African-specific improvement of a polygenic hazard score for age at diagnosis of prostate cancer
Roshan A. Karunamuni
(1)
,
Minh-Phuong Huynh-Le
(1)
,
Chun C Fan
(2)
,
W T Thompson
(1)
,
Rosalind A. Eeles
(3, 4)
,
Zsofia Kote-Jarai
(4)
,
Kenneth Muir
(5, 6)
,
Artitaya Lophatananon
(5)
,
Catherine M. Tangen
(7)
,
Phyllis J. Goodman
(7)
,
Ian M. Thompson
,
William J. Blot
(8, 9)
,
Wei Zheng
(8)
,
Adam S. Kibel
(10)
,
Bettina F. Drake
(11)
,
Olivier Cussenot
(12)
,
Géraldine Cancel-Tassin
(12)
,
Florence Menegaux
(13, 14)
,
Thérèse Truong
(13, 14)
,
Jong Y. Park
(15)
,
Hui-Yi Lin
(16)
,
Jeannette T. Bensen
(17)
,
Elizabeth T. H. Fontham
(16)
,
James L. Mohler
(17)
,
Jack A Taylor
(18)
,
Luc Multigner
(19)
,
Pascal Blanchet
(19)
,
Laurent Brureau
(19)
,
Marc Romana
(20)
,
Robin J Leach
(21)
,
Esther M. John
(22)
,
Jay Fowke
(8, 23)
,
William S. Bush
(24)
,
Melinda Aldrich
(8)
,
Dana C. Crawford
(24)
,
Shiv Srivastava
(9)
,
Jennifer C. Cullen
(9)
,
Gyorgy Petrovics
(9)
,
Marie-Elise Parent
(25, 26)
,
Jennifer J. Hu
(27)
,
Maureen Sanderson
,
Ian G. Mills
(28)
,
Ole A. Andreassen
(29)
,
Anders M. Dale
(1)
,
Tyler M. Seibert
(1)
1
UC San Diego -
University of California [San Diego]
2 Healthlytix [San Diego]
3 The Royal Marsden
4 The institute of cancer research [London]
5 University of Manchester [Manchester]
6 University of Warwick [Coventry]
7 FHCRC - Fred Hutchinson Cancer Research Center [Seattle]
8 VUSE - Vanderbilt University School of Engineering [Nashville]
9 GeneDx [Gaithersburg, MD, USA]
10 BWH - Brigham & Women’s Hospital [Boston]
11 WUSTL - Washington University in Saint Louis
12 Hôpital Cochin [AP-HP]
13 UVSQ - Université de Versailles Saint-Quentin-en-Yvelines
14 CESP - Centre de recherche en épidémiologie et santé des populations
15 H. Lee Moffitt Cancer Center and Research Institute
16 LSU - Louisiana State University
17 UNC - University of North Carolina [Chapel Hill]
18 NIEHS-NIH - National Institute of Environmental Health Sciences [Durham, NC, USA]
19 Irset - Institut de recherche en santé, environnement et travail
20 BIGR (UMR_S_1134 / U1134) - Biologie Intégrée du Globule Rouge
21 UTSA - The University of Texas at San Antonio
22 Stanford University
23 Vanderbilt University [Nashville]
24 Case Western Reserve University [Cleveland]
25 eResearch Collaboratory [Quebec City]
26 McGill University = Université McGill [Montréal, Canada]
27 UMMSM - University of Miami Leonard M. Miller School of Medicine
28 School of Medicine, Dentistry and Biomedical Sciences [Belfast]
29 UiO - University of Oslo
2 Healthlytix [San Diego]
3 The Royal Marsden
4 The institute of cancer research [London]
5 University of Manchester [Manchester]
6 University of Warwick [Coventry]
7 FHCRC - Fred Hutchinson Cancer Research Center [Seattle]
8 VUSE - Vanderbilt University School of Engineering [Nashville]
9 GeneDx [Gaithersburg, MD, USA]
10 BWH - Brigham & Women’s Hospital [Boston]
11 WUSTL - Washington University in Saint Louis
12 Hôpital Cochin [AP-HP]
13 UVSQ - Université de Versailles Saint-Quentin-en-Yvelines
14 CESP - Centre de recherche en épidémiologie et santé des populations
15 H. Lee Moffitt Cancer Center and Research Institute
16 LSU - Louisiana State University
17 UNC - University of North Carolina [Chapel Hill]
18 NIEHS-NIH - National Institute of Environmental Health Sciences [Durham, NC, USA]
19 Irset - Institut de recherche en santé, environnement et travail
20 BIGR (UMR_S_1134 / U1134) - Biologie Intégrée du Globule Rouge
21 UTSA - The University of Texas at San Antonio
22 Stanford University
23 Vanderbilt University [Nashville]
24 Case Western Reserve University [Cleveland]
25 eResearch Collaboratory [Quebec City]
26 McGill University = Université McGill [Montréal, Canada]
27 UMMSM - University of Miami Leonard M. Miller School of Medicine
28 School of Medicine, Dentistry and Biomedical Sciences [Belfast]
