Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing

被引：500

作者：

Leary, Rebecca J. ^{[1
,2
]}

Sausen, Mark ^{[1
,2
]}

Kinde, Isaac ^{[1
,2
]}

Papadopoulos, Nickolas ^{[1
,2
]}

Carpten, John D. ^{[3
]}

Craig, David ^{[3
]}

O'Shaughnessy, Joyce ^{[4
]}

Kinzler, Kenneth W. ^{[1
,2
]}

Parmigiani, Giovanni ^{[5
,6
]}

Vogelstein, Bert ^{[1
,2
]}

Diaz, Luis A., Jr. ^{[1
,2
]}

Velculescu, Victor E. ^{[1
,2
]}

机构：

[1] Johns Hopkins Kimmel Canc Ctr, Ludwig Ctr Canc Genet, Baltimore, MD 21287 USA

[2] Johns Hopkins Kimmel Canc Ctr, Howard Hughes Med Inst, Baltimore, MD 21287 USA

[3] Translat Genom Res Inst, Phoenix, AZ 85044 USA

[4] US Oncol, Texas Oncol, Baylor Sammons Canc Ctr, Dallas, TX 75246 USA

[5] Dana Farber Canc Inst, Dept Biostat & Comp Biol, Boston, MA 02215 USA

[6] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

来源：

SCIENCE TRANSLATIONAL MEDICINE | 2012年 / 4卷 / 162期

关键词：

MINIMAL RESIDUAL DISEASE; ACUTE LYMPHOBLASTIC-LEUKEMIA; DETECTABLE CLONAL MOSAICISM; COPY-NUMBER; MUTATIONS; REARRANGEMENTS; PLASMA; BREAST; DNA; IDENTIFICATION;

D O I：

10.1126/scitranslmed.3004742

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

Clinical management of cancer patients could be improved through the development of noninvasive approaches for the detection of incipient, residual, and recurrent tumors. We describe an approach to directly identify tumor-derived chromosomal alterations through analysis of circulating cell-free DNA from cancer patients. Whole-genome analyses of DNA from the plasma of 10 colorectal and breast cancer patients and 10 healthy individuals with massively parallel sequencing identified, in all patients, structural alterations that were not present in plasma DNA from healthy subjects. Detected alterations comprised chromosomal copy number changes and rearrangements, including amplification of cancer driver genes such as ERBB2 and CDK6. The level of circulating tumor DNA in the cancer patients ranged from 1.4 to 47.9%. The sensitivity and specificity of this approach are dependent on the amount of sequence data obtained and are derived from the fact that most cancers harbor multiple chromosomal alterations, each of which is unlikely to be present in normal cells. Given that chromosomal abnormalities are present in nearly all human cancers, this approach represents a useful method for the noninvasive detection of human tumors that is not dependent on the availability of tumor biopsies.

引用

页数：12

共 42 条

[1] Personalized copy number and segmental duplication maps using next-generation sequencing [J].

Alkan, Can ;

Kidd, Jeffrey M. ;

Marques-Bonet, Tomas ;

Aksay, Gozde ;

Antonacci, Francesca ;

Hormozdiari, Fereydoun ;

Kitzman, Jacob O. ;

Baker, Carl ;

Malig, Maika ;

Mutlu, Onur ;

Sahinalp, S. Cenk ;

Gibbs, Richard A. ;

Eichler, Evan E. .

NATURE GENETICS, 2009, 41 (10) :1061-U29

[2] A map of human genome variation from population-scale sequencing [J].

Altshuler, David ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Collins, Francis S. ;

De la Vega, Francisco M. ;

Donnelly, Peter ;

Egholm, Michael ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Knoppers, Bartha M. ;

Lander, Eric S. ;

Lehrach, Hans ;

Mardis, Elaine R. ;

McVean, Gil A. ;

Nickerson, DebbieA. ;

Peltonen, Leena ;

Schafer, Alan J. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Deiros, David ;

Metzker, Mike ;

Muzny, Donna ;

Reid, Jeff ;

Wheeler, David ;

Wang, Jun ;

Li, Jingxiang ;

Jian, Min ;

Li, Guoqing ;

Li, Ruiqiang ;

Liang, Huiqing ;

Tian, Geng ;

Wang, Bo ;

Wang, Jian ;

Wang, Wei ;

Yang, Huanming ;

Zhang, Xiuqing ;

Zheng, Huisong ;

Lander, Eric S. ;

Altshuler, David L. ;

Ambrogio, Lauren ;

Bloom, Toby ;

Cibulskis, Kristian ;

Fennell, Tim J. ;

Gabriel, Stacey B. .

NATURE, 2010, 467 (7319) :1061-1073

[3] CHROMOSOME-17 DELETIONS AND P53 GENE-MUTATIONS IN COLORECTAL CARCINOMAS [J].

