Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation

Robert Lucito, John Healy, Joan Alexander, Andrew Reiner, Diane Esposito, Maoyen Chi, Linda Rodgers, Amy Brady, Jonathan Sebat, Jennifer Troge, Joseph A. West, Seth Rostan, Ken C Q Nguyen, Scott Powers, Qian K. Ye, Adam Olshen, Ennapadam Venkatraman, Larry Norton, Michael Wigler

Research output: Contribution to journalArticle

324 Citations (Scopus)

Abstract

We have developed a methodology we call ROMA (representational oligonucleotide microarray analysis), for the detection of the genomic aberrations in cancer and normal humans. By arraying oligonucleotide probes designed from the human genome sequence, and hybridizing with "representations" from cancer and normal cells, we detect regions of the genome with altered "copy number." We achieve an average resolution of 30 kb throughout the genome, and resolutions as high as a probe every 15 kb are practical. We illustrate the characteristics of probes on the array and accuracy of measurements obtained using ROMA. Using this methodology, we identify variation between cancer and normal genomes, as well as between normal human genomes. In cancer genomes, we readily detect amplifications and large and small homozygous and hemizygous deletions. Between normal human genomes, we frequently detect large (100 kb to 1 Mb) deletions or duplications. Many of these changes encompass known genes. ROMA will assist in the discovery of genes and markers important in cancer, and the discovery of loci that may be important in inherited predispositions to disease.

Original languageEnglish (US)
Pages (from-to)2291-2305
Number of pages15
JournalGenome Research
Volume13
Issue number10
DOIs
StatePublished - Oct 1 2003
Externally publishedYes

Fingerprint

Microarray Analysis
Oligonucleotide Array Sequence Analysis
Genome
Human Genome
Neoplasms
Oligonucleotide Probes
Genetic Association Studies
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Lucito, R., Healy, J., Alexander, J., Reiner, A., Esposito, D., Chi, M., ... Wigler, M. (2003). Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation. Genome Research, 13(10), 2291-2305. https://doi.org/10.1101/gr.1349003

Representational oligonucleotide microarray analysis : A high-resolution method to detect genome copy number variation. / Lucito, Robert; Healy, John; Alexander, Joan; Reiner, Andrew; Esposito, Diane; Chi, Maoyen; Rodgers, Linda; Brady, Amy; Sebat, Jonathan; Troge, Jennifer; West, Joseph A.; Rostan, Seth; Nguyen, Ken C Q; Powers, Scott; Ye, Qian K.; Olshen, Adam; Venkatraman, Ennapadam; Norton, Larry; Wigler, Michael.

In: Genome Research, Vol. 13, No. 10, 01.10.2003, p. 2291-2305.

Research output: Contribution to journalArticle

Lucito, R, Healy, J, Alexander, J, Reiner, A, Esposito, D, Chi, M, Rodgers, L, Brady, A, Sebat, J, Troge, J, West, JA, Rostan, S, Nguyen, KCQ, Powers, S, Ye, QK, Olshen, A, Venkatraman, E, Norton, L & Wigler, M 2003, 'Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation', Genome Research, vol. 13, no. 10, pp. 2291-2305. https://doi.org/10.1101/gr.1349003
Lucito, Robert ; Healy, John ; Alexander, Joan ; Reiner, Andrew ; Esposito, Diane ; Chi, Maoyen ; Rodgers, Linda ; Brady, Amy ; Sebat, Jonathan ; Troge, Jennifer ; West, Joseph A. ; Rostan, Seth ; Nguyen, Ken C Q ; Powers, Scott ; Ye, Qian K. ; Olshen, Adam ; Venkatraman, Ennapadam ; Norton, Larry ; Wigler, Michael. / Representational oligonucleotide microarray analysis : A high-resolution method to detect genome copy number variation. In: Genome Research. 2003 ; Vol. 13, No. 10. pp. 2291-2305.
@article{1b3b51a2ffaa4ad1b7f8bcb273e1e558,
title = "Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation",
abstract = "We have developed a methodology we call ROMA (representational oligonucleotide microarray analysis), for the detection of the genomic aberrations in cancer and normal humans. By arraying oligonucleotide probes designed from the human genome sequence, and hybridizing with {"}representations{"} from cancer and normal cells, we detect regions of the genome with altered {"}copy number.{"} We achieve an average resolution of 30 kb throughout the genome, and resolutions as high as a probe every 15 kb are practical. We illustrate the characteristics of probes on the array and accuracy of measurements obtained using ROMA. Using this methodology, we identify variation between cancer and normal genomes, as well as between normal human genomes. In cancer genomes, we readily detect amplifications and large and small homozygous and hemizygous deletions. Between normal human genomes, we frequently detect large (100 kb to 1 Mb) deletions or duplications. Many of these changes encompass known genes. ROMA will assist in the discovery of genes and markers important in cancer, and the discovery of loci that may be important in inherited predispositions to disease.",
author = "Robert Lucito and John Healy and Joan Alexander and Andrew Reiner and Diane Esposito and Maoyen Chi and Linda Rodgers and Amy Brady and Jonathan Sebat and Jennifer Troge and West, {Joseph A.} and Seth Rostan and Nguyen, {Ken C Q} and Scott Powers and Ye, {Qian K.} and Adam Olshen and Ennapadam Venkatraman and Larry Norton and Michael Wigler",
year = "2003",
month = "10",
day = "1",
doi = "10.1101/gr.1349003",
language = "English (US)",
volume = "13",
pages = "2291--2305",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "10",

