Cancer Research Translational Cancer Medicine 2008: Cancer Clinical Trials and Personalized Medicine AACR Conference on Molecular Diagnostics
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Cancer Research Clinical Cancer Research
Cancer Epidemiology Biomarkers & Prevention Molecular Cancer Therapeutics
Molecular Cancer Research Cancer Prevention Research
Cancer Prevention Journals Portal Cancer Reviews Online
Annual Meeting Education Book Cell Growth & Differentiation
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplementary Data
Right arrow Supplementary Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Zhao, X.
Right arrow Articles by Meyerson, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zhao, X.
Right arrow Articles by Meyerson, M.
[Cancer Research 64, 3060-3071, May 1, 2004]
© 2004 American Association for Cancer Research

Regular Articles

An Integrated View of Copy Number and Allelic Alterations in the Cancer Genome Using Single Nucleotide Polymorphism Arrays

Xiaojun Zhao1,4, Cheng Li2,5, J. Guillermo Paez1,3, Koei Chin7, Pasi A. Jänne1,3, Tzu-Hsiu Chen1, Luc Girard8,9, John Minna8,9, David Christiani6, Chris Leo1, Joe W. Gray7, William R. Sellers1,3 and Matthew Meyerson1,4

1 Departments of Medical Oncology and 2 Biostatistical Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts; 3 Departments of Medicine and 4 Pathology, Harvard Medical School, Boston, Massachusetts; 5 Departments of Biostatistics and 6 Environmental Health, Harvard School of Public Health, Boston, Massachusetts; 7 Department of Laboratory Medicine, University of California, San Francisco, California, 8 Hamon Center for Therapeutic Oncology Research, and 9 Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas

Changes in DNA copy number contribute to cancer pathogenesis. We now show that high-density single nucleotide polymorphism (SNP) arrays can detect copy number alterations. By hybridizing genomic representations of breast and lung carcinoma cell line and lung tumor DNA to SNP arrays, and measuring locus-specific hybridization intensity, we detected both known and novel genomic amplifications and homozygous deletions in these cancer samples. Moreover, by combining genotyping with SNP quantitation, we could distinguish loss of heterozygosity events caused by hemizygous deletion from those that occur by copy-neutral events. The simultaneous measurement of DNA copy number changes and loss of heterozygosity events by SNP arrays should strengthen our ability to discover cancer-causing genes and to refine cancer diagnosis.




This article has been cited by other articles:


Home page
 J. Clin. Pathol.Home page
E Korsching, S S Jeffrey, W Meinerz, T Decker, W Boecker, and H Buerger
Basal carcinoma of the breast revisited: an old entity with new interpretations
J. Clin. Pathol., May 1, 2008; 61(5): 553 - 560.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Cahan, L. E. Godfrey, P. S. Eis, T. A. Richmond, R. R. Selzer, M. Brent, H. L. McLeod, T. J. Ley, and T. A. Graubert
wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data
Nucleic Acids Res., April 1, 2008; 36(7): e41 - e41.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
I. G. Yulug and B. Gur-Dedeoglu
Functional genomics in translational cancer research: focus on breast cancer
Brief Funct Genomic Proteomic, March 7, 2008; (2008) eln009v1.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
P. Ouillette, H. Erba, L. Kujawski, M. Kaminski, K. Shedden, and S. N. Malek
Integrated Genomic Profiling of Chronic Lymphocytic Leukemia Identifies Subtypes of Deletion 13q14
Cancer Res., February 15, 2008; 68(4): 1012 - 1021.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
W. M. Lin, A. C. Baker, R. Beroukhim, W. Winckler, W. Feng, J. M. Marmion, E. Laine, H. Greulich, H. Tseng, C. Gates, et al.
Modeling Genomic Diversity and Tumor Dependency in Malignant Melanoma
Cancer Res., February 1, 2008; 68(3): 664 - 673.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Pique-Regi, J. Monso-Varona, A. Ortega, R. C. Seeger, T. J. Triche, and S. Asgharzadeh
Sparse representation and Bayesian detection of genome copy number alterations from microarray data
Bioinformatics, February 1, 2008; 24(3): 309 - 318.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
C. Saddler, P. Ouillette, L. Kujawski, S. Shangary, M. Talpaz, M. Kaminski, H. Erba, K. Shedden, S. Wang, and S. N. Malek
Comprehensive biomarker and genomic analysis identifies p53 status as the major determinant of response to MDM2 inhibitors in chronic lymphocytic leukemia
Blood, February 1, 2008; 111(3): 1584 - 1593.
[Abstract] [Full Text] [PDF]

