Genome remodelling in a basal-like breast cancer metastasis and xenograft

Li Ding; Matthew J. Ellis; Shunqiang Li; David E. Larson; Ken Chen; John W. Wallis; Christopher C. Harris; Michael D. McLellan; Robert S. Fulton; Lucinda L. Fulton; Rachel M. Abbott; Jeremy Hoog; David J. Dooling; Daniel C. Koboldt; Heather Schmidt; Joelle Kalicki; Qunyuan Zhang; Lei Chen; Ling Lin; Michael C. Wendl; Joshua F. McMichael; Vincent J. Magrini; Lisa Cook; Sean D. McGrath; Tammi L. Vickery; Elizabeth Appelbaum; Katherine Deschryver; Sherri Davies; Therese Guintoli; Li Lim; Robert Crowder; Yu Tao; Jacqueline E. Snider; Scott M. Smith; Adam F. Dukes; Gabriel E. Sanderson; Craig S. Pohl; Kim D. Delehaunty; Catrina C. Fronick; Kimberley A. Pape; Jerry S. Reed; Jody S. Robinson; Jennifer S. Hodges; William Schierding; Nathan D. Dees; Dong Shen; Devin P. Locke; Madeline E. Wiechert; James M. Eldred; Josh B. Peck; Benjamin J. Oberkfell; Justin T. Lolofie; Feiyu Du; Amy E. Hawkins; Michelle D. Oĝlaughlin; Kelly E. Bernard; Mark Cunningham; Glendoria Elliott; Mark D. Mason; Dominic M. Thompson; Jennifer L. Ivanovich; Paul J. Goodfellow; Charles M. Perou; George M. Weinstock; Rebecca Aft; Mark Watson; Timothy J. Ley; Richard K. Wilson; Elaine R. Mardis

doi:10.1038/nature08989

Genome remodelling in a basal-like breast cancer metastasis and xenograft

Li Ding, Matthew J. Ellis, Shunqiang Li, David E. Larson, Ken Chen, John W. Wallis, Christopher C. Harris, Michael D. McLellan, Robert S. Fulton, Lucinda L. Fulton, Rachel M. Abbott, Jeremy Hoog, David J. Dooling, Daniel C. Koboldt, Heather Schmidt, Joelle Kalicki, Qunyuan Zhang, Lei Chen, Ling Lin, Michael C. WendlJoshua F. McMichael, Vincent J. Magrini, Lisa Cook, Sean D. McGrath, Tammi L. Vickery, Elizabeth Appelbaum, Katherine Deschryver, Sherri Davies, Therese Guintoli, Li Lim, Robert Crowder, Yu Tao, Jacqueline E. Snider, Scott M. Smith, Adam F. Dukes, Gabriel E. Sanderson, Craig S. Pohl, Kim D. Delehaunty, Catrina C. Fronick, Kimberley A. Pape, Jerry S. Reed, Jody S. Robinson, Jennifer S. Hodges, William Schierding, Nathan D. Dees, Dong Shen, Devin P. Locke, Madeline E. Wiechert, James M. Eldred, Josh B. Peck, Benjamin J. Oberkfell, Justin T. Lolofie, Feiyu Du, Amy E. Hawkins, Michelle D. Oĝlaughlin, Kelly E. Bernard, Mark Cunningham, Glendoria Elliott, Mark D. Mason, Dominic M. Thompson, Jennifer L. Ivanovich, Paul J. Goodfellow, Charles M. Perou, George M. Weinstock, Rebecca Aft, Mark Watson, Timothy J. Ley, Richard K. Wilson, Elaine R. Mardis

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

1013 Scopus citations

Abstract

Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The metastasis contained two de novo mutations and a large deletion not present in the primary tumour, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumour mutations and displayed a mutation enrichment pattern that resembled the metastasis. Two overlapping large deletions, encompassing CTNNA1, were present in all three tumour samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour.

Original language	English (US)
Pages (from-to)	999-1005
Number of pages	7
Journal	Nature
Volume	464
Issue number	7291
DOIs	https://doi.org/10.1038/nature08989
State	Published - Apr 15 2010
Externally published	Yes

ASJC Scopus subject areas

General

Access to Document

10.1038/nature08989

Cite this

Ding, L., Ellis, M. J., Li, S., Larson, D. E., Chen, K., Wallis, J. W., Harris, C. C., McLellan, M. D., Fulton, R. S., Fulton, L. L., Abbott, R. M., Hoog, J., Dooling, D. J., Koboldt, D. C., Schmidt, H., Kalicki, J., Zhang, Q., Chen, L., Lin, L., ... Mardis, E. R. (2010). Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature, 464(7291), 999-1005. https://doi.org/10.1038/nature08989

