Genome-wide association study identifies novel breast cancer susceptibility loci

TLDR: To identify further susceptibility alleles, a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls was conducted, followed by a third stage in which 30 single nucleotide polymorphisms were tested for confirmation.

Abstract: Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r2.0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P,1027). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P,0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach.

Figures

Figure 3. The FGFR2 locus a, Map of the whole FGFR2 gene, viewed relative to common SNPs on HapMap. The gene is 126 kb long and in reverse 3′–5′ orientation on chromosome 10. Exon positions are illustrated with respect to the 67 SNPs with m.a.f.>5% in HapMap CEU (therefore the map is not to physical scale). Numbered SNPs are those tested in the genomewide study. SNPs in black were not significant in stage 1. Those in red were significant at P<0.0001 after stage 2. rs10510097 (orange) was significant in stage 1, but failed quality control in stage 2 owing to deviation from Hardy–Weinberg equilibrium. Squares indicate pairwise r2 on a greyscale (black=1, white=0). Red circle indicates rs2981582. b, Resequenced 32 kb region, shown relative to SNPs in CEU with m.a.f.>5%, showing pairwise LD for SNPs in HapMap CEU (left panel) and JPT/CHB (right panel). Red circle indicates rs2981582, shown in bold black. c, Sequence conservation of 32 kb region in five species, relative to human sequence (http:// pipeline.lbl.gov/methods.shtml)35. Red circle indicates rs2981582. SNPs in grey are those used in the initial tagging of known common HapMap SNPs within the block. SNPs in black are correlated with rs2981582 with r2>0.6 in European samples. Six SNPs in red were those consistent with being the causative variant on the basis of the genetic data (not excluded at odds of 100:1 relative to the SNP with the strongest association, rs7895676).

Figure 2. Forest plots of the per-allele odds ratios for each of the five SNPs reaching genomewide significance a, rs2981582; b, rs3803662; c, rs889312; d, rs13281615; and e, rs3817198. The x-axis gives the per-allele odds ratio. Each row represents one study (see Supplementary Table 2), with summary odds ratios for all European and all Asian studies, and all studies combined. The area of the square for each study is proportional to the inverse of the variance of the estimate. Horizontal lines represent 95% confidence intervals. Diamonds represent the summary odds ratios, with 95% confidence intervals, based on the stage 3 studies only.

Figure 1. Quantile–quantile plots for the test statistics (Cochran-Armitage 1 d.f. χ2 trend tests) for stages 1 and 2 a, Stage 1; b, stage 2. Black dots are the uncorrected test statistics. Red dots are the statistics corrected by the genomic control method (λ=1.03 for stage 1, λ=1.06 for stage 2). Under the null hypothesis of no association at any locus, the points would be expected to follow the black line.

Table 1 Number of significant associations after stage 2

Full text

Genome-wide association study identifies novel breast
cancer susceptibility loci
Author
Easton, DF, Pooley, KA, Dunning, AM, Pharoah, PDP, Thompson, D, Ballinger, DG, Struewing,
JP, Morrison, J, Field, H, Luben, R, Wareham, N, Ahmed, S, Healey, CS, Bowman, R, Meyer,
KB, Haiman, CA, Kolonel, LK, Henderson, BE, Le Marchand, L, Brennan, P, Sangrajrang,
S, Gaborieau, V, Odefrey, F, Shen, CY, Wu, PE, Wang, HC, Eccles, D, Evans, DG, Peto, J,
Fletcher, O, Johnson, N, Seal, S, Stratton, MR, Rahman, N, Chenevix-Trench, G, Bojesen,
SE, Nordestgaard, BG, Axelsson, CK, Garcia-Closas, M, Brinton, L, Chanock, S, Lissowska,
J, Peplonska, B, Nevanlinna, H, Fagerholm, R, Eerola, H, Kang, D, Yoo, KY, Noh, DY, Ahn,
SH, Hunter, DJ, Hankinson, SE, Cox, DG, Hall, P, Wedren, S, Liu, J, Low, YL, Bogdanova,
N, Schürmann, P, Dörk, T, Tollenaar, RAEM, Jacobi, CE, Devilee, P, Klijn, JGM, Sigurdson,
AJ, Doody, MM, Alexander, BH, Zhang, J, Cox, A, Brock, IW, MacPherson, G, Reed, MWR,
Couch, FJ, Goode, EL, Olson, JE, Meijers-Heijboer, H, Van Den Ouweland, A, Uitterlinden, A,
Rivadeneira, F, Milne, RL, Ribas, G, Gonzalez-Neira, A, Benitez, J, Hopper, JL, McCredie, M,
Southey, M, Giles, G, Schroen, C, Justenhoven, C, Brauch, H, Hamann, U, Ko, YD, Spurdle,
AB, Beesley, J, Chen, X, Mannermaa, A, Kosma, VM, Kataja, V, Hartikainen, J, Day, NE
Published
2007
Journal Title
Nature
Version
Accepted Manuscript (AM)
DOI
https://doi.org/10.1038/nature05887
Copyright Statement
© 2007 Nature Publishing Group. This is the author-manuscript version of this paper.
Reproduced in accordance with the copyright policy of the publisher. Please refer to the journal
website for access to the definitive, published version.
Downloaded from
http://hdl.handle.net/10072/27478
Link to published version

