F, Friedman E, Frost D, Gago-Dominguez M, Gapstur SM, Garber J, García-Sáenz JA, Gaudet MM, Gayther SA, Giles GG, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Gronwald J, Guénel P, Häberle L, Hahnen E, Haiman CA, Hake CR, Hall P, Hamann U, Harkness EF, Heemskerk-Gerritsen BAM, Hillemanns P, Hogervorst FBL, Holleczek B, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Howell A, Huebner H, Hulick PJ, Imyanitov EN, kConFab Investigators, ABCTB Investigators, Isaacs C, Izatt L, Jager A, Jakimovska M, Jakubowska A, James P, Janavicius R, Janni W, John EM, Jones ME, Jung A, Kaaks R, Kapoor PM, Karlan BY, Keeman R, Khan S, Khusnutdinova E, Kitahara CM, Ko YD, Konstantopoulou I, Koppert LB, Koutros S, Kristensen VN, Laenkholm AV, Lambrechts D, Larsson SC, Laurent-Puig P, Lazaro C, Lazarova E, Lejbkowicz F, Leslie G, Lesueur F, Lindblom A, Lissowska J, Lo WY, Loud JT, Lubinski J, Lukomska A, MacInnis RJ, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Matricardi L, McGuffog L, McLean C, Mebirouk N, Meindl A, Menon U, Miller A, Mingazheva E, Montagna M, Mulligan AM, Mulot C, Muranen TA, Nathanson KL, Neuhausen SL, Nevanlinna H, Neven P, Newman WG, Nielsen FC, Nikitina-Zake L, Nodora J, Offit K, Olah E, Olopade OI, Olsson H, Orr N, Papi L, Papp J, Park-Simon TW, Parsons MT, Peissel B, Peixoto A, Peshkin B, Peterlongo P, Peto J, Phillips KA, Piedmonte M, Plaseska-Karanfilska D, Prajzendanc K, Prentice R, Prokofyeva D, Rack B, Radice P, Ramus SJ, Rantala J, Rashid MU, Rennert G, Rennert HS, Risch HA, Romero A, Rookus MA, Rübner M, Rüdiger T, Saloustros E, Sampson S, Sandler DP, Sawyer EJ, Scheuner MT, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schöttker B, Schürmann P, Senter L, Sharma P, Sherman ME, Shu XO, Singer CF, Smichkoska S, Soucy P, Southey MC, Spinelli JJ, Stone J, Stoppa-Lyonnet D, EMBRACE Study, GEMO Study Collaborators, Swerdlow AJ, Szabo CI, Tamimi RM, Tapper WJ, Taylor JA, Teixeira MR, Terry M, Thomassen M, Thull DL, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Torres D, Troester MA, Truong T, Tung N, Untch M, Vachon CM, van den Ouweland AMW, van der Kolk LE, van Veen EM, vanRensburg EJ, Vega A, Wappenschmidt B, Weinberg CR, Weitzel JN, Wildiers H, Winqvist R, Wolk A, Yang XR, Yannoukakos D, Zheng W, Zorn KK, Milne RL, Kraft P, Simard J, Pharoah PDP, Michailidou K, Antoniou AC, Schmidt MK, Chenevix-Trench G, Easton DF, Chatterjee N, García-Closas M.
