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Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers

Zhang, Yan Dora ; Hurson, Amber N. ; Zhang, Haoyu ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Nature Communications Vol. 11, No. 1 ( 2020-07-03)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2020-07-03)

Abstract: Genome-wide association studies (GWAS) have led to the identification of hundreds of susceptibility loci across cancers, but the impact of further studies remains uncertain. Here we analyse summary-level data from GWAS of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) and underlying effect-size distribution. All cancers show a high degree of polygenicity, involving at a minimum of thousands of loci. We project that sample sizes required to explain 80% of GWAS heritability vary from 60,000 cases for testicular to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores (PRS), compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-020-16483-3

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2553671-0

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Author Correction: A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Coignard, Juliette ; Lush, Michael ; Beesley, Jonathan ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Nature Communications Vol. 12, No. 1 ( 2021-05-14)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-05-14)

Abstract: A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-23162-4

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-021-23162-4

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2553671-0

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Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer

Couch, Fergus J. ; Kuchenbaecker, Karoline B. ; Michailidou, Kyriaki ; [et al.]

Springer Science and Business Media LLC ; 2016

In: Nature Communications Vol. 7, No. 1 ( 2016-04-27)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2016-04-27)

Abstract: Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations ( P 〈 5 × 10 −8 ) with oestrogen receptor (ER)-negative breast cancer and BRCA1 -associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5 , a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations ( P 〈 0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and PPIL3 at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for ∼11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and BRCA1 breast cancer risk prediction.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/ncomms11375

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 2553671-0

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Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus

Lawrenson, Kate ; Kar, Siddhartha ; McCue, Karen ; [et al.]

Springer Science and Business Media LLC ; 2016

In: Nature Communications Vol. 7, No. 1 ( 2016-09-07)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2016-09-07)

Abstract: A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC ( P =9.2 × 10 −20 ), ER-negative BC ( P =1.1 × 10 −13 ), BRCA1 -associated BC ( P =7.7 × 10 −16 ) and triple negative BC ( P -diff=2 × 10 −5 ). Genotype-gene expression associations are identified for candidate target genes ANKLE1 ( P =2 × 10 −3 ) and ABHD8 ( P 〈 2 × 10 −3 ). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8 , and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/ncomms12675

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 2553671-0

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Evidence of Gene–Environment Interactions between Common Breast Cancer Susceptibility Loci and Established Environmental Risk Factors

Nickels, Stefan ; Truong, Thérèse ; Hein, Rebecca ; [et al.]

Public Library of Science (PLoS) ; 2013

In: PLoS Genetics Vol. 9, No. 3 ( 2013-3-27), p. e1003284-

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In: PLoS Genetics, Public Library of Science (PLoS), Vol. 9, No. 3 ( 2013-3-27), p. e1003284-

Type of Medium: Online Resource

ISSN: 1553-7404

URL: Article

DOI: 10.1371/journal.pgen.1003284

DOI: 10.1371/journal.pgen.1003284.g001

DOI: 10.1371/journal.pgen.1003284.g002

DOI: 10.1371/journal.pgen.1003284.t001

DOI: 10.1371/journal.pgen.1003284.t002

DOI: 10.1371/journal.pgen.1003284.t003

DOI: 10.1371/journal.pgen.1003284.t004

DOI: 10.1371/journal.pgen.1003284.s001

DOI: 10.1371/journal.pgen.1003284.s002

DOI: 10.1371/journal.pgen.1003284.s003

DOI: 10.1371/journal.pgen.1003284.s004

DOI: 10.1371/journal.pgen.1003284.s005

DOI: 10.1371/journal.pgen.1003284.s006

DOI: 10.1371/journal.pgen.1003284.s007

DOI: 10.1371/journal.pgen.1003284.s008

DOI: 10.1371/journal.pgen.1003284.s009

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2013

detail.hit.zdb_id: 2186725-2

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Large-scale genotyping identifies 41 new loci associated with breast cancer risk

Michailidou, Kyriaki ; The Breast and Ovarian Cancer Susceptibility Collaboration ; Hall, Per ; [et al.]