http://www.nature.com/nature/index.html
Griffith Research Online
https://research-repository.griffith.edu.au

Genome-wide association study identifies novel breast cancer
susceptibility loci
Douglas F. Easton
1
, Karen A. Pooley
2
, Alison M. Dunning
2
, Paul D. P. Pharoah
2
, Deborah
Thompson
1
, Dennis G. Ballinger
3
, Jeffery P. Struewing
4
, Jonathan Morrison
2
, Helen Field
2
,
Robert Luben
5
, Nicholas Wareham
5
, Shahana Ahmed
2
, Catherine S. Healey
2
, Richard
Bowman
6
, the SEARCH collaborators
2
, Kerstin B. Meyer
7
, Christopher A. Haiman
8
,
Laurence K. Kolonel
9
, Brian E. Henderson
8
, Loic Le Marchand
9
, Paul Brennan
10
,
Suleeporn Sangrajrang
11
, Valerie Gaborieau
10
, Fabrice Odefrey
10
, Chen-Yang Shen
12
, Pei-
Ei Wu
12
, Hui-Chun Wang
12
, Diana Eccles
13
, D. Gareth Evans
14
, Julian Peto
15
, Olivia
Fletcher
16
, Nichola Johnson
16
, Sheila Seal
17
, Michael R. Stratton
17,18
, Nazneen Rahman
17
,
Georgia Chenevix-Trench
19
, Stig E. Bojesen
20
, Børge G. Nordestgaard
20
, Christen K.
Axelsson
21
, Montserrat Garcia-Closas
22
, Louise Brinton
22
, Stephen Chanock
23
, Jolanta
Lissowska
24
, Beata Peplonska
25
, Heli Nevanlinna
26
, Rainer Fagerholm
26
, Hannaleena
Eerola
26,27
, Daehee Kang
28
, Keun-Young Yoo
28,29
, Dong-Young Noh
28
, Sei-Hyun Ahn
30
,
David J. Hunter
31,32
, Susan E. Hankinson
32
, David G. Cox
31
, Per Hall
33
, Sara Wedren
33
,
Jianjun Liu
34
, Yen-Ling Low
34
, Natalia Bogdanova
35,36
, Peter Schürmann
36
, Thilo Dörk
36
,
Rob A. E. M. Tollenaar
37
, Catharina E. Jacobi
38
, Peter Devilee
39
, Jan G. M. Klijn
40
, Alice J.
Sigurdson
41
, Michele M. Doody
41
, Bruce H. Alexander
42
, Jinghui Zhang
4
, Angela Cox
43
, Ian
W. Brock
43
, Gordon MacPherson
43
, Malcolm W. R. Reed
44
, Fergus J. Couch
45
, Ellen L.
Goode
45
, Janet E. Olson
45
, Hanne Meijers-Heijboer
46,47
, Ans van den Ouweland
47
, André
Uitterlinden
48
, Fernando Rivadeneira
48
, Roger L. Milne
49
, Gloria Ribas
49
, Anna Gonzalez-
Neira
49
, Javier Benitez
49
, John L. Hopper
50
, Margaret McCredie
51
, Melissa Southey
50
,
Graham G. Giles
52
, Chris Schroen
53
, Christina Justenhoven
54
, Hiltrud Brauch
54
, Ute
Hamann
55
, Yon-Dschun Ko
56
, Amanda B. Spurdle
19
, Jonathan Beesley
19
, Xiaoqing Chen
19
,
kConFab
57
, AOCS Management Group
19,57
, Arto Mannermaa
58,59
, Veli-Matti Kosma
58,59
,
Vesa Kataja
58,60
, Jaana Hartikainen
58,59
, Nicholas E. Day
5
, David R. Cox
3
, and Bruce A. J.
Ponder
2,7
Author affiliations: 1
CR-UK Genetic Epidemiology Unit, Department of Public Health and Primary Care,
University of Cambridge, Cambridge CB1 8RN, UK.
2
Department of Oncology, University of
Cambridge, Cambridge CB1 8RN, UK.
3
Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain
View, California 94043, USA.
4
Laboratory of Population Genetics, US National Cancer Institute,
©2007 Nature Publishing Group
Correspondence and requests for materials should be addressed to D.F.E. (d.easton@srl.cam.ac.uk)..
Author Contributions D.F.E., A.M.D., P.D.P.P., D.R.C. and B.A.J.P. designed the study and obtained financial support. D.G.B. and
D.R.C. directed the genotyping of stages 1 and 2. D.F.E. and D.T. conducted the statistical analysis. K.A.P. and A.M.D. coordinated
the genotyping for stage 3 and the fine-scale mapping of the
FGFR2
and
TNRC9
loci. J.P.S. and J.Z. performed resequencing and
analysis of the
FGFR2
locus. K.A.P., S.A., C.S.H., R.B., C.A.H., L.K.K., B.E.H., L.L.M., P.B., S.S., V.G., F.O., C-Y. S., P-E.W. and
H-C.W. conducted genotyping for the fine-scale mapping. R.L., J.M., H.F. and K.B.M. provided bioinformatics support. D.E., D.G.E.,
J.P., O.F., N.J., S.S., M.R.S. and N.R. coordinated the studies used in stage 1. N.W. and N.E.D. coordinated the EPIC study used in
stages 1 and 2. The remaining authors coordinated the studies in stage 3 and undertook genotyping in those studies. D.F.E. drafted the
manuscript, with substantial contributions from K.A.P., A.M.D., P.D.P.P. and B.A.J.P. All authors contributed to the final paper.
Full Methods and any associated references are available in the online version of the paper at www.nature.com/nature.
Supplementary Information is linked to the online version of the paper at www.nature.com/nature.
Reprints and permissions information is available at www.nature.com/reprints.
The authors declare no competing financial interests.

