Accurate and reliable high-throughput detection of copy number variation in the human genome

Genome Research

Volumn 16, Issue 12, 2006, Pages 1566-1574

  Fiegler, Heike ^a   Redon, Richard ^a   Andrews, Dan ^a   Scott, Carol ^a   Andrews, Robert ^a   Carder, Carol ^a   Clark, Richard ^a   Dovey, Oliver ^a   Ellis, Peter ^a   Feuk, Lars ^b,c   French, Lisa ^a   Hunt, Paul ^a   Kalaitzopoulos, Dimitrios ^a   Larkin, James ^a   Montgomery, Lyndal ^a   Perry, George H ^d   Plumb, Bob W ^a   Porter, Keith ^a   Rigby, Rachel E ^a   Rigler, Diane ^a   Valsesia, Armand ^a   Langford, Cordelia ^a   Humphray, Sean J ^a   Scherer, Stephen W ^b,c   Lee, Charles ^d,e   Hurles, Matthew E ^a   Carter, Nigel P ^a   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; EUCHROMATIN; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; HYBRIDIZATION; MOLECULAR CLONING; PRIORITY JOURNAL;

ALGORITHMS; CHROMOSOME MAPPING; DNA; DNA FINGERPRINTING; EUCHROMATIN; FALSE NEGATIVE REACTIONS; FALSE POSITIVE REACTIONS; GENE DOSAGE; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; VARIATION (GENETICS);

EID: 33751349817     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5630906     Document Type: Article

References (21)

1. Adams, D.J., Quail, M.A., Cox, T., van der Weyden, L., Gorick, B.D., Su, Q., Chan, W.I., Davies, R., Bonfield, J.K., Law, F., et al. 2005. A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction. Genomics 86: 753-758.
2. Charbonnier, F., Raux, G., Wang, Q., Drouot, N., Cordier, F., Limacher, J.M., Saurin, J.C., Puisieux, A., Olschwang, S., and Frebourg, T. 2000. Detection of exon deletions and duplications of the mismatch repair genes in hereditary nonpolyposis colorectal cancer families using multiplex polymerase chain reaction of short fluorescent fragments. Cancer Res. 60: 2760-2763.
3. Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E., and Pritchard, J.K. 2006. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38: 75-81.
4. Fiegler, H., Carr, P., Douglas, E.J., Burford, D.C., Hunt, S., Scott, C.E., Smith, J., Vetrie, D., Gorman, P., Tomlinson, I.P., et al. 2003. DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 36: 361-374.
5. Humphray, S.J., Knaggs, S.J., and Ragoussis, I. 2001. Contiguation of bacterial clones. Methods Mol. Biol. 175: 69-108.
6. 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.
7. Ishkanian, A.S., Malloff, C.A., Watson, S.K., DeLeeuw, R.J., Chi, B., Coe, B.P., Snijders, A., Albertson, D.G., Pinkel, D., Marra, M.A., et al. 2004. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet. 36: 299-303.
8. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
9. Marra, M.A., Kucaba, T.A., Dietrich, N.L., Green, E.D., Brownstein, B., Wilson, R.K., McDonald, K.M., Hillier, L.W., McPherson, J.D., and Waterston, R.H. 1997. High throughput fingerprint analysis of large-insert clones. Genome Res. 7: 1072-1084.
10. Newman, T.L., Tuzun, E., Morrison, V.A., Hayden, K.E., Ventura, M., McGrath, S.D., Rocchi, M., and Eichler, E.E. 2005. A genome-wide survey of structural variation between human and chimpanzee. Genome Res. 15: 1344-1356.
11. 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.
12. 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. 103: 8006-8011.
13. Price, T.S., Regan, R., Mott, R., Hedman, A., Honey, B., Daniels, R.J., Smith, L., Greenfield, A., Tiganescu, A., Buckle, V., et al. 2005. SW-ARRAY: A dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res. 33: 3455-3464.
14. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., Fiegler, H., Shapero, M.H., Chen, W., et al. 2006. Global variation in copy number in the human genome. Nature (in press).
15. Rickman, L., Fiegler, H., Shaw-Smith, C., Nash, R., Cirigliano, V., Voglino, G., Ng, B.L., Scott, C., Whittaker, J., Adinolfi, M., et al. 2006. Prenatal detection of unbalanced chromosomal rearrangements by array CGH. J. Med. Genet. 43: 353-361.
16. 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.
17. Sharp, A.J., Locke, D.P., McGrath, S.D., Cheng, Z., Bailey, J.A., Vallente, R.U., Pertz, L.M., Clark, R.A., Schwartz, S., Segraves, R., et al. 2005. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77: 78-88.
18. Smith, T.F. and Waterman, M.S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197.
19. Soderlund, C., Humphray, S., Dunham, A., and French, L. 2000. Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10: 1772-1787.
20. Tuzun, E., Sharp, A.J., Bailey, J.A., Kaul, R., Morrison, V.A., Pertz, L.M., Haugen, E., Hayden, H., Albertson, D., Pinkel, D., et al. 2005. Fine-scale structural variation of the human genome. Nat. Genet. 37: 727-732.
21. Ylstra, B., van den Ijssel, P., Carvalho, B., Brakenhoff, R.H., and Meijer, G.A. 2006. BAC to the future! Or oligonucleotides: A perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 34: 445-450.