Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry.
Breast cancer susceptibility
Diverse ancestry
Gene regulation
Genome-wide association study
Rare variants
Journal
Genome medicine
ISSN: 1756-994X
Titre abrégé: Genome Med
Pays: England
ID NLM: 101475844
Informations de publication
Date de publication:
26 01 2023
26 01 2023
Historique:
received:
05
05
2022
accepted:
16
12
2022
entrez:
26
1
2023
pubmed:
27
1
2023
medline:
31
1
2023
Statut:
epublish
Résumé
Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes. We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry. In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10 Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10
Sections du résumé
BACKGROUND
Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.
METHODS
We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.
RESULTS
In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10
CONCLUSIONS
Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10
Identifiants
pubmed: 36703164
doi: 10.1186/s13073-022-01152-5
pii: 10.1186/s13073-022-01152-5
pmc: PMC9878779
doi:
Substances chimiques
FMNL3 protein, human
0
Formins
0
Types de publication
Meta-Analysis
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, P.H.S.
Research Support, N.I.H., Intramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
7Subventions
Organisme : NCI NIH HHS
ID : UM1 CA164917
Pays : United States
Organisme : Cancer Research UK
ID : C12292/A11174
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : P50 CA116201
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : Cancer Research UK
ID : C1287/A10118
Pays : United Kingdom
Organisme : Intramural NIH HHS
ID : Z01 ES044005
Pays : United States
Organisme : Intramural NIH HHS
ID : Z01 ES049033
Pays : United States
Organisme : Cancer Research UK
ID : C1275/A19187
Pays : United Kingdom
Organisme : Cancer Research UK
ID : C8221/A19170
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA148667
Pays : United States
Organisme : NCI NIH HHS
ID : HHSN261201800032I
Pays : United States
Organisme : NCI NIH HHS
ID : U19 CA148112
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA058223
Pays : United States
Organisme : Cancer Research UK
ID : C1287/A10710
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA120120
Pays : United States
Organisme : Cancer Research UK
ID : 14136
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : HHSN261201800015I
Pays : United States
Organisme : Cancer Research UK
ID : 29186
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : HHSN261201800009I
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA176726
Pays : United States
Organisme : Cancer Research UK
ID : C1275/C22524
Pays : United Kingdom
Organisme : Intramural NIH HHS
ID : Z01 CP010119
Pays : United States
Organisme : Cancer Research UK
ID : C1287/A16563
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_00004/01
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : P30 CA033572
Pays : United States
Organisme : Cancer Research UK
ID : C5047/A10692
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : P30 CA023100
Pays : United States
Organisme : Cancer Research UK
ID : C490/A16561
Pays : United Kingdom
Organisme : Medical Research Council
ID : 1000143
Pays : United Kingdom
Organisme : Cancer Research UK
ID : C490/A10124
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA192393
Pays : United States
Organisme : Cancer Research UK
ID : C5047/A8384
Pays : United Kingdom
Organisme : NCCDPHP CDC HHS
ID : NU58DP006344
Pays : United States
Organisme : Cancer Research UK
ID : C570/A16491
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : U19 CA148065
Pays : United States
Organisme : Cancer Research UK
ID : C1275/A11699
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : UM1 CA186107
Pays : United States
Organisme : Medical Research Council
ID : MR/M012190/1
Pays : United Kingdom
Organisme : Cancer Research UK
ID : C5047/A15007
Pays : United Kingdom
Organisme : Department of Health
ID : PGFAR 0707-10031
Pays : United Kingdom
Organisme : Intramural NIH HHS
ID : Z01 ES049030
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA125183
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA176785
Pays : United States
Organisme : FIC NIH HHS
ID : D43 TW009112
Pays : United States
Organisme : Department of Health
ID : IS-BRC-1215-20007
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : K24 CA169004
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA156733
Pays : United States
Organisme : NCI NIH HHS
ID : R35 CA253187
Pays : United States
Organisme : Cancer Research UK
ID : 10118
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA077398
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA100374
Pays : United States
Organisme : Cancer Research UK
ID : C1275/A15956
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : U01 CA164920
Pays : United States
Organisme : NCI NIH HHS
ID : UM1 CA176726
Pays : United States
Organisme : Cancer Research UK
ID : C1281/A12014
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : U01 CA199277
Pays : United States
Organisme : NCI NIH HHS
ID : UM1 CA164920
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA179715
Pays : United States
Organisme : Cancer Research UK
ID : C8197/A16565
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA116167
Pays : United States
Organisme : NCI NIH HHS
ID : U19 CA148537
Pays : United States
Organisme : Wellcome Trust
ID : 203477/Z/16/Z
Pays : United Kingdom
Investigateurs
Kristine K Sahlberg
(KK)
Anne-Lise Børresen-Dale
(AL)
Lars Ottestad
(L)
Rolf Kåresen
(R)
Ellen Schlichting
(E)
Marit Muri Holmen
(MM)
Toril Sauer
(T)
Vilde Haakensen
(V)
Olav Engebråten
(O)
Bjørn Naume
(B)
Alexander Fosså
(A)
Cecile E Kiserud
(CE)
Kristin V Reinertsen
(KV)
Åslaug Helland
(Å)
Margit Riis
(M)
Jürgen Geisler
(J)
Grethe I Grenaker Alnaes
(GI)
Deborah Marsh
(D)
Rodney Scott
(R)
Robert Baxter
(R)
Desmond Yip
(D)
Jane Carpenter
(J)
Alison Davis
(A)
Nirmala Pathmanathan
(N)
Peter Simpson
(P)
Dinny Graham
(D)
Mythily Sachchithananthan
(M)
Informations de copyright
© 2023. The Author(s).
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