Bethesda, Maryland 20892, USA.
5
EPIC, Department of Public Health and Primary Care,
University of Cambridge, Cambridge CB1 8RN, UK.
6
MRC Dunn Clinical Nutrition Centre,
Cambridge CB2 0XY, UK.
7
Cancer Research UK Cambridge Research Institute, Cambridge CB2
0RE, UK.
8
Department of Preventive Medicine, Keck School of Medicine, University of Southern
California, Los Angeles, California 90033, USA.
9
Epidemiology Program, Cancer Research
Center of Hawaii, University of Hawaii, Honolulu, Hawaii 96813, USA.
10
International Agency for
Research on Cancer, 150 Cours Albert Thomas, Lyon 69008, France.
11
National Cancer Institute,
Bangkok 10400, Thailand.
12
Institute of Biomedical Sciences, Academia Sinica, Taipei 11529,
Taiwan.
13
Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton SO16 5YA,
UK.
14
Regional Genetic Service, St Mary's Hospital, Manchester M13 0JH, UK.
15
London School
of Hygiene and Tropical Medicine, London WC1E 7HT, UK, and Institute of Cancer Research,
Sutton, Surrey SM2 5NG, UK.
16
Breakthrough Breast Cancer Research Centre, London SW3
6JB, UK.
17
Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey SM2 5NG,
UK.
18
Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome
Campus, Hinxton, Cambridge CB10 1SA, UK.
19
Queensland Institute of Medical Research,
Brisbane, Queensland 4006, Australia
20
Departments of Clinical Biochemistry, Herlev and
Bispebjerg University Hospitals, University of Copenhagen, DK-2730 Herlev, Denmark.
21
Department of Breast Surgery, Herlev and Bispebjerg University Hospitals, University of
Copenhagen, DK-2730 Herlev, Denmark.
22
Division of Cancer Epidemiology and Genetics,
National Cancer Institute, Rockville, Maryland 20852, USA.
23
Advanced Technology Center,
National Cancer Institute, Gaithersburg, Maryland 20877, USA.
24
Cancer Center and M.
Sklodowska-Curie Institute of Oncology, Warsaw 02781, Poland.
25
Nofer Institute of Occupational
Medicine, Lodz 90950, Poland.
26
Departments of Obstetrics and Gynecology, Helsinki University
Central Hospital, Helsinki 00029, Finland.
27
Department of Oncology, Helsinki University Central
Hospital, Helsinki 00029, Finland.
28
Seoul National University College of Medicine, Seoul
151-742, Korea.
29
National Cancer Center, Goyang 411-769, Korea.
30
Ulsan University College
of Medicine, Ulsan 680-749, Korea.
31
Program in Molecular and Genetic Epidemiology, Harvard
School of Public Health, 677 Huntington Ave., Boston, Massachusetts 02115, USA.
32
Channing
Laboratory, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Ave.,
Boston, Massachusetts 02115, USA.
33
Department of Medical Epidemiology and Biostatistics,
Karolinska Institute, Stockholm SE-171 77, Sweden.
34
Population Genetics, Genome Institute of
Singapore, 60 Biopolis Street, Singapore 138672, Republic of Singapore.
35
Department of
Radiation Oncology, Hannover Medical School, D-30625 Hannover, Germany.
36
Department of
Gynecology and Obstetrics, Hannover Medical School, D-30625 Hannover, Germany.
37
Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the
Netherlands.
38
Department of Medical Decision Making, Leiden University Medical Center,
Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
39
Departments of Human Genetics and
Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
40
Family Cancer Clinic, Department of Medical Oncology, Erasmus MC-Daniel den Hoed Cancer
Center, Groene Hilledijk 301, 3075 EA Rotterdam, the Netherlands.
41
Radiation Epidemiology
Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS,
Bethesda, Maryland 20892, USA.
42
Environmental Health Sciences, University of Minnesota,
Minneapolis, Minnesota 55455, USA.
43
Institute for Cancer Studies, Sheffield University Medical
School, Sheffield S10 2RX, UK.
44
Academic Unit of Surgical Oncology, Sheffield University
Medical School, Sheffield S10 2RX, UK.
45
Mayo Clinic College of Medicine, Rochester,
Minnesota 55905, USA.
46
VU University Medical Center, 1007 MB Amsterdam, the Netherlands.
47
Department of Clinical Genetics, Erasmus University, Rotterdam NL-3015-GE, the Netherlands.
48
Internal Medicine, Erasmus University, Rotterdam NL-3015-GE, the Netherlands.
49
Spanish
National Cancer Centre (CNIO), Madrid E-28029, Spain.
50
Centre for Molecular, Environmental,
Genetic and Analytical Epidemiology, University of Melbourne, Carlton, Victoria 3053, Australia.
51
Department of Preventive and Social Medicine, University of Otago, Dunedin 9001, New
Easton et al. Page 2