Springer Science and Business Media LLC ; 2013

In: Nature Genetics Vol. 45, No. 4 ( 2013-4), p. 353-361

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 45, No. 4 ( 2013-4), p. 353-361

Type of Medium: Online Resource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/ng.2563

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2013

detail.hit.zdb_id: 1494946-5

SSG: 12

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Transcriptome‐wide association study of breast cancer risk by estrogen‐receptor status

Feng, Helian ; Gusev, Alexander ; Pasaniuc, Bogdan ; [et al.]

Wiley ; 2020

In: Genetic Epidemiology Vol. 44, No. 5 ( 2020-07), p. 442-468

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In: Genetic Epidemiology, Wiley, Vol. 44, No. 5 ( 2020-07), p. 442-468

Abstract: Previous transcriptome‐wide association studies (TWAS) have identified breast cancer risk genes by integrating data from expression quantitative loci and genome‐wide association studies (GWAS), but analyses of breast cancer subtype‐specific associations have been limited. In this study, we conducted a TWAS using gene expression data from GTEx and summary statistics from the hitherto largest GWAS meta‐analysis conducted for breast cancer overall, and by estrogen receptor subtypes (ER+ and ER−). We further compared associations with ER+ and ER− subtypes, using a case‐only TWAS approach. We also conducted multigene conditional analyses in regions with multiple TWAS associations. Two genes, STXBP4 and HIST2H2BA , were specifically associated with ER+ but not with ER– breast cancer. We further identified 30 TWAS‐significant genes associated with overall breast cancer risk, including four that were not identified in previous studies. Conditional analyses identified single independent breast‐cancer gene in three of six regions harboring multiple TWAS‐significant genes. Our study provides new information on breast cancer genetics and biology, particularly about genomic differences between ER+ and ER− breast cancer.

Type of Medium: Online Resource

ISSN: 0741-0395 , 1098-2272

URL: Issue

URL: Article

DOI: 10.1002/gepi.v44.5

DOI: 10.1002/gepi.22288

Language: English

Publisher: Wiley

Publication Date: 2020

detail.hit.zdb_id: 1492643-X

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Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Milne, Roger L ; ABCTB Investigators ; Kuchenbaecker, Karoline B ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Nature Genetics Vol. 49, No. 12 ( 2017-12-01), p. 1767-1778

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 49, No. 12 ( 2017-12-01), p. 1767-1778

Type of Medium: Online Resource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/ng.3785

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 1494946-5

SSG: 12

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A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Coignard, Juliette ; Lush, Michael ; Beesley, Jonathan ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Nature Communications Vol. 12, No. 1 ( 2021-02-17)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-02-17)

Abstract: Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P 〈 10 −8 , at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD , SP11 and EIF1 , genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-020-20496-3

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2553671-0

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Large-Scale Genomic Analyses Link Reproductive Aging to Hypothalamic Signaling, Breast Cancer Susceptibility, and BRCA1-Mediated DNA Repair

Day, Felix R. ; Ruth, Katherine S. ; Thompson, Deborah J. ; [et al.]

Ovid Technologies (Wolters Kluwer Health) ; 2015

In: Obstetrical & Gynecological Survey Vol. 70, No. 12 ( 2015-12), p. 758-762

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In: Obstetrical & Gynecological Survey, Ovid Technologies (Wolters Kluwer Health), Vol. 70, No. 12 ( 2015-12), p. 758-762

Type of Medium: Online Resource

ISSN: 0029-7828

URL: Article

DOI: 10.1097/01.ogx.0000473766.71624.99

Language: English

Publisher: Ovid Technologies (Wolters Kluwer Health)

Publication Date: 2015

detail.hit.zdb_id: 2043471-6

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