Representational Oligonucleotide Microarray Analysis: a High-resolution Method to Detect Genome Copy Number Variation

Overview

Journal Genome Res

Specialty Genetics

Date 2003 Sep 17

PMID 12975311

Citations 131

Authors

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

Kenneth Q Ye

Adam Olshen

Ennapadam Venkatraman

Larry Norton

Michael Wigler

Affiliations

Soon will be listed here.

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.

Citing Articles

Genomic complexity and clinical significance of the RCCX locus.

Shiryagin V, Devyatkin A, Fateev O, Petriaikina E, Bogdanov V, Antysheva Z PeerJ. 2024; 12:e18243.

PMID: 39512309 PMC: 11542561. DOI: 10.7717/peerj.18243.

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits.

Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X Front Vet Sci. 2024; 10:1334434.

PMID: 38274664 PMC: 10808162. DOI: 10.3389/fvets.2023.1334434.

Detection of Single-Nucleotide and Copy Number Defects Underlying Hyperphenylalaninemia by Next-Generation Sequencing.

Tendi E, Morello G, Guarnaccia M, La Cognata V, Petralia S, Messina M Biomedicines. 2023; 11(7).

PMID: 37509538 PMC: 10377317. DOI: 10.3390/biomedicines11071899.

Genetic variation in placental insufficiency: What have we learned over time?.

Wang L, Fernandez-Boyano I, Robinson W Front Cell Dev Biol. 2022; 10:1038358.

PMID: 36313546 PMC: 9613937. DOI: 10.3389/fcell.2022.1038358.

Tool and techniques study to plant microbiome current understanding and future needs: an overview.

Enespa , Chandra P Commun Integr Biol. 2022; 15(1):209-225.

PMID: 35967908 PMC: 9367660. DOI: 10.1080/19420889.2022.2082736.

References

Mu D, Chen L, Zhang X, See L, Koch C, Yen C . Genomic amplification and oncogenic properties of the KCNK9 potassium channel gene. Cancer Cell. 2003; 3(3):297-302. DOI: 10.1016/s1535-6108(03)00054-0. View

Snijders A, Nowee M, Fridlyand J, Piek J, Dorsman J, Jain A . Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma. Oncogene. 2003; 22(27):4281-6. DOI: 10.1038/sj.onc.1206621. View

Healy J, Thomas E, Schwartz J, Wigler M . Annotating large genomes with exact word matches. Genome Res. 2003; 13(10):2306-15. PMC: 403711. DOI: 10.1101/gr.1350803. View

Tkachuk D, Westbrook C, Andreeff M, Donlon T, Cleary M, Suryanarayan K . Detection of bcr-abl fusion in chronic myelogeneous leukemia by in situ hybridization. Science. 1990; 250(4980):559-62. DOI: 10.1126/science.2237408. View

Lisitsyn N, Wigler M . Cloning the differences between two complex genomes. Science. 1993; 259(5097):946-51. DOI: 10.1126/science.8438152. View

CHEE M, Yang R, Hubbell E, Berno A, Huang X, Stern D . Accessing genetic information with high-density DNA arrays. Science. 1996; 274(5287):610-4. DOI: 10.1126/science.274.5287.610. View

Derisi J, Penland L, Brown P, Bittner M, Meltzer P, Ray M . Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996; 14(4):457-60. DOI: 10.1038/ng1296-457. View

Li J, Yen C, Liaw D, Podsypanina K, Bose S, Wang S . PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science. 1997; 275(5308):1943-7. DOI: 10.1126/science.275.5308.1943. View

Lucito R, Nakimura M, West J, Han Y, Chin K, Jensen K . Genetic analysis using genomic representations. Proc Natl Acad Sci U S A. 1998; 95(8):4487-92. PMC: 22516. DOI: 10.1073/pnas.95.8.4487. View

10.

Bartlett J, Mallon E, Cooke T . The clinical evaluation of HER-2 status: which test to use?. J Pathol. 2003; 199(4):411-7. DOI: 10.1002/path.1354. View

11.

Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E . Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res. 2002; 62(21):6240-5. View

12.

Hamaguchi M, Meth J, von Klitzing C, Wei W, Esposito D, Rodgers L . DBC2, a candidate for a tumor suppressor gene involved in breast cancer. Proc Natl Acad Sci U S A. 2002; 99(21):13647-52. PMC: 129730. DOI: 10.1073/pnas.212516099. View

13.

Yang Y, Dudoit S, Luu P, Lin D, Peng V, Ngai J . Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002; 30(4):e15. PMC: 100354. DOI: 10.1093/nar/30.4.e15. View

14.

J van t Veer L, Dai H, van de Vijver M, He Y, Hart A, Mao M . Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002; 415(6871):530-6. DOI: 10.1038/415530a. View

15.

Nurnberg P, Thiele H, Chandler D, Hohne W, Cunningham M, Ritter H . Heterozygous mutations in ANKH, the human ortholog of the mouse progressive ankylosis gene, result in craniometaphyseal dysplasia. Nat Genet. 2001; 28(1):37-41. DOI: 10.1038/ng0501-37. View

16.

Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J . Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860-921. DOI: 10.1038/35057062. View

17.

Lucito R, West J, Reiner A, Alexander J, Esposito D, Mishra B . Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations. Genome Res. 2000; 10(11):1726-36. PMC: 310939. DOI: 10.1101/gr.138300. View

18.

Ilyin G, Rialland M, Pigeon C, Guguen-Guillouzo C . cDNA cloning and expression analysis of new members of the mammalian F-box protein family. Genomics. 2000; 67(1):40-7. DOI: 10.1006/geno.2000.6211. View

19.

Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D . High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998; 20(2):207-11. DOI: 10.1038/2524. View

20.

Golub T, Slonim D, Tamayo P, Huard C, Gaasenbeek M, Mesirov J . Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999; 286(5439):531-7. DOI: 10.1126/science.286.5439.531. View