Zealand.
52
Cancer Epidemiology Centre, Cancer Council Victoria, Carlton, Victoria 3053,
Australia.
53
Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne,
Parkville, Victoria 3052, Australia.
54
Dr. Margarete Fischer-Bosch-Institute of Clinical
Pharamcology, 70376 Stuttgart and University of Tuebingen, 72074 Tuebingen, Germany.
55
Deutsches Krebsforschungszentrum, Heidelberg 69120, Germany.
56
Evangelische Kliniken
Bonn gGmbH Johanniter Krankenhaus, 53113 Bonn, Germany.
57
Peter MacCallum Cancer
Centre, Melbourne, Victoria 3002, Australia.
58
Insitute of Clinical Medicine, Pathology and
Forensic Medicine, University of Kuopio, Kuopio FIN-70210, Finland.
59
Departments of Oncology
and Pathology, University Hospital of Kuopio, Kuopio FIN-70211, Finland.
60
Department of
Oncology, Vaasa Central Hospital, Vaasa 65130, Finland.
Craig Luccarini
1
, Don Conroy
1
, Mitul Shah
1
, Hannah Munday
1
, Clare Jordan
1
, Barbara
Perkins
1
, Judy West
1
, Karen Redman
1
, and Kristy Driver
1
The SEARCH collaborators
Morteza Aghmesheh
2
, David Amor
2
, Lesley Andrews
2
, Yoland Antill
5
, Jane Armes
6
, Shane
Armitage
7
, Leanne Arnold
7
, Rosemary Balleine
8
, Glenn Begley
9
, John Beilby
10
, Ian
Bennett
11
, Barbara Bennett
2
, Geoffrey Berry
12
, Anneke Blackburn
13
, Meagan Brennan
14
,
Melissa Brown
15
, Michael Buckley
16
, Jo Burke
17
, Phyllis Butow
18
, Keith Byron
19
, David
Callen
20
, Ian Campbell
21
, Georgia Chenevix-Trench
22
, Christine Clarke
23
, Alison Colley
24
,
Dick Cotton
25
, Jisheng Cui
26
, Bronwyn Culling
27
, Margaret Cummings
28
, Sarah-Jane
Dawson
5
, Joanne Dixon
29
, Alexander Dobrovic
30
, Tracy Dudding
31
, Ted Edkins
32
, Maurice
Eisenbruch
33
, Gelareh Farshid
34
, Susan Fawcett
35
, Michael Field
36
, Frank Firgaira
37
, Jean
Fleming
38
, John Forbes
39
, Michael Friedlander
40
, Clara Gaff
41
, Mac Gardner
41
, Mike
Gattas
42
, Peter George
43
, Graham Giles
44
, Grantley Gill
45
, Jack Goldblatt
46
, Sian
Greening
47
, Scott Grist
37
, Eric Haan
48
, Marion Harris
49
, Stewart Hart
50
, Nick Hayward
22
,
John Hopper
51
, Evelyn Humphrey
17
, Mark Jenkins
52
, Alison Jones
7
, Rick Kefford
53
, Judy
Kirk
54
, James Kollias