Home page
 JNCI J Natl Cancer InstHome page
M. A. Bollet, N. Servant, P. Neuvial, C. Decraene, I. Lebigot, J.-P. Meyniel, Y. De Rycke, A. Savignoni, G. Rigaill, P. Hupe, et al.
High-Resolution Mapping of DNA Breakpoints to Define True Recurrences Among Ipsilateral Breast Cancers
J Natl Cancer Inst, January 2, 2008; 100(1): 48 - 58.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
L. M. Hansford, A. E. McKee, L. Zhang, R. E. George, J. T. Gerstle, P. S. Thorner, K. M. Smith, A. T. Look, H. Yeger, F. D. Miller, et al.
Neuroblastoma Cells Isolated from Bone Marrow Metastases Contain a Naturally Enriched Tumor-Initiating Cell
Cancer Res., December 1, 2007; 67(23): 11234 - 11243.
[Abstract] [Full Text] [PDF]

Home page
 J. Mol. Diagn.Home page
C. Spittle, M. R. Ward, K. L. Nathanson, P. A. Gimotty, E. Rappaport, M. S. Brose, A. Medina, R. Letrero, M. Herlyn, and R. H. Edwards
Application of a BRAF Pyrosequencing Assay for Mutation Detection and Copy Number Analysis in Malignant Melanoma
J. Mol. Diagn., September 1, 2007; 9(4): 464 - 471.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
C. W. Ross, P. D. Ouillette, C. M. Saddler, K. A. Shedden, and S. N. Malek
Comprehensive Analysis of Copy Number and Allele Status Identifies Multiple Chromosome Defects Underlying Follicular Lymphoma Pathogenesis
Clin. Cancer Res., August 15, 2007; 13(16): 4777 - 4785.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Laakso, S. Tuupanen, A. Karhu, R. Lehtonen, L. A. Aaltonen, and S. Hautaniemi
Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays
Bioinformatics, August 1, 2007; 23(15): 1952 - 1961.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Pathol.Home page
J. R. Pollack
A Perspective on DNA Microarrays in Pathology Research and Practice
Am. J. Pathol., August 1, 2007; 171(2): 375 - 385.
[Abstract] [Full Text] [PDF]

Home page
 BiostatisticsHome page
B. Xing, C. M. T. Greenwood, and S. B. Bull
A hierarchical clustering method for estimating copy number variation
Biostat., July 1, 2007; 8(3): 632 - 653.
[Abstract] [Full Text] [PDF]

Home page
 Endocr Relat CancerHome page
Y. Nagano, D. H. Kim, L. Zhang, J. A White, J. C Yao, S. R Hamilton, and A. Rashid
Allelic alterations in pancreatic endocrine tumors identified by genome-wide single nucleotide polymorphism analysis
Endocr. Relat. Cancer, June 1, 2007; 14(2): 483 - 492.
[Abstract] [Full Text] [PDF]