29 UiO - University of Oslo
Ian M. Thompson
- Fonction : Auteur
Wei Zheng
- Fonction : Auteur
- PersonId : 756070
- ORCID : 0000-0003-1226-070X
Florence Menegaux
- Fonction : Auteur
- PersonId : 852869
- IdHAL : florence-menegaux
Thérèse Truong
- Fonction : Auteur
- PersonId : 989756
- IdHAL : therese-truong
Luc Multigner
- Fonction : Auteur
- PersonId : 181193
- IdHAL : luc-multigner
- ORCID : 0000-0003-3205-8568
- IdRef : 155909010
Pascal Blanchet
- Fonction : Auteur
- PersonId : 874252
Marc Romana
- Fonction : Auteur
- PersonId : 178737
- IdHAL : marc-romana
- ORCID : 0000-0002-8715-9836
- IdRef : 149209827
Jennifer J. Hu
- Fonction : Auteur
- PersonId : 1079035
Maureen Sanderson
- Fonction : Auteur
Résumé
Polygenic hazard score (PHS) models are associated with age at diagnosis of prostate cancer. Our model developed in Europeans (PHS46) showed reduced performance in men with African genetic ancestry. We used a cross-validated search to identify single nucleotide polymorphisms (SNPs) that might improve performance in this population. Anonymized genotypic data were obtained from the PRACTICAL consortium for 6253 men with African genetic ancestry. Ten iterations of a 10-fold cross-validation search were conducted to select SNPs that would be included in the final PHS46+African model. The coefficients of PHS46+African were estimated in a Cox proportional hazards framework using age at diagnosis as the dependent variable and PHS46, and selected SNPs as predictors. The performance of PHS46 and PHS46+African was compared using the same cross-validated approach. Three SNPs (rs76229939, rs74421890 and rs5013678) were selected for inclusion in PHS46+African. All three SNPs are located on chromosome 8q24. PHS46+African showed substantial improvements in all performance metrics measured, including a 75% increase in the relative hazard of those in the upper 20% compared to the bottom 20% (2.47-4.34) and a 20% reduction in the relative hazard of those in the bottom 20% compared to the middle 40% (0.65-0.53). In conclusion, we identified three SNPs that substantially improved the association of PHS46 with age at diagnosis of prostate cancer in men with African genetic ancestry to levels comparable to Europeans.
Format du dépôt | Fichier |
---|---|
Type de dépôt | Article dans une revue |
Résumé |
en
Polygenic hazard score (PHS) models are associated with age at diagnosis of prostate cancer. Our model developed in Europeans (PHS46) showed reduced performance in men with African genetic ancestry. We used a cross-validated search to identify single nucleotide polymorphisms (SNPs) that might improve performance in this population. Anonymized genotypic data were obtained from the PRACTICAL consortium for 6253 men with African genetic ancestry. Ten iterations of a 10-fold cross-validation search were conducted to select SNPs that would be included in the final PHS46+African model. The coefficients of PHS46+African were estimated in a Cox proportional hazards framework using age at diagnosis as the dependent variable and PHS46, and selected SNPs as predictors. The performance of PHS46 and PHS46+African was compared using the same cross-validated approach. Three SNPs (rs76229939, rs74421890 and rs5013678) were selected for inclusion in PHS46+African. All three SNPs are located on chromosome 8q24. PHS46+African showed substantial improvements in all performance metrics measured, including a 75% increase in the relative hazard of those in the upper 20% compared to the bottom 20% (2.47-4.34) and a 20% reduction in the relative hazard of those in the bottom 20% compared to the middle 40% (0.65-0.53). In conclusion, we identified three SNPs that substantially improved the association of PHS46 with age at diagnosis of prostate cancer in men with African genetic ancestry to levels comparable to Europeans.