55
, Sergey Kovalenko
56
, Sunil Lakhani
57
, Jennifer Leary
54
, Jacqueline
Lim
58
, Geoff Lindeman
59
, Lara Lipton
60
, Liz Lobb
61
, Mariette Maclurcan
62
, Graham Mann
23
,
Deborah Marsh
63
, Margaret McCredie
64
, Michael McKay
49
, Sue Anne McLachlan
65
, Bettina
Meiser
2
, Roger Milne
26
, Gillian Mitchell
49
, Beth Newman
66
, Imelda O'Loughlin
67
, Richard
Osborne
51
, Lester Peters
68
, Kelly Phillips
5
, Melanie Price
62
, Jeanne Reeve
69
, Tony
Reeve
70
, Robert Richards
71
, Gina Rinehart
72
, Bridget Robinson
73
, Barney Rudzki
74
,
Elizabeth Salisbury
75
, Joe Sambrook
21
, Christobel Saunders
76
, Clare Scott
5
, Elizabeth
Scott
77
, Rodney Scott
31
, Ram Seshadri
37
, Andrew Shelling
78
, Melissa Southey
26
, Amanda
Spurdle
22
, Graeme Suthers
48
, Donna Taylor
79
, Christopher Tennant
58
, Heather Thorne
21
,
Sharron Townshend
46
, Kathy Tucker
2
, Janet Tyler
2
, Deon Venter
80
, Jane Visvader
81
, Ian
Walpole
46
, Robin Ward
82
, Paul Waring
30
, Bev Warner
83
, Graham Warren
67
, Elizabeth
Watson
67
, Rachael Williams
84
, Judy Wilson
85
, Ingrid Winship
69
, and Mary Ann Young
49
kConFab
David Bowtell
86
, Adele Green
22
, Anna deFazio
87
, Georgia Chenevix-Trench
22
, Dorota
Gertig
51
, and Penny Webb
22
AOCS Management Group
Consortia affiliations: 1
Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK.
2
Oncology Research Centre, Prince of Wales Hospital, Randwick, New South Wales 2031,
Australia.
3
Genetic Health Services Victoria, Royal Children's Hospital, Melbourne, Victoria 3050,
Australia.
4
Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, New South Wales
2031, Australia.
5
Department of Haematology and Medical Oncology, Peter MacCallum Cancer
Centre, St Andrews Place, East Melbourne, Victoria 3002, Australia.
6
Anatomical Pathology,
Royal Women's Hospital, Carlton, Victoria 3053, Australia.
7
Molecular Genetics Laboratory, Royal
Brisbane and Women's Hospital, Herston, Queensland 4029, Australia.
8
Departments of
Translational and Medical Oncology, Westmead Hospital, Westmead, New South Wales 2145,
Australia.
9
Cancer Biology Laboratory, TVW Institute for Child Health Research, Subiaco,
Easton et al. Page 3