Ding, L, Ellis, MJ, Li, S, Larson, DE, Chen, K, Wallis, JW, Harris, CC, McLellan, MD, Fulton, RS, Fulton, LL, Abbott, RM, Hoog, J, Dooling, DJ, Koboldt, DC, Schmidt, H, Kalicki, J, Zhang, Q, Chen, L, Lin, L, Wendl, MC, McMichael, JF, Magrini, VJ, Cook, L, McGrath, SD, Vickery, TL, Appelbaum, E, Deschryver, K, Davies, S, Guintoli, T, Lim, L, Crowder, R, Tao, Y, Snider, JE, Smith, SM, Dukes, AF, Sanderson, GE, Pohl, CS, Delehaunty, KD, Fronick, CC, Pape, KA, Reed, JS, Robinson, JS, Hodges, JS, Schierding, W, Dees, ND, Shen, D, Locke, DP, Wiechert, ME, Eldred, JM, Peck, JB, Oberkfell, BJ, Lolofie, JT, Du, F, Hawkins, AE, Oĝlaughlin, MD, Bernard, KE, Cunningham, M, Elliott, G, Mason, MD, Thompson, DM, Ivanovich, JL, Goodfellow, PJ, Perou, CM, Weinstock, GM, Aft, R, Watson, M, Ley, TJ, Wilson, RK & Mardis, ER 2010, 'Genome remodelling in a basal-like breast cancer metastasis and xenograft', Nature, vol. 464, no. 7291, pp. 999-1005. https://doi.org/10.1038/nature08989

@article{292592a34d474e79b04f0c3fb23550d7,

title = "Genome remodelling in a basal-like breast cancer metastasis and xenograft",

abstract = "Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The metastasis contained two de novo mutations and a large deletion not present in the primary tumour, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumour mutations and displayed a mutation enrichment pattern that resembled the metastasis. Two overlapping large deletions, encompassing CTNNA1, were present in all three tumour samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour.",

author = "Li Ding and Ellis, {Matthew J.} and Shunqiang Li and Larson, {David E.} and Ken Chen and Wallis, {John W.} and Harris, {Christopher C.} and McLellan, {Michael D.} and Fulton, {Robert S.} and Fulton, {Lucinda L.} and Abbott, {Rachel M.} and Jeremy Hoog and Dooling, {David J.} and Koboldt, {Daniel C.} and Heather Schmidt and Joelle Kalicki and Qunyuan Zhang and Lei Chen and Ling Lin and Wendl, {Michael C.} and McMichael, {Joshua F.} and Magrini, {Vincent J.} and Lisa Cook and McGrath, {Sean D.} and Vickery, {Tammi L.} and Elizabeth Appelbaum and Katherine Deschryver and Sherri Davies and Therese Guintoli and Li Lim and Robert Crowder and Yu Tao and Snider, {Jacqueline E.} and Smith, {Scott M.} and Dukes, {Adam F.} and Sanderson, {Gabriel E.} and Pohl, {Craig S.} and Delehaunty, {Kim D.} and Fronick, {Catrina C.} and Pape, {Kimberley A.} and Reed, {Jerry S.} and Robinson, {Jody S.} and Hodges, {Jennifer S.} and William Schierding and Dees, {Nathan D.} and Dong Shen and Locke, {Devin P.} and Wiechert, {Madeline E.} and Eldred, {James M.} and Peck, {Josh B.} and Oberkfell, {Benjamin J.} and Lolofie, {Justin T.} and Feiyu Du and Hawkins, {Amy E.} and Oĝlaughlin, {Michelle D.} and Bernard, {Kelly E.} and Mark Cunningham and Glendoria Elliott and Mason, {Mark D.} and Thompson, {Dominic M.} and Ivanovich, {Jennifer L.} and Goodfellow, {Paul J.} and Perou, {Charles M.} and Weinstock, {George M.} and Rebecca Aft and Mark Watson and Ley, {Timothy J.} and Wilson, {Richard K.} and Mardis, {Elaine R.}",

note = "Funding Information: Acknowledgements We thank the many members of The Genome Center and Siteman Cancer Center at Washington University in St Louis for support. This work was funded by grants to R.K.W. from Washington University in St Louis and the National Human Genome Research Institute (NHGRI U54 HG003079), and grants to M.J.E. from the National Cancer Institute (NCI 1 U01 CA114722-01), the Susan G Komen Breast Cancer Foundation (BCTR0707808), and the Fashion Footwear Charitable Foundation, Inc. NCI U10 CA076001 and a Breast Cancer Research Foundation grant awarded to the American College of Surgeons Oncology Group supported the acquisition of samples for recurrence testing. The tissue procurement core was supported by an NCI core grant to the Siteman Cancer Center (NCI 3P50 CA68438). The Human and Mouse Linked Evaluation of Tumors Core was supported by the Institute of Clinical and Translational Sciences at Washington University (CTSA grant UL1 RR024992). We also thank Illumina, Inc. for their support and role in the Washington University Cancer Genome Initiative.",

year = "2010",

month = apr,

day = "15",

doi = "10.1038/nature08989",

language = "English (US)",

volume = "464",

pages = "999--1005",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7291",

}

TY - JOUR

T1 - Genome remodelling in a basal-like breast cancer metastasis and xenograft

AU - Ding, Li

AU - Ellis, Matthew J.

