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

Deanery of Molecular, Genetic and Population Health Sciences

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

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. Single-marker 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
Pages (from-to)	479-90
Number of pages	12
Journal	Human Genetics
Volume	131
Issue number	3
DOIs	https://doi.org/10.1007/s00439-011-1088-4
Publication status	Published - Mar 2012

Keywords / Materials (for Non-textual outputs)

Breast Neoplasms
Case-Control Studies
Chromosome Mapping
Chromosomes, Human, Pair 14
Female
Genetic Predisposition to Disease
HapMap Project
Haplotypes
Humans
Polymorphism, Single Nucleotide

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10.1007/s00439-011-1088-4

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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), 479-90. https://doi.org/10.1007/s00439-011-1088-4

@article{ebefaba5a60d4286a9d3d7859d138693,

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. Single-marker 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.",

keywords = "Breast Neoplasms, Case-Control Studies, Chromosome Mapping, Chromosomes, Human, Pair 14, Female, Genetic Predisposition to Disease, HapMap Project, Haplotypes, Humans, Polymorphism, Single Nucleotide",

author = "Phoebe Lee and Yi-Ping Fu 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 Marie-Jos{\`e}phe Horner 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}",

year = "2012",

month = mar,

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

language = "English",

volume = "131",

pages = "479--90",

journal = "Human Genetics",

issn = "0340-6717",

publisher = "Springer",

number = "3",

}

Lee, P, Fu, Y-P, Figueroa, JD, Prokunina-Olsson, L, Gonzalez-Bosquet, J, Kraft, P, Wang, Z, Jacobs, KB, Yeager, M, Horner, M-J, 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. 479-90. https://doi.org/10.1007/s00439-011-1088-4

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

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. Single-marker 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. Single-marker 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.

KW - Breast Neoplasms

KW - Case-Control Studies

KW - Chromosome Mapping

KW - Chromosomes, Human, Pair 14

KW - Female

KW - Genetic Predisposition to Disease

KW - HapMap Project

KW - Haplotypes

KW - Humans

KW - Polymorphism, Single Nucleotide

U2 - 10.1007/s00439-011-1088-4

DO - 10.1007/s00439-011-1088-4

M3 - Article

C2 - 21959381

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

Keywords / Materials (for Non-textual outputs)

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