Frequently asked questions

Q1. What have the authors contributed in "Genome-wide association study identifies novel breast cancer susceptibility loci author" ?

To identify further susceptibility alleles, the authors conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms ( SNPs ) were tested for confirmation in 21,860 cases and 22,578 Easton et al. 

Q2. What future works have the authors mentioned in the paper "Genome-wide association study identifies novel breast cancer susceptibility loci author" ?

The detection of further susceptibility loci will require genome-wide studies with more complete coverage and using larger numbers of cases and controls, together with the combination of results across multiple studies. 

Q3. Why are neighbouring polymorphisms often strongly correlated with each other?

because recombination tends to occur at distinct ‘hot-spots’, neighbouring polymorphisms are often strongly correlated (in ‘linkage disequilibrium’, LD) with each other. 

Q4. What is the reason for the low risk of breast cancer?

Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. 

Q5. What are the common genes in the breast cancer susceptibility study?

Most previously identified breast cancer susceptibility genes are involved in DNA repair, and many association studies in breast cancer have concentrated on genes in DNA repair and sex hormone synthesis and metabolism pathways. 

Q6. What was the method used for the mapping of the FGFR2 locus?

Genotyping for stage 3, and for the fine-scale mapping of the FGFR2 locus, was conducted using either a 5′ nuclease assay (Taqman, Applied Biosystems) or MALDITOF mass spectrometry using the Sequenom iPLEX system. 

Q7. How many SNPs can be analysed in association studies?

Recent technological advances have provided platforms that allow hundreds of thousands of SNPs to be analysed in association studies, thus providing a basis for identifying moderate risk alleles without prior knowledge of position or function. 

Q8. What is the likelihood of a similar study being required to identify common alleles for other?

As most common cancers have similar familial relative risks to breast cancer, it is likely that similarly large studies will be required to identify common alleles for other cancers. 

Q9. How many cases of breast cancer were selected?

The cases were selected to have a strong family history of breast cancer, equivalent to at least two affected female first-degree relatives, because such cases are more likely to carry susceptibility alleles20. 

Q10. How many SNPs are found in HapMap?

On the basis of their staged design and the estimated distribution of linkage disequilibrium between the typed SNPs and those in HapMap, the authors estimate that the power to identify the five most significant associations at P<10−7 (rs2981582, rs3803662, rs889312, rs13281615 and rs3817198) was 93%, 71%, 25%, 3% and 1% respectively. 

Q11. How many variants need to be subjected to functional analysis?

the use of studies from multiple populations with different patterns of LD can substantially reduce the number of variants that need to be subjected to functional analysis. 

Q12. What is the significance of the association between FGFR2 and breast cancer?

It is notable that three of the five loci contain genes related to control of cell growth or to cell signalling, but only one (FGFR2) had a clear priorEaston et al. 

Q13. How many SNPs showed some evidence of association in stage 3?

In particular, three SNPs showed some evidence of association in stage 3 (P<0.05, in each case in the same direction as in stages 1Easton et al.