|
Titre |
en
African-specific improvement of a polygenic hazard score for age at diagnosis of prostate cancer
|
Auteur(s) |
Roshan A. Karunamuni
1
, Minh-Phuong Huynh-Le
1
, Chun C Fan
2
, W T Thompson
1
, Rosalind A. Eeles
3, 4
, Zsofia Kote-Jarai
4
, Kenneth Muir
5, 6
, Artitaya Lophatananon
5
, Catherine M. Tangen
7
, Phyllis J. Goodman
7
, Ian M. Thompson
, William J. Blot
8, 9
, Wei Zheng
8
, Adam S. Kibel
10
, Bettina F. Drake
11
, Olivier Cussenot
12
, Géraldine Cancel-Tassin
12
, Florence Menegaux
13, 14
, Thérèse Truong
13, 14
, Jong Y. Park
15
, Hui-Yi Lin
16
, Jeannette T. Bensen
17
, Elizabeth T. H. Fontham
16
, James L. Mohler
17
, Jack A Taylor
18
, Luc Multigner
19
, Pascal Blanchet
19
, Laurent Brureau
19
, Marc Romana
20
, Robin J Leach
21
, Esther M. John
22
, Jay Fowke
8, 23
, William S. Bush
24
, Melinda Aldrich
8
, Dana C. Crawford
24
, Shiv Srivastava
9
, Jennifer C. Cullen
9
, Gyorgy Petrovics
9
, Marie-Elise Parent
25, 26
, Jennifer J. Hu
27
, Maureen Sanderson
, Ian G. Mills
28
, Ole A. Andreassen
29
, Anders M. Dale
1
, Tyler M. Seibert
1
1
UC San Diego -
University of California [San Diego]
( 300717 )
- UCSD, 9500 Gilman Dr., La Jolla, CA 92093 USA
- États-Unis
2
Healthlytix [San Diego]
( 1054079 )
- États-Unis
3
The Royal Marsden
( 302879 )
-
- France
4
The institute of cancer research [London]
( 412235 )
- 123 Old Brompton Road
London SW7 3RP
- Royaume-Uni
5
University of Manchester [Manchester]
( 121172 )
- Oxford Rd, Manchester M13 9PL
- Royaume-Uni
6
University of Warwick [Coventry]
( 302824 )
- Coventry CV4 7AL
- Royaume-Uni
7
FHCRC -
Fred Hutchinson Cancer Research Center [Seattle]
( 41823 )
- 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
- États-Unis
8
VUSE -
Vanderbilt University School of Engineering [Nashville]
( 85378 )
- 2201 West End Avenue, Nashville, TN 37232, USA
- États-Unis
9
GeneDx [Gaithersburg, MD, USA]
( 536296 )
- 207 Perry Parkway
Gaithersburg, MD 20877
- États-Unis
10
BWH -
Brigham & Women’s Hospital [Boston]
( 538529 )
- 75 Francis street, Boston MA 02115
- États-Unis
11
WUSTL -
Washington University in Saint Louis
( 508210 )
- 1 Brookings Dr, St. Louis, MO 63130
- États-Unis
12
Hôpital Cochin [AP-HP]
( 300123 )
- 27 Rue du Faubourg Saint-Jacques 75014 Paris
- France
13
UVSQ -
Université de Versailles Saint-Quentin-en-Yvelines
( 81173 )
- 55 avenue de Paris - 78035 Versailles cedex
- France
14
CESP -
Centre de recherche en épidémiologie et santé des populations
( 1051097 )
- 16 avenue Paul Vaillant Couturier 94807 Villejuif Cedex, France
- France
15
H. Lee Moffitt Cancer Center and Research Institute
( 306973 )
- Tampa, Florida, USA
- États-Unis
16
LSU -
Louisiana State University
( 303524 )
- États-Unis
17
UNC -
University of North Carolina [Chapel Hill]
( 44261 )
- 250 East Franklin Street, Chapel Hill, NC,
- États-Unis
18
NIEHS-NIH -
National Institute of Environmental Health Sciences [Durham, NC, USA]
( 59763 )
- Research Triangle Park, Durham, NC, 27709
- États-Unis
19
Irset -
Institut de recherche en santé, environnement et travail
( 182194 )
- 263 avenue Général Leclerc 35042 Rennes Cedex
- France
20
BIGR (UMR_S_1134 / U1134) -
Biologie Intégrée du Globule Rouge
( 1005032 )
- 6 rue Alexandre Cabanel - 75739 Paris cedex 15
- France
21
UTSA -
The University of Texas at San Antonio
( 335543 )
- 1 UTSA Circle, San Antonio, TX 78249
- États-Unis
22
Stanford University
( 73500 )
- 450 Serra Mall, Stanford, CA 94305-2004
- États-Unis
23
Vanderbilt University [Nashville]
( 168363 )
- Nashville, Tennessee, TN 37240
- États-Unis
24
Case Western Reserve University [Cleveland]
( 365163 )
- 10900 Euclid Ave., Cleveland, Ohio 44106
- États-Unis
25
eResearch Collaboratory [Quebec City]
( 485127 )
- Canada
26
McGill University = Université McGill [Montréal, Canada]
( 134741 )
- 845, rue Sherbrooke O. Montréal (Québec) Canada H3A 0G4
- Canada
27
UMMSM -
University of Miami Leonard M. Miller School of Medicine
( 116558 )
- Miami, Florida, USA
- États-Unis
28
School of Medicine, Dentistry and Biomedical Sciences [Belfast]
( 220509 )
- Whitla Medical Building,
97 Lisburn Road,
Belfast, BT9 7BL
- Royaume-Uni
29
UiO -
University of Oslo
( 50791 )
- P.O 1072 Blindern 0316 Oslo
- Norvège
|
Nom de la revue |
|
Date de publication |
2021-01
|
Date de publication électronique |
2020-09-22
|
Volume |
148
|
Numéro |
1
|
Page/Identifiant |
99-105
|
Langue du document |
Anglais
|
Vulgarisation |
Non
|
Comité de lecture |
Oui
|
Audience |
Internationale
|
Domaine(s) |
|
Financement |
|
Mots-clés |
en
African, genome wide association study, genomics, genotypic ancestry, health disparities, polygenic risk, prostate cancer
|
DOI | 10.1002/ijc.33282 |
Pubmed Id | 32930425 |
Fichier principal
Karunamuni et al-2020-African-specific improvement of a polygenic hazard score for age at diagnosis.pdf ( 1.09 Mo
)
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