}

TY - JOUR

T1 - Representational oligonucleotide microarray analysis

T2 - A high-resolution method to detect genome copy number variation

AU - Lucito, Robert

AU - Healy, John

AU - Alexander, Joan

AU - Reiner, Andrew

AU - Esposito, Diane

AU - Chi, Maoyen

AU - Rodgers, Linda

AU - Brady, Amy

AU - Sebat, Jonathan

AU - Troge, Jennifer

AU - West, Joseph A.

AU - Rostan, Seth

AU - Nguyen, Ken C Q

AU - Powers, Scott

AU - Ye, Qian K.

AU - Olshen, Adam

AU - Venkatraman, Ennapadam

AU - Norton, Larry

AU - Wigler, Michael

PY - 2003/10/1

Y1 - 2003/10/1

N2 - We have developed a methodology we call ROMA (representational oligonucleotide microarray analysis), for the detection of the genomic aberrations in cancer and normal humans. By arraying oligonucleotide probes designed from the human genome sequence, and hybridizing with "representations" from cancer and normal cells, we detect regions of the genome with altered "copy number." We achieve an average resolution of 30 kb throughout the genome, and resolutions as high as a probe every 15 kb are practical. We illustrate the characteristics of probes on the array and accuracy of measurements obtained using ROMA. Using this methodology, we identify variation between cancer and normal genomes, as well as between normal human genomes. In cancer genomes, we readily detect amplifications and large and small homozygous and hemizygous deletions. Between normal human genomes, we frequently detect large (100 kb to 1 Mb) deletions or duplications. Many of these changes encompass known genes. ROMA will assist in the discovery of genes and markers important in cancer, and the discovery of loci that may be important in inherited predispositions to disease.

AB - We have developed a methodology we call ROMA (representational oligonucleotide microarray analysis), for the detection of the genomic aberrations in cancer and normal humans. By arraying oligonucleotide probes designed from the human genome sequence, and hybridizing with "representations" from cancer and normal cells, we detect regions of the genome with altered "copy number." We achieve an average resolution of 30 kb throughout the genome, and resolutions as high as a probe every 15 kb are practical. We illustrate the characteristics of probes on the array and accuracy of measurements obtained using ROMA. Using this methodology, we identify variation between cancer and normal genomes, as well as between normal human genomes. In cancer genomes, we readily detect amplifications and large and small homozygous and hemizygous deletions. Between normal human genomes, we frequently detect large (100 kb to 1 Mb) deletions or duplications. Many of these changes encompass known genes. ROMA will assist in the discovery of genes and markers important in cancer, and the discovery of loci that may be important in inherited predispositions to disease.

UR - http://www.scopus.com/inward/record.url?scp=10744231187&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=10744231187&partnerID=8YFLogxK

U2 - 10.1101/gr.1349003

DO - 10.1101/gr.1349003

M3 - Article

C2 - 12975311

AN - SCOPUS:10744231187

VL - 13

SP - 2291

EP - 2305

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 10

ER -