Released in PGS: July 14, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000212 PRS330_LumA PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (luminal A-like) breast tumor luminal 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000212/ScoringFiles/PGS000212.txt.gz
PGS000213 PRS330_LumBHER2neg PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like) Her2-receptor negative breast cancer 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000213/ScoringFiles/PGS000213.txt.gz
PGS000214 PRS330_LumB PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (luminal B-like) breast tumor luminal 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000214/ScoringFiles/PGS000214.txt.gz
PGS000215 PRS330_HER2 PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (HER2-enriched-like) HER2 Positive Breast Carcinoma 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000215/ScoringFiles/PGS000215.txt.gz
PGS000216 PRS330_TN PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (triple negative) triple-negative breast cancer 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000216/ScoringFiles/PGS000216.txt.gz

External PGS Evaluated By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000004 PRS313_BC PGP000002
Mavaddat N et al. Am J Hum Genet (2018)
Breast Cancer breast carcinoma 313 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.txt.gz
PGS000005 PRS313_ERpos PGP000002
Mavaddat N et al. Am J Hum Genet (2018)
ER-positive Breast Cancer estrogen-receptor positive breast cancer 313 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000005/ScoringFiles/PGS000005.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000663 PGS000005 (PRS313_ERpos) PSS000363 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (triple negative) OR: 1.59[1.51, 1.66] AUROC: 0.6276
PPM000662 PGS000004 (PRS313_BC) PSS000363 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (triple negative) OR: 1.38[1.31, 1.44] AUROC: 0.5877
PPM000661 PGS000216 (PRS330_TN) PSS000363 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (triple negative) OR: 1.65[1.57, 1.73] AUROC: 0.6358
PPM000660 PGS000005 (PRS313_ERpos) PSS000359 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (HER2-enriched-like) OR: 1.59[1.48, 1.71] AUROC: 0.6291
PPM000659 PGS000004 (PRS313_BC) PSS000359 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (HER2-enriched-like) OR: 1.49[1.38, 1.6] AUROC: 0.6093
PPM000658 PGS000215 (PRS330_HER2) PSS000359 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (HER2-enriched-like) OR: 1.53[1.42, 1.65] AUROC: 0.6208
PPM000657 PGS000005 (PRS313_ERpos) PSS000362 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal B-like) OR: 1.66[1.58, 1.75] AUROC: 0.64
PPM000656 PGS000004 (PRS313_BC) PSS000362 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal B-like) OR: 1.68[1.6, 1.77] AUROC: 0.6432
PPM000655 PGS000214 (PRS330_LumB) PSS000362 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (luminal B-like) OR: 1.69[1.61, 1.77] AUROC: 0.6431
PPM000654 PGS000005 (PRS313_ERpos) PSS000361 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like) OR: 1.62[1.54, 1.7] AUROC: 0.6323
PPM000653 PGS000004 (PRS313_BC) PSS000361 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like) OR: 1.62[1.55, 1.71] AUROC: 0.6336
PPM000652 PGS000213 (PRS330_LumBHER2neg) PSS000361 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like) OR: 1.62[1.54, 1.7] AUROC: 0.633
PPM000651 PGS000005 (PRS313_ERpos) PSS000360 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal A-like) OR: 1.82[1.77, 1.87] AUROC: 0.6595
PPM000650 PGS000004 (PRS313_BC) PSS000360 PGP000088
Zhang H et al. (2020)
Ext.
Reported Trait: Breast cancer intrinsic-like subtype (luminal A-like) OR: 1.8[1.75, 1.86] AUROC: 0.6573
PPM000649 PGS000212 (PRS330_LumA) PSS000360 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (luminal A-like) OR: 1.83[1.78, 1.88] AUROC: 0.6609

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000359 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (4) HER2-enriched-like (ER- and PR-, HER2+)
[
  • 718 cases
  • , 20,815 controls
]
,
0.0 % Male samples
European 6 cohorts
  • BCAC
  • ,MMHS
  • ,PLCO
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data
PSS000360 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (1) luminal A-like (ER+ and/or PR+, HER2-, grade 1 & 2); 
[
  • 7,325 cases
  • , 20,815 controls
]
,
0.0 % Male samples
European 6 cohorts
  • BCAC
  • ,MMHS
  • ,PLCO
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data
PSS000361 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (2) luminal B/HER2-negative-like (ER+ and/or PR+, HER2-, grade 3)
[
  • 1,779 cases
  • , 20,815 controls
]
,
0.0 % Male samples
European 6 cohorts
  • BCAC
  • ,MMHS
  • ,PLCO
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data
PSS000362 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (3) luminal B-like (ER+ and/or PR+, HER2+); 
[
  • 1,682 cases
  • , 20,815 controls
]
,
0.0 % Male samples
European 6 cohorts
  • BCAC
  • ,MMHS
  • ,PLCO
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data
PSS000363 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (5) triple-negative ( ER-, PR-, HER2-). 
[
  • 2,006 cases
  • , 20,815 controls
]
,
0.0 % Male samples
European 6 cohorts
  • BCAC
  • ,MMHS
  • ,PLCO
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data