Home page
 J. Mol. Diagn.Home page
C. M. Heaphy, W. C. Hines, K. S. Butler, C. M. Haaland, G. Heywood, E. G. Fischer, M. Bisoffi, and J. K. Griffith
Assessment of the Frequency of Allelic Imbalance in Human Tissue Using a Multiplex Polymerase Chain Reaction System
J. Mol. Diagn., April 1, 2007; 9(2): 266 - 271.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Colella, C. Yau, J. M. Taylor, G. Mirza, H. Butler, P. Clouston, A. S. Bassett, A. Seller, C. C. Holmes, and J. Ragoussis
QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data
Nucleic Acids Res., March 27, 2007; (2007) gkm076v3.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
M. Stark and N. Hayward
Genome-Wide Loss of Heterozygosity and Copy Number Analysis in Melanoma Using High-Density Single-Nucleotide Polymorphism Arrays
Cancer Res., March 15, 2007; 67(6): 2632 - 2642.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. Oosting, E. H. Lips, R. van Eijk, P. H.C. Eilers, K. Szuhai, C. Wijmenga, H. Morreau, and T. van Wezel
High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays
Genome Res., March 1, 2007; 17(3): 368 - 376.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
D. Pfeifer, M. Pantic, I. Skatulla, J. Rawluk, C. Kreutz, U. M. Martens, P. Fisch, J. Timmer, and H. Veelken
Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays
Blood, February 1, 2007; 109(3): 1202 - 1210.
[Abstract] [Full Text] [PDF]

Home page
 CarcinogenesisHome page
C. L. Andersen, C. Wiuf, M. Kruhoffer, M. Korsgaard, S. Laurberg, and T. F. Orntoft
Frequent occurrence of uniparental disomy in colorectal cancer
Carcinogenesis, January 1, 2007; 28(1): 38 - 48.
[Abstract] [Full Text] [PDF]

Home page
 Endocr Relat CancerHome page
S. K Gruvberger-Saal, H. E Cunliffe, K. M Carr, and I. A Hedenfalk
Microarrays in breast cancer research and clinical practice - the future lies ahead
Endocr. Relat. Cancer, December 1, 2006; 13(4): 1017 - 1031.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
K.-K. Wong, Y. T.M. Tsang, Y.-M. Chang, J. Su, A. M. Di Francesco, D. Meco, R. Riccardi, L. Perlaky, R. C. Dauser, A. Adesina, et al.
Genome-Wide Allelic Imbalance Analysis of Pediatric Gliomas by Single Nucleotide Polymorphic Allele Array
Cancer Res., December 1, 2006; 66(23): 11172 - 11178.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
D. Komura, F. Shen, S. Ishikawa, K. R. Fitch, W. Chen, J. Zhang, G. Liu, S. Ihara, H. Nakamura, M. E. Hurles, et al.
Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
Genome Res., December 1, 2006; 16(12): 1575 - 1584.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Lamy, C. L. Andersen, F. P. Wikman, and C. Wiuf
Genotyping and annotation of Affymetrix SNP arrays
Nucleic Acids Res., September 1, 2006; 34(14): e100 - e100.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
D. A. Peiffer, J. M. Le, F. J. Steemers, W. Chang, T. Jenniges, F. Garcia, K. Haden, J. Li, C. A. Shaw, J. Belmont, et al.
High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
Genome Res., September 1, 2006; 16(9): 1136 - 1148.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
J. M. Amann, P. Chaurand, A. Gonzalez, J. A. Mobley, P. P. Massion, D. P. Carbone, and R. M. Caprioli
Selective Profiling of Proteins in Lung Cancer Cells from Fine-Needle Aspirates by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Clin. Cancer Res., September 1, 2006; 12(17): 5142 - 5150.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
R. K. Thomas, B. Weir, and M. Meyerson
Genomic approaches to lung cancer.
Clin. Cancer Res., July 15, 2006; 12(14): 4384s - 4391s.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
A. Dutt and K.-K. Wong
Mouse models of lung cancer.
Clin. Cancer Res., July 15, 2006; 12(14): 4396s - 4402s.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
J. T. Park, M. Li, K. Nakayama, T.-L. Mao, B. Davidson, Z. Zhang, R. J. Kurman, C. G. Eberhart, I.-M. Shih, and T.-L. Wang
Notch3 gene amplification in ovarian cancer.
Cancer Res., June 15, 2006; 66(12): 6312 - 6318.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
E. Yuan, F. Haghighi, S. White, R. Costa, J. McMinn, K. Chun, M. Minden, and B. Tycko
A single nucleotide polymorphism chip-based method for combined genetic and epigenetic profiling: validation in decitabine therapy and tumor/normal comparisons.
Cancer Res., April 1, 2006; 66(7): 3443 - 3451.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
C. A. Baron, C. G. Tepper, S. Y. Liu, R. R. Davis, N. J. Wang, N. C. Schanen, and J. P. Gregg
Genomic and functional profiling of duplicated chromosome 15 cell lines reveal regulatory alterations in UBE3A-associated ubiquitin-proteasome pathway processes
Hum. Mol. Genet., March 15, 2006; 15(6): 853 - 869.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Ylstra, P. van den IJssel, B. Carvalho, R. H. Brakenhoff, and G. A. Meijer
BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)
Nucleic Acids Res., January 26, 2006; 34(2): 445 - 450.
[Abstract] [Full Text] [PDF]