AU - Li, Shunqiang

AU - Larson, David E.

AU - Chen, Ken

AU - Wallis, John W.

AU - Harris, Christopher C.

AU - McLellan, Michael D.

AU - Fulton, Robert S.

AU - Fulton, Lucinda L.

AU - Abbott, Rachel M.

AU - Hoog, Jeremy

AU - Dooling, David J.

AU - Koboldt, Daniel C.

AU - Schmidt, Heather

AU - Kalicki, Joelle

AU - Zhang, Qunyuan

AU - Chen, Lei

AU - Lin, Ling

AU - Wendl, Michael C.

AU - McMichael, Joshua F.

AU - Magrini, Vincent J.

AU - Cook, Lisa

AU - McGrath, Sean D.

AU - Vickery, Tammi L.

AU - Appelbaum, Elizabeth

AU - Deschryver, Katherine

AU - Davies, Sherri

AU - Guintoli, Therese

AU - Lim, Li

AU - Crowder, Robert

AU - Tao, Yu

AU - Snider, Jacqueline E.

AU - Smith, Scott M.

AU - Dukes, Adam F.

AU - Sanderson, Gabriel E.

AU - Pohl, Craig S.

AU - Delehaunty, Kim D.

AU - Fronick, Catrina C.

AU - Pape, Kimberley A.

AU - Reed, Jerry S.

AU - Robinson, Jody S.

AU - Hodges, Jennifer S.

AU - Schierding, William

AU - Dees, Nathan D.

AU - Shen, Dong

AU - Locke, Devin P.

AU - Wiechert, Madeline E.

AU - Eldred, James M.

AU - Peck, Josh B.

AU - Oberkfell, Benjamin J.

AU - Lolofie, Justin T.

AU - Du, Feiyu

AU - Hawkins, Amy E.

AU - Oĝlaughlin, Michelle D.

AU - Bernard, Kelly E.

AU - Cunningham, Mark

AU - Elliott, Glendoria

AU - Mason, Mark D.

AU - Thompson, Dominic M.

AU - Ivanovich, Jennifer L.

AU - Goodfellow, Paul J.

AU - Perou, Charles M.

AU - Weinstock, George M.

AU - Aft, Rebecca

AU - Watson, Mark

AU - Ley, Timothy J.

AU - Wilson, Richard K.

AU - Mardis, Elaine R.

N1 - Funding Information: Acknowledgements We thank the many members of The Genome Center and Siteman Cancer Center at Washington University in St Louis for support. This work was funded by grants to R.K.W. from Washington University in St Louis and the National Human Genome Research Institute (NHGRI U54 HG003079), and grants to M.J.E. from the National Cancer Institute (NCI 1 U01 CA114722-01), the Susan G Komen Breast Cancer Foundation (BCTR0707808), and the Fashion Footwear Charitable Foundation, Inc. NCI U10 CA076001 and a Breast Cancer Research Foundation grant awarded to the American College of Surgeons Oncology Group supported the acquisition of samples for recurrence testing. The tissue procurement core was supported by an NCI core grant to the Siteman Cancer Center (NCI 3P50 CA68438). The Human and Mouse Linked Evaluation of Tumors Core was supported by the Institute of Clinical and Translational Sciences at Washington University (CTSA grant UL1 RR024992). We also thank Illumina, Inc. for their support and role in the Washington University Cancer Genome Initiative.

PY - 2010/4/15

Y1 - 2010/4/15

N2 - Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The metastasis contained two de novo mutations and a large deletion not present in the primary tumour, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumour mutations and displayed a mutation enrichment pattern that resembled the metastasis. Two overlapping large deletions, encompassing CTNNA1, were present in all three tumour samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour.

AB - Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The metastasis contained two de novo mutations and a large deletion not present in the primary tumour, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumour mutations and displayed a mutation enrichment pattern that resembled the metastasis. Two overlapping large deletions, encompassing CTNNA1, were present in all three tumour samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour.

UR - http://www.scopus.com/inward/record.url?scp=77951139631&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77951139631&partnerID=8YFLogxK

U2 - 10.1038/nature08989

DO - 10.1038/nature08989

M3 - Article

C2 - 20393555

AN - SCOPUS:77951139631

SN - 0028-0836

VL - 464

SP - 999

EP - 1005

JO - Nature

JF - Nature

IS - 7291

ER -

Genome remodelling in a basal-like breast cancer metastasis and xenograft

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this