Fine mapping of 14q24.1 breast cancer susceptibility locus

Phoebe Lee; Yi Ping Fu; Jonine D. Figueroa; Ludmila Prokunina-Olsson; Jesus Gonzalez-Bosquet; Peter Kraft; Zhaoming Wang; Kevin B. Jacobs; Meredith Yeager; Marie Josèphe Horner; Susan E. Hankinson; Amy Hutchinson; Nilanjan Chatterjee; Montserrat Garcia-Closas; Regina G. Ziegler; Christine D. Berg; Saundra S. Buys; Catherine A. McCarty; Heather Spencer Feigelson; Michael J. Thun; Ryan Diver; Ross Prentice; Rebecca Jackson; Charles Kooperberg; Rowan Chlebowski; Jolanta Lissowska; Beata Peplonska; Louise A. Brinton; Margaret Tucker; Joseph F. Fraumeni; Robert N. Hoover; Gilles Thomas; David J. Hunter; Stephen J. Chanock

doi:10.1007/s00439-011-1088-4

Fine mapping of 14q24.1 breast cancer susceptibility locus

Phoebe Lee, Yi Ping Fu, Jonine D. Figueroa, Ludmila Prokunina-Olsson, Jesus Gonzalez-Bosquet, Peter Kraft, Zhaoming Wang, Kevin B. Jacobs, Meredith Yeager, Marie Josèphe Horner, Susan E. Hankinson, Amy Hutchinson, Nilanjan Chatterjee, Montserrat Garcia-Closas, Regina G. Ziegler, Christine D. Berg, Saundra S. Buys, Catherine A. McCarty, Heather Spencer Feigelson, Michael J. ThunRyan Diver, Ross Prentice, Rebecca Jackson, Charles Kooperberg, Rowan Chlebowski, Jolanta Lissowska, Beata Peplonska, Louise A. Brinton, Margaret Tucker, Joseph F. Fraumeni, Robert N. Hoover, Gilles Thomas, David J. Hunter, Stephen J. Chanock

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

In the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) genome-wide association study of breast cancer, a single nucleotide polymorphism (SNP) marker, rs999737, in the 14q24.1 interval, was associated with breast cancer risk. In order to fine map this region, we imputed a 3.93 MB region flanking rs999737 for Stages 1 and 2 of the CGEMS study (5,692 cases, 5,576 controls) using the combined reference panels of the HapMap 3 and the 1000 Genomes Project. Singlemarker association testing and variable-sized sliding-window haplotype analysis were performed, and for both analyses the initial tagging SNP rs999737 retained the strongest association with breast cancer risk. Investigation of contiguous regions did not reveal evidence for an additional independent signal. Therefore, we conclude that rs999737 is an optimal tag SNP for common variants in the 14q24.1 region and thus narrow the candidate variants that should be investigated in follow-up laboratory evaluation.

Original language	English (US)
Pages (from-to)	479-490
Number of pages	12
Journal	Human genetics
Volume	131
Issue number	3
DOIs	https://doi.org/10.1007/s00439-011-1088-4
State	Published - Mar 2012
Externally published	Yes

ASJC Scopus subject areas

Genetics
Genetics(clinical)

Access to Document

10.1007/s00439-011-1088-4

Cite this

Lee, P., Fu, Y. P., Figueroa, J. D., Prokunina-Olsson, L., Gonzalez-Bosquet, J., Kraft, P., Wang, Z., Jacobs, K. B., Yeager, M., Horner, M. J., Hankinson, S. E., Hutchinson, A., Chatterjee, N., Garcia-Closas, M., Ziegler, R. G., Berg, C. D., Buys, S. S., McCarty, C. A., Feigelson, H. S., ... Chanock, S. J. (2012). Fine mapping of 14q24.1 breast cancer susceptibility locus. Human genetics, 131(3), 479-490. https://doi.org/10.1007/s00439-011-1088-4