Home page
 ASH Education BookHome page
J. R. Downing and C. G. Mullighan
Tumor-Specific Genetic Lesions and Their Influence on Therapy in Pediatric Acute Lymphoblastic Leukemia
Hematology, January 1, 2006; 2006(1): 118 - 122.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Wang, M. Moorhead, G. Karlin-Neumann, M. Falkowski, C. Chen, F. Siddiqui, R. W. Davis, T. D. Willis, and M. Faham
Allele quantification using molecular inversion probes (MIP)
Nucleic Acids Res., November 28, 2005; 33(21): e183 - e183.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
E. H. Lips, J. W. F. Dierssen, R. van Eijk, J. Oosting, P. H.C. Eilers, R. A.E.M. Tollenaar, E. J. de Graaf, R. van't Slot, C. Wijmenga, H. Morreau, et al.
Reliable High-Throughput Genotyping and Loss-of-Heterozygosity Detection in Formalin-Fixed, Paraffin-Embedded Tumors Using Single Nucleotide Polymorphism Arrays
Cancer Res., November 15, 2005; 65(22): 10188 - 10191.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Willenbrock and J. Fridlyand
A comparison study: applying segmentation to array CGH data for downstream analyses
Bioinformatics, November 15, 2005; 21(22): 4084 - 4091.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
P. L.M. Dahia, K. Hao, J. Rogus, C. Colin, M. A.G. Pujana, K. Ross, D. Magoffin, N. Aronin, A. Cascon, C. Y. Hayashida, et al.
Novel Pheochromocytoma Susceptibility Loci Identified by Integrative Genomics
Cancer Res., November 1, 2005; 65(21): 9651 - 9658.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
K. Zieger, L. Dyrskjot, C. Wiuf, J. L. Jensen, C. L. Andersen, K. M.-E. Jensen, and T. F. Orntoft
Role of Activating Fibroblast Growth Factor Receptor 3 Mutations in the Development of Bladder Tumors
Clin. Cancer Res., November 1, 2005; 11(21): 7709 - 7719.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Huang, B. Wu, P. Lizardi, and H. Zhao
Detection of DNA copy number alterations using penalized least squares regression
Bioinformatics, October 15, 2005; 21(20): 3811 - 3817.
[Abstract] [Full Text] [PDF]

