Methods and strategies for analyzing copy number variation using DNA microarrays (original) (raw)
Jacobs, P.A., Baikie, A.G., Court Brown, W.M. & Strong, J.A. The somatic chromosomes in mongolism. Lancet1, 710 (1959). ArticleCAS Google Scholar
Kunze, J. Neurological disorders in patients with chromosomal anomalies. Neuropediatrics11, 203–249 (1980). ArticleCAS Google Scholar
Lejeune, J., Lafourcade, J., Berger, R. & Rethore, M.A. [The crying cat syndrome and its reciprocal] [in French] Ann. Genet.8, 11–15 (1965). CASPubMed Google Scholar
Sedano, H.O., Look, R.A., Carter, C. & Cohen, M.M. Jr. B group short-arm deletion syndrome. Birth Defects Orig. Artic. Ser.7, 89–97 (1971). CASPubMed Google Scholar
Morton, C.C., Corey, L.A., Nance, W.E. & Brown, J.A. Quinacrine mustard and nucleolar organizer region heteromorphisms in twins. Acta Genet. Med. Gemellol. (Roma)30, 39–49 (1981). ArticleCAS Google Scholar
Verma, R.S., Dosik, H. & Lubs, H.A. Size variation polymorphisms of the short arm of human acrocentric chromosomes determined by R-banding by fluorescence using acridine orange (RFA). Hum. Genet.38, 231–234 (1977). ArticleCAS Google Scholar
Edwards, A., Civitello, A., Hammond, H.A. & Caskey, C.T. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet.49, 746–756 (1991). CASPubMedPubMed Central Google Scholar
Kwok, P.Y., Deng, Q., Zakeri, H., Taylor, S.L. & Nickerson, D.A. Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics31, 123–126 (1996). ArticleCAS Google Scholar
Mir, K.U. & Southern, E.M. Sequence variation in genes and genomic DNA: methods for large-scale analysis. Annu. Rev. Genomics Hum. Genet.1, 329–360 (2000). ArticleCAS Google Scholar
Taillon-Miller, P., Gu, Z., Li, Q., Hillier, L. & Kwok, P.Y. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res.8, 748–754 (1998). ArticleCAS Google Scholar
Wang, D.G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science280, 1077–1082 (1998). ArticleCAS Google Scholar
Freeman, