Copy Number Variants Are Ovarian Cancer Risk Alleles at Known and Novel Risk Loci.
Journal
Journal of the National Cancer Institute
ISSN: 1460-2105
Titre abrégé: J Natl Cancer Inst
Pays: United States
ID NLM: 7503089
Informations de publication
Date de publication:
14 11 2022
14 11 2022
Historique:
received:
28
01
2022
revised:
13
04
2022
accepted:
18
08
2022
pubmed:
11
10
2022
medline:
18
11
2022
entrez:
10
10
2022
Statut:
ppublish
Résumé
Known risk alleles for epithelial ovarian cancer (EOC) account for approximately 40% of the heritability for EOC. Copy number variants (CNVs) have not been investigated as EOC risk alleles in a large population cohort. Single nucleotide polymorphism array data from 13 071 EOC cases and 17 306 controls of White European ancestry were used to identify CNVs associated with EOC risk using a rare admixture maximum likelihood test for gene burden and a by-probe ratio test. We performed enrichment analysis of CNVs at known EOC risk loci and functional biofeatures in ovarian cancer-related cell types. We identified statistically significant risk associations with CNVs at known EOC risk genes; BRCA1 (PEOC = 1.60E-21; OREOC = 8.24), RAD51C (Phigh-grade serous ovarian cancer [HGSOC] = 5.5E-4; odds ratio [OR]HGSOC = 5.74 del), and BRCA2 (PHGSOC = 7.0E-4; ORHGSOC = 3.31 deletion). Four suggestive associations (P < .001) were identified for rare CNVs. Risk-associated CNVs were enriched (P < .05) at known EOC risk loci identified by genome-wide association study. Noncoding CNVs were enriched in active promoters and insulators in EOC-related cell types. CNVs in BRCA1 have been previously reported in smaller studies, but their observed frequency in this large population-based cohort, along with the CNVs observed at BRCA2 and RAD51C gene loci in EOC cases, suggests that these CNVs are potentially pathogenic and may contribute to the spectrum of disease-causing mutations in these genes. CNVs are likely to occur in a wider set of susceptibility regions, with potential implications for clinical genetic testing and disease prevention.
Sections du résumé
BACKGROUND
Known risk alleles for epithelial ovarian cancer (EOC) account for approximately 40% of the heritability for EOC. Copy number variants (CNVs) have not been investigated as EOC risk alleles in a large population cohort.
METHODS
Single nucleotide polymorphism array data from 13 071 EOC cases and 17 306 controls of White European ancestry were used to identify CNVs associated with EOC risk using a rare admixture maximum likelihood test for gene burden and a by-probe ratio test. We performed enrichment analysis of CNVs at known EOC risk loci and functional biofeatures in ovarian cancer-related cell types.
RESULTS
We identified statistically significant risk associations with CNVs at known EOC risk genes; BRCA1 (PEOC = 1.60E-21; OREOC = 8.24), RAD51C (Phigh-grade serous ovarian cancer [HGSOC] = 5.5E-4; odds ratio [OR]HGSOC = 5.74 del), and BRCA2 (PHGSOC = 7.0E-4; ORHGSOC = 3.31 deletion). Four suggestive associations (P < .001) were identified for rare CNVs. Risk-associated CNVs were enriched (P < .05) at known EOC risk loci identified by genome-wide association study. Noncoding CNVs were enriched in active promoters and insulators in EOC-related cell types.
CONCLUSIONS
CNVs in BRCA1 have been previously reported in smaller studies, but their observed frequency in this large population-based cohort, along with the CNVs observed at BRCA2 and RAD51C gene loci in EOC cases, suggests that these CNVs are potentially pathogenic and may contribute to the spectrum of disease-causing mutations in these genes. CNVs are likely to occur in a wider set of susceptibility regions, with potential implications for clinical genetic testing and disease prevention.