Lee, P, Fu, YP, Figueroa, JD, Prokunina-Olsson, L, Gonzalez-Bosquet, J, Kraft, P, Wang, Z, Jacobs, KB, Yeager, M, Horner, MJ, Hankinson, SE, Hutchinson, A, Chatterjee, N, Garcia-Closas, M, Ziegler, RG, Berg, CD, Buys, SS, McCarty, CA, Feigelson, HS, Thun, MJ, Diver, R, Prentice, R, Jackson, R, Kooperberg, C, Chlebowski, R, Lissowska, J, Peplonska, B, Brinton, LA, Tucker, M, Fraumeni, JF, Hoover, RN, Thomas, G, Hunter, DJ & Chanock, SJ 2012, 'Fine mapping of 14q24.1 breast cancer susceptibility locus', Human genetics, vol. 131, no. 3, pp. 479-490. https://doi.org/10.1007/s00439-011-1088-4

@article{91a128ee89a644808a220d1402c89719,

title = "Fine mapping of 14q24.1 breast cancer susceptibility locus",

abstract = "In the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) genome-wide association study of breast cancer, a single nucleotide polymorphism (SNP) marker, rs999737, in the 14q24.1 interval, was associated with breast cancer risk. In order to fine map this region, we imputed a 3.93 MB region flanking rs999737 for Stages 1 and 2 of the CGEMS study (5,692 cases, 5,576 controls) using the combined reference panels of the HapMap 3 and the 1000 Genomes Project. Singlemarker association testing and variable-sized sliding-window haplotype analysis were performed, and for both analyses the initial tagging SNP rs999737 retained the strongest association with breast cancer risk. Investigation of contiguous regions did not reveal evidence for an additional independent signal. Therefore, we conclude that rs999737 is an optimal tag SNP for common variants in the 14q24.1 region and thus narrow the candidate variants that should be investigated in follow-up laboratory evaluation.",

author = "Phoebe Lee and Fu, {Yi Ping} and Figueroa, {Jonine D.} and Ludmila Prokunina-Olsson and Jesus Gonzalez-Bosquet and Peter Kraft and Zhaoming Wang and Jacobs, {Kevin B.} and Meredith Yeager and Horner, {Marie Jos{\`e}phe} and Hankinson, {Susan E.} and Amy Hutchinson and Nilanjan Chatterjee and Montserrat Garcia-Closas and Ziegler, {Regina G.} and Berg, {Christine D.} and Buys, {Saundra S.} and McCarty, {Catherine A.} and Feigelson, {Heather Spencer} and Thun, {Michael J.} and Ryan Diver and Ross Prentice and Rebecca Jackson and Charles Kooperberg and Rowan Chlebowski and Jolanta Lissowska and Beata Peplonska and Brinton, {Louise A.} and Margaret Tucker and Fraumeni, {Joseph F.} and Hoover, {Robert N.} and Gilles Thomas and Hunter, {David J.} and Chanock, {Stephen J.}",

note = "Funding Information: The WHI program is supported by contracts from the National Heart, Lung and Blood Institute, NIH. The authors thank the WHI investigators and staff for their dedication, and the study participants for making the program possible. A full listing of WHI investigators can be found at http://www.whi.org. Funding Information: The PLCO study is supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics and contracts from the Division of Cancer Prevention, National Cancer Institute, NIH, DHHS. The authors thank Dr Philip Prorok, Division of Cancer Prevention, National Cancer Institute; the Screening Center investigators and staff of the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). Most importantly, we acknowledge the study participants for their contributions to making this study possible. Funding Information: Acknowledgments The Nurses{\textquoteright} Health Studies are supported by NIH grants CA 65725, CA87969, CA49449, CA67262, CA50385 and 5UO1CA098233. The authors thank Barbara Egan, Lori Egan, Helena Judge Ellis, Hardeep Ranu, and Pati Soule for assistance, and the participants in the Nurses{\textquoteright} Health Studies.",

year = "2012",

month = mar,

doi = "10.1007/s00439-011-1088-4",

language = "English (US)",

volume = "131",

pages = "479--490",

journal = "Human genetics",

issn = "0340-6717",

publisher = "Springer Science and Business Media Deutschland GmbH",

number = "3",

}

TY - JOUR

T1 - Fine mapping of 14q24.1 breast cancer susceptibility locus

AU - Lee, Phoebe

AU - Fu, Yi Ping

AU - Figueroa, Jonine D.

AU - Prokunina-Olsson, Ludmila

AU - Gonzalez-Bosquet, Jesus

AU - Kraft, Peter

AU - Wang, Zhaoming

AU - Jacobs, Kevin B.

