Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays

Nucleic Acids Research

Volumn 38, Issue 10, 2010, Pages 3275-3286

  Oldridge, Derek A ^a   Banerjee, Samprit ^a   Setlur, Sunita R ^b   Sboner, Andrea ^c   Demichelis, Fancesca ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA MICROARRAY; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GENETIC ASSOCIATION; HAPLOTYPE MAP; HUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; CHEMISTRY; EVALUATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; STANDARD;

ALGORITHMS; BASE SEQUENCE; DNA COPY NUMBER VARIATIONS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77953694663     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq073     Document Type: Article

References (24)

1. Iafrate, A.J., Feuk, L., Rivera, M.N., Listewnik, M.L., Donahoe, P.K., Qi, Y., Scherer, S.W. and Lee, C. (2004) Detection of large-scale variation in the human genome. Nat Genet., 36, 949-951.
2. Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Maner, S., Massa, H., Walker, M., Chi, M. et al. (2004) Large-scale copy number polymorphism in the human genome. Science, 305, 525-528.
3. de Smith, A.J., Tsalenko, A., Sampas, N., Scheffer, A., Yamada, N.A., Tsang, P., Ben-Dor, A., Yakhini, Z., Ellis, R.J., Bruhn, L. et al. (2007) Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases. Hum. Mol. Genet., 16, 2783-2794.
4. McCarroll, S.A., Kuruvilla, F.G., Korn, J.M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M.H., de Bakker, P.I., Maller, J.B., Kirby, A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., 40, 1166-1174.
5. Shaikh, T.H., Gai, X., Perin, J.C., Glessner, J.T., Xie, H., Murphy, K., O'Hara, R., Casalunovo, T., Conlin, L.K., D'Arcy, M. et al. (2009) High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. Genome Res., 19, 1682-1690.
6. Gokcumen, O. and Lee, C. (2009) Copy number variants (CNVs) in primate species using array-based comparative genomic hybridization. Methods, 49, 18-25.
7. Lee, A.S., Gutierrez-Arcelus, M., Perry, G.H., Vallender, E.J., Johnson, W.E., Miller, G.M., Korbel, J.O. and Lee, C. (2008) Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Hum. Mol. Genet., 17, 1127-1136.
8. Perry, G.H. (2008) The evolutionary significance of copy number variation in the human genome. Cytogenet. Genome Res., 123, 283-287.
9. Perry, G.H., Tchinda, J., McGrath, S.D., Zhang, J., Picker, S.R., Caceres, A.M., Iafrate, A.J., Tyler-Smith, C., Scherer, S.W., Eichler, E.E. et al. (2006) Hotspots for copy number variation in chimpanzees and humans. Proc. Natl Acad. Sci. USA, 103, 8006-8011.
10. McCarroll, S.A. and Altshuler, D.M. (2007) Copy-number variation and association studies of human disease. Nat. Genet., 39, S37-S42.
11. Brennan, C., Zhang, Y., Leo, C., Feng, B., Cauwels, C., Aguirre, A.J., Kim, M., Protopopov, A. and Chin, L. (2004) High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res., 64, 4744-4748.
12. Greshock, J., Feng, B., Nogueira, C., Ivanova, E., Perna, I., Nathanson, K., Protopopov, A., Weber, B.L. and Chin, L. (2007) A comparison of DNA copy number profiling platforms. Cancer Res., 67, 10173-10180.
13. Perry, G.H., Ben-Dor, A., Tsalenko, A., Sampas, N., Rodriguez-Revenga, L., Tran, C.W., Scheffer, A., Steinfeld, I., Tsang, P., Yamada, N.A. et al. (2008) The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet., 82, 685-695.
14. Hupe, P., Stransky, N., Thiery, J.P., Radvanyi, F. and Barillot, E. (2004) Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics, 20, 3413-3422.
15. Olshen, A.B., Venkatraman, E.S., Lucito, R. and Wigler, M. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572.
16. International HapMap Consortium. (2003) The International HapMap Project. Nature, 426, 789-796.
17. Carter, N.P. (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet., 39, S16-S21.
18. Itsara, A., Cooper, G.M., Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R.M., Myers, R.M., Ridker, P.M., Chasman, D.I. et al. (2009) Population analysis of large copy number variants and hotspots of human genetic disease. Am. J. Hum. Genet., 84, 148-161.
19. Korn, J.M., Kuruvilla, F.G., McCarroll, S.A., Wysoker, A., Nemesh, J., Cawley, S., Hubbell, E., Veitch, J., Collins, P.J., Darvishi, K. et al. (2008) Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet., 40, 1253-1260.
20. Demichelis, F., Setlur, S.R., Beroukhim, R., Perner, S., Korbel, J.O., Lafargue, C.J., Pflueger, D., Pina, C., Hofer, M.D., Sboner, A. et al. (2009) Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer, 48, 366-380.
21. Weir, B.A., Woo, M.S., Getz, G., Perner, S., Ding, L., Beroukhim, R., Lin, W.M., Province, M.A., Kraja, A., Johnson, L.A. et al. (2007) Characterizing the cancer genome in lung adenocarcinoma. Nature, 450, 893-898.
22. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
23. Demichelis, F., Greulich, H., Macoska, J.A., Beroukhim, R., Sellers, W.R., Garraway, L. and Rubin, M.A. (2008) SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Res., 36, 2446-2456.
24. Leutenegger, A.L., Prum, B., Genin, E., Verny, C., Lemainque, A., Clerget-Darpoux, F. and Thompson, E.A. (2003) Estimation of the inbreeding coefficient through use of genomic data. Am. J. Hum. Genet., 73, 516-523.