Home page
 JCOHome page
L. J. Wirth, R. I. Haddad, N. I. Lindeman, X. Zhao, J. C. Lee, V. A. Joshi, C. M. Norris Jr, and M. R. Posner
Phase I Study of Gefitinib Plus Celecoxib in Recurrent or Metastatic Squamous Cell Carcinoma of the Head and Neck
J. Clin. Oncol., October 1, 2005; 23(28): 6976 - 6981.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
Y. Nannya, M. Sanada, K. Nakazaki, N. Hosoya, L. Wang, A. Hangaishi, M. Kurokawa, S. Chiba, D. K. Bailey, G. C. Kennedy, et al.
A Robust Algorithm for Copy Number Detection Using High-Density Oligonucleotide Single Nucleotide Polymorphism Genotyping Arrays
Cancer Res., July 15, 2005; 65(14): 6071 - 6079.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
X. Zhao, B. A. Weir, T. LaFramboise, M. Lin, R. Beroukhim, L. Garraway, J. Beheshti, J. C. Lee, K. Naoki, W. G. Richards, et al.
Homozygous Deletions and Chromosome Amplifications in Human Lung Carcinomas Revealed by Single Nucleotide Polymorphism Array Analysis
Cancer Res., July 1, 2005; 65(13): 5561 - 5570.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
N. Hu, C. Wang, Y. Hu, H. H. Yang, C. Giffen, Z.-Z. Tang, X.-Y. Han, A. M. Goldstein, M. R. Emmert-Buck, K. H. Buetow, et al.
Genome-Wide Association Study in Esophageal Cancer Using GeneChip Mapping 10K Array
Cancer Res., April 1, 2005; 65(7): 2542 - 2546.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
M. Raghavan, D. M. Lillington, S. Skoulakis, S. Debernardi, T. Chaplin, N. J. Foot, T. A. Lister, and B. D. Young
Genome-Wide Single Nucleotide Polymorphism Analysis Reveals Frequent Partial Uniparental Disomy Due to Somatic Recombination in Acute Myeloid Leukemias
Cancer Res., January 15, 2005; 65(2): 375 - 378.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
A. Forche, G. May, and P. T. Magee
Demonstration of Loss of Heterozygosity by Single-Nucleotide Polymorphism Microarray Analysis and Alterations in Strain Morphology in Candida albicans Strains during Infection
Eukaryot. Cell, January 1, 2005; 4(1): 156 - 165.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. T. Barrett, A. Scheffer, A. Ben-Dor, N. Sampas, D. Lipson, R. Kincaid, P. Tsang, B. Curry, K. Baird, P. S. Meltzer, et al.
Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA
PNAS, December 21, 2004; 101(51): 17765 - 17770.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Cardoso, L. Molenaar, R. X. de Menezes, C. Rosenberg, H. Morreau, G. Moslein, R. Fodde, and J. M. Boer
Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH
Nucleic Acids Res., October 28, 2004; 32(19): e146 - e146.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Tengs, T. LaFramboise, R. B. Den, D. N. Hayes, J. Zhang, S. DebRoy, R. C. Gentleman, K. O'Neill, B. Birren, and M. Meyerson
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Nucleic Acids Res., August 25, 2004; 32(15): e121 - e121.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
C. Brennan, Y. Zhang, C. Leo, B. Feng, C. Cauwels, A. J. Aguirre, M. Kim, A. Protopopov, and L. Chin
High-Resolution Global Profiling of Genomic Alterations with Long Oligonucleotide Microarray
Cancer Res., July 15, 2004; 64(14): 4744 - 4748.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. G. Paez, M. Lin, R. Beroukhim, J. C. Lee, X. Zhao, D. J. Richter, S. Gabriel, P. Herman, H. Sasaki, D. Altshuler, et al.
Genome coverage and sequence fidelity of {phi}29 polymerase-based multiple strand displacement whole genome amplification
Nucleic Acids Res., May 18, 2004; 32(9): e71 - e71.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Cancer Research Clinical Cancer Research
Cancer Epidemiology Biomarkers & Prevention Molecular Cancer Therapeutics
Molecular Cancer Research Cancer Prevention Research
Cancer Prevention Journals Portal Cancer Reviews Online
Annual Meeting Education Book Cell Growth & Differentiation
Copyright © 2004 by the American Association for Cancer Research.