AU - Yeager, Meredith

AU - Horner, Marie Josèphe

AU - Hankinson, Susan E.

AU - Hutchinson, Amy

AU - Chatterjee, Nilanjan

AU - Garcia-Closas, Montserrat

AU - Ziegler, Regina G.

AU - Berg, Christine D.

AU - Buys, Saundra S.

AU - McCarty, Catherine A.

AU - Feigelson, Heather Spencer

AU - Thun, Michael J.

AU - Diver, Ryan

AU - Prentice, Ross

AU - Jackson, Rebecca

AU - Kooperberg, Charles

AU - Chlebowski, Rowan

AU - Lissowska, Jolanta

AU - Peplonska, Beata

AU - Brinton, Louise A.

AU - Tucker, Margaret

AU - Fraumeni, Joseph F.

AU - Hoover, Robert N.

AU - Thomas, Gilles

AU - Hunter, David J.

AU - Chanock, Stephen J.

N1 - Funding Information: The WHI program is supported by contracts from the National Heart, Lung and Blood Institute, NIH. The authors thank the WHI investigators and staff for their dedication, and the study participants for making the program possible. A full listing of WHI investigators can be found at http://www.whi.org. Funding Information: The PLCO study is supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics and contracts from the Division of Cancer Prevention, National Cancer Institute, NIH, DHHS. The authors thank Dr Philip Prorok, Division of Cancer Prevention, National Cancer Institute; the Screening Center investigators and staff of the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). Most importantly, we acknowledge the study participants for their contributions to making this study possible. Funding Information: Acknowledgments The Nurses’ Health Studies are supported by NIH grants CA 65725, CA87969, CA49449, CA67262, CA50385 and 5UO1CA098233. The authors thank Barbara Egan, Lori Egan, Helena Judge Ellis, Hardeep Ranu, and Pati Soule for assistance, and the participants in the Nurses’ Health Studies.

PY - 2012/3

Y1 - 2012/3

N2 - In the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) genome-wide association study of breast cancer, a single nucleotide polymorphism (SNP) marker, rs999737, in the 14q24.1 interval, was associated with breast cancer risk. In order to fine map this region, we imputed a 3.93 MB region flanking rs999737 for Stages 1 and 2 of the CGEMS study (5,692 cases, 5,576 controls) using the combined reference panels of the HapMap 3 and the 1000 Genomes Project. Singlemarker association testing and variable-sized sliding-window haplotype analysis were performed, and for both analyses the initial tagging SNP rs999737 retained the strongest association with breast cancer risk. Investigation of contiguous regions did not reveal evidence for an additional independent signal. Therefore, we conclude that rs999737 is an optimal tag SNP for common variants in the 14q24.1 region and thus narrow the candidate variants that should be investigated in follow-up laboratory evaluation.

AB - In the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) genome-wide association study of breast cancer, a single nucleotide polymorphism (SNP) marker, rs999737, in the 14q24.1 interval, was associated with breast cancer risk. In order to fine map this region, we imputed a 3.93 MB region flanking rs999737 for Stages 1 and 2 of the CGEMS study (5,692 cases, 5,576 controls) using the combined reference panels of the HapMap 3 and the 1000 Genomes Project. Singlemarker association testing and variable-sized sliding-window haplotype analysis were performed, and for both analyses the initial tagging SNP rs999737 retained the strongest association with breast cancer risk. Investigation of contiguous regions did not reveal evidence for an additional independent signal. Therefore, we conclude that rs999737 is an optimal tag SNP for common variants in the 14q24.1 region and thus narrow the candidate variants that should be investigated in follow-up laboratory evaluation.

UR - http://www.scopus.com/inward/record.url?scp=84859489770&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84859489770&partnerID=8YFLogxK

U2 - 10.1007/s00439-011-1088-4

DO - 10.1007/s00439-011-1088-4

M3 - Article

C2 - 21959381

AN - SCOPUS:84859489770

SN - 0340-6717

VL - 131

SP - 479

EP - 490

JO - Human genetics

JF - Human genetics

IS - 3

ER -

Fine mapping of 14q24.1 breast cancer susceptibility locus

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this