Identifiants
pubmed: 36210504
pii: 6751998
doi: 10.1093/jnci/djac160
pmc: PMC9949586
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1533-1544Subventions
Organisme : NCI NIH HHS
ID : P01 CA017054
Pays : United States
Organisme : NCI NIH HHS
ID : UM1 CA176726
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA058860
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA105009
Pays : United States
Organisme : NIH HHS
ID : R01-CA122443
Pays : United States
Organisme : Wellcome Trust
ID : 076113
Pays : United Kingdom
Organisme : Medical Research Council
ID : G0401527
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : U19-CA148112
Pays : United States
Organisme : NCI NIH HHS
ID : N01 CN025403
Pays : United States
Organisme : Intramural NIH HHS
ID : Z01 ES049033
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA136393
Pays : United States
Organisme : Cancer Research UK
ID : C490/A10119 C490/A10124
Pays : United Kingdom
Organisme : Medical Research Council
ID : 1000143
Pays : United Kingdom
Organisme : NIH HHS
ID : R01-CA54419
Pays : United States
Organisme : Cancer Research UK
ID : C8221/A19170
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA049449
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA159981
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM118288
Pays : United States
Organisme : NIH HHS
ID : CA1X01HG007491-01
Pays : United States
Organisme : NIEHS NIH HHS
ID : Z01-ES044005
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA106414
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA095023
Pays : United States
Organisme : NCI NIH HHS
ID : N01 PC067010
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA058598
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA176726
Pays : United States
Organisme : NCRR NIH HHS
ID : S10 RR025141
Pays : United States
Organisme : NCRR NIH HHS
ID : M01 RR000056
Pays : United States
Organisme : Department of Health
Pays : United Kingdom
Organisme : NIH HHS
ID : 5T32GM118288-03
Pays : United States
Organisme : Medical Research Council
ID : MR/N003284/1
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : P30 CA014089
Pays : United States
Organisme : NCI NIH HHS
ID : K07-CA080668
Pays : United States
Organisme : Cancer Research UK
ID : 14136
Pays : United Kingdom
Organisme : Worldwide Cancer Research
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR_UU_12023
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA067262
Pays : United States
Organisme : NCI NIH HHS
ID : UM1 CA186107
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA015083
Pays : United States
Organisme : Medical Research Council
ID : G1000143
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA076016
Pays : United States
Organisme : NHGRI NIH HHS
Pays : United States
Organisme : NCI NIH HHS
ID : P01 CA087969
Pays : United States
Organisme : NCI NIH HHS
ID : R01- CA61107
Pays : United States
Organisme : NIH HHS
ID : R01-CA58598
Pays : United States
Organisme : NCI NIH HHS
ID : U19 CA148112
Pays : United States
Organisme : NCATS NIH HHS
ID : ULTR000445
Pays : United States
Organisme : NCI NIH HHS
ID : R03 CA115195
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Breast Cancer Now
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA160669
Pays : United States
Organisme : NIH HHS
ID : R01-CA058860
Pays : United States
Organisme : Cancer Research UK
ID : C570/A16491
Pays : United Kingdom
Organisme : NIH HHS
ID : R01-CA76016
Pays : United States
Organisme : NIH HHS
ID : R01-CA106414-A2
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA126841
Pays : United States
Organisme : Medical Research Council
ID : MR/M012190/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 209057
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R03 CA113148
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA149429
Pays : United States
Investigateurs
P Webb
(P)
A DeFazio
(A)
M Friedlander
(M)
A Obermair
(A)
P Grant
(P)
C Nagle
(C)
V Beesley
(V)
G Chevenix-Trench
(G)
D Bowtell
(D)
P Blomfield
(P)
A Brand
(A)
A Davis
(A)
Y Leung
(Y)
J Nicklin
(J)
M Quinn
(M)
K Livingstone
(K)
H O'Neill
(H)
M Williams
(M)
A Black
(A)
A Hadley
(A)
A Glasgow
(A)
A Garrett
(A)
A Rao
(A)
C Shannon
(C)
C Steer
(C)
D Allen
(D)
D Neesham
(D)
G Otton
(G)
G Au-Yeung
(G)
G Goss
(G)
G Wain
(G)
G Gard
(G)
G Robertson
(G)
J Lombard
(J)
J Tan
(J)
J McNeilage
(J)
J Power
(J)
J Coward
(J)
J Miller
(J)
J Carter
(J)
J Lamont
(J)
K M Wong
(KM)
K Reid
(K)
L Perrin
(L)
L Milishkin
(L)
M Nascimento
(M)
M Buck
(M)
M Bunting
(M)
M Harrison
(M)
N Chetty
(N)
N Hacker
(N)
O McNally
(O)
P Harnett
(P)
P Beale
(P)
R Awad
(R)
R Mohan
(R)
R Farrell
(R)
R McIntosh
(R)
R Rome
(R)
R Sayer
(R)
R Houghton
(R)
R Hogg
(R)
R Land
(R)
S Baron-Hay
(S)
S Paramasivum
(S)
S Pather
(S)
S Hyde
(S)
S Salfinger
(S)
S Valmadre
(S)
T Jobling
(T)
T Manolitsas
(T)
T Bonaventura
(T)
V Arora
(V)
D Bowtell
(D)
G Chenevix-Trench
(G)
A Green
(A)
P Webb
(P)
A DeFazio
(A)
D Gertig
(D)
N Traficante
(N)
S Fereday
(S)
S Moore
(S)
J Hung
(J)
K Harrap
(K)
T Sadkowsky
(T)
N Pandeya
(N)
M Malt
(M)
R Robertson
(R)
T Vanden Bergh
(TV)
M Jones
(M)
P McKenzie
(P)
J Maidens
(J)
K Nattress
(K)
Y E Chiew
(YE)
A Stenlake
(A)
H Sullivan
(H)
B Alexander
(B)
P Ashover
(P)
S Brown
(S)
T Corrish
(T)
L Green
(L)
L Jackman
(L)
K Ferguson
(K)
K Martin
(K)
A Martyn
(A)
B Ranieri
(B)
J White
(J)
V Jayde
(V)
L Bowes
(L)
P Mamers
(P)
L Galletta
(L)
D Giles
(D)
J Hendley
(J)
K Alsop
(K)
T Schmidt
(T)
H Shirley
(H)
C Ball
(C)
C Young
(C)
S Viduka
(S)
H Tran
(H)
S Bilic
(S)
L Glavinas
(L)
J Brooks
(J)
R Stuart-Harris
(R)
F Kirsten
(F)
J Rutovitz
(J)
P Clingan
(P)
A Glasgow
(A)
A Proietto
(A)
S Braye
(S)
G Otton
(G)
J Shannon
(J)
T Bonaventura
(T)
J Stewart
(J)
S Begbie
(S)
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
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