Publication Information (EuropePMC) | |
Title | Polygenic hazard score predicts aggressive and fatal prostate cancer in multi-ethnic populations |
doi | 10.1101/19012237 |
Publication Date | Nov. 19, 2019 |
Journal | medRxiv Preprint |
Author(s) | Huynh-Le M, Fan CC, Karunamuni R, Martinez ME, Eeles RA, Kote-Jarai Z, Muir K, Schleutker J, Pashayan N, Batra J, Grönberg H, Neal DE, Donovan J, Hamdy FC, Martin RM, Nielsen SF, Nordestgaard BG, Wiklund F, Tangen CM, Giles GG, Wolk A, Albanes D, Haiman CA, Travis RC, Blot WJ, Zheng W, Sanderson M, Stanford JL, Mucci LA, West CML, Kibel AS, Cussenot O, Berndt SI, Koutros S, Sørensen KD, Cybulski C, Grindedal EM, Menegaux F, Khaw K, Park JY, Ingles SA, Maier C, Hamilton RJ, Thibodeau SN, Rosenstein BS, Lu Y, Watya S, Vega A, Kogevinas M, Penney KL, Huff C, Teixeira MR, Multigner L, Leach RJ, Cannon-Albright L, Brenner H, John EM, Kaneva R, Logothetis CJ, Neuhausen SL, De Ruyck K, Pandha H, Razack A, Newcomb LF, Fowke J, Gamulin M, Usmani N, Claessens F, Gago-Dominguez M, Townsend PA, Bush WS, Srivastava S, Roobol M, Parent M, Hu JJ, Mills IG, Andreassen OA, Dale AM, Seibert TM, UKGPCS collaborators, APCB (Australian Prostate Cancer BioResource), NC-LA PCaP Investigators, The IMPACT Study Steering Committee and Collaborators, Canary P ASS Investigators, The Profile Study Steering Committee, The PRACTICAL Consortium. |
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000067 (PCa_PHS) |
PGP000047 | Seibert TM et al. BMJ (2018) |
Prostate cancer | prostate carcinoma | 54 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000067/ScoringFiles/PGS000067.txt.gz |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM000393 | PGS000067 (PCa_PHS) |
PSS000221| African Ancestry| 4,437 individuals |
PGP000058 | Huynh-Le M et al. medRxiv (2019) |Ext.|Pre |
Reported Trait: Age of aggressive prostate cancer onset | — | — | Hazard Ratio (HR; top 20% vs. rest): 2.4 [2.3, 2.6] | — | Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94). |
PPM000392 | PGS000067 (PCa_PHS) |
PSS000222| Additional Asian Ancestries| 1,901 individuals |
PGP000058 | Huynh-Le M et al. medRxiv (2019) |Ext.|Pre |
Reported Trait: Age of aggressive prostate cancer onset | — | — | Hazard Ratio (HR; top 20% vs. rest): 5.2 [4.8, 5.6] | — | Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94). |
PPM000391 | PGS000067 (PCa_PHS) |
PSS000223| European Ancestry| 50,656 individuals |
PGP000058 | Huynh-Le M et al. medRxiv (2019) |Ext.|Pre |
Reported Trait: Age of aggressive prostate cancer onset | — | — | Hazard Ratio (HR; top 20% vs. rest): 5.6 [5.2, 6.0] | — | Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94). |
PPM000390 | PGS000067 (PCa_PHS) |
PSS000220| Multi-ancestry (including European)| 56,994 individuals |
PGP000058 | Huynh-Le M et al. medRxiv (2019) |Ext.|Pre |
Reported Trait: Age of aggressive prostate cancer onset | — | — | Hazard Ratio (HR; top 20% vs. rest): 5.9 [5.5, 6.3] | — | Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94). |
PPM000394 | PGS000067 (PCa_PHS) |
PSS000224| Multi-ancestry (including European)| 34,558 individuals |
PGP000058 | Huynh-Le M et al. medRxiv (2019) |Ext.|Pre |
Reported Trait: Age of prostate cancer death | — | — | Hazard Ratio (HR; top 20% vs. rest): 5.7 [4.6, 7.0] | — | Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94). |
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 |
---|---|---|---|---|---|---|---|---|
PSS000220 | Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases | — | [ ,
100.0 % Male samples |
— | European, East Asian, African American or Afro-Caribbean, Oceanian, Hispanic or Latin American, South Asian, African unspecified, NR | Combined analysis of multiple ancestries, including: European, East Asian, African American, Hawaiian, Hispanic American, South Asian, Black African, Black Caribbean, and Other (not specified) | OncoArray_Prostate | List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1 |
PSS000221 | Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases | — | [ ,
100.0 % Male samples |
— | African unspecified | Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop | OncoArray_Prostate | List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1 |
PSS000222 | Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases | — | [ ,
100.0 % Male samples |
— | Asian unspecified | Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop | OncoArray_Prostate | List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1 |
PSS000223 | Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases | — | [ ,
100.0 % Male samples |
— | European | Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop | OncoArray_Prostate | List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1 |
PSS000224 | Age at death due to prostate cancer. | — | [ ,
100.0 % Male samples |
Mean = 70.0 years IQR = [63.0, 76.0] years |
European, East Asian, African American or Afro-Caribbean, Oceanian, Hispanic or Latin American, South Asian, African unspecified, NR | Combined analysis of multiple ancestries, including: European, East Asian, African American, Hawaiian, Hispanic American, South Asian, Black African, Black Caribbean, and Other (not specified) | OncoArray_Prostate | List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1 |