BAKER, SJ ;

FEARON, ER ;

NIGRO, JM ;

HAMILTON, SR ;

PREISINGER, AC ;

JESSUP, JM ;

VANTUINEN, P ;

LEDBETTER, DH ;

BARKER, DF ;

NAKAMURA, Y ;

WHITE, R ;

VOGELSTEIN, B .

SCIENCE, 1989, 244 (4901) :217-221

[4] Leukemia- and lymphoma-associated genetic aberrations in healthy individuals [J].

Bäsecke, J ;

Griesinger, F ;

Trümper, L ;

Brittinger, G .

ANNALS OF HEMATOLOGY, 2002, 81 (02) :64-75

[5] The landscape of somatic copy-number alteration across human cancers [J].

Beroukhim, Rameen ;

Mermel, Craig H. ;

Porter, Dale ;

Wei, Guo ;

Raychaudhuri, Soumya ;

Donovan, Jerry ;

Barretina, Jordi ;

Boehm, Jesse S. ;

Dobson, Jennifer ;

Urashima, Mitsuyoshi ;

Mc Henry, Kevin T. ;

Pinchback, Reid M. ;

Ligon, Azra H. ;

Cho, Yoon-Jae ;

Haery, Leila ;

Greulich, Heidi ;

Reich, Michael ;

Winckler, Wendy ;

Lawrence, Michael S. ;

Weir, Barbara A. ;

Tanaka, Kumiko E. ;

Chiang, Derek Y. ;

Bass, Adam J. ;

Loo, Alice ;

Hoffman, Carter ;

Prensner, John ;

Liefeld, Ted ;

Gao, Qing ;

Yecies, Derek ;

Signoretti, Sabina ;

Maher, Elizabeth ;

Kaye, Frederic J. ;

Sasaki, Hidefumi ;

Tepper, Joel E. ;

Fletcher, Jonathan A. ;

Tabernero, Josep ;

Baselga, Jose ;

Tsao, Ming-Sound ;

Demichelis, Francesca ;

Rubin, Mark A. ;

Janne, Pasi A. ;

Daly, Mark J. ;

Nucera, Carmelo ;

Levine, Ross L. ;

Ebert, Benjamin L. ;

Gabriel, Stacey ;

Rustgi, Anil K. ;

Antonescu, Cristina R. ;

Ladanyi, Marc ;

Letai, Anthony .

NATURE, 2010, 463 (7283) :899-905

[6] MINIMAL RESIDUAL DISEASE IN ACUTE LYMPHOBLASTIC-LEUKEMIA DETECTED BY IMMUNE SELECTION AND GENE REARRANGEMENT ANALYSIS [J].

BREGNI, M ;

SIENA, S ;

NERI, A ;

BASSAN, R ;

BARBUI, T ;

DELIA, D ;

BONADONNA, G ;

FAVERA, RD ;

GIANNI, AM .

JOURNAL OF CLINICAL ONCOLOGY, 1989, 7 (03) :338-343

[7] GENE AMPLIFICATION IN HUMAN NEUROBLASTOMAS - BASIC MECHANISMS AND CLINICAL IMPLICATIONS [J].

BRODEUR, GM ;

SEEGER, RC .

CANCER GENETICS AND CYTOGENETICS, 1986, 19 (1-2) :101-111

[8] Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing [J].

Campbell, Peter J. ;

Stephens, Philip J. ;

Pleasance, Erin D. ;

O'Meara, Sarah ;

Li, Heng ;

Santarius, Thomas ;

Stebbings, Lucy A. ;

Leroy, Catherine ;

Edkins, Sarah ;

Hardy, Claire ;

Teague, Jon W. ;

Menzies, Andrew ;

Goodhead, Ian ;

Turner, Daniel J. ;

Clee, Christopher M. ;

Quail, Michael A. ;

Cox, Antony ;

Brown, Clive ;

Durbin, Richard ;

Hurles, Matthew E. ;

Edwards, Paul A. W. ;

Bignell, Graham R. ;

Stratton, Michael R. ;

Futreal, P. Andrew .

NATURE GENETICS, 2008, 40 (06) :722-729

[9] Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma [J].

Chiu, Rossa W. K. ;

Chan, K. C. Allen ;

Gao, Yuan ;

Lau, Virginia Y. M. ;

Zheng, Wenli ;

Leung, Tak Y. ;

Foo, Chris H. F. ;

Xie, Bin ;

Tsui, Nancy B. Y. ;

Lun, Fiona M. F. ;

Zee, Benny C. Y. ;

Lau, Tze K. ;

Cantor, Charles R. ;

Lo, Y. M. Dennis .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (51) :20458-20463

[10] Detection and quantification of mutations in the plasma of patients with colorectal tumors [J].

Diehl, F ;

Li, M ;

Dressman, D ;

He, YP ;

Shen, D ;

Szabo, S ;

Diaz, LA ;

Goodman, SN ;

David, KA ;

Juhl, H ;

Kinzler, KW ;

Vogelstein, B .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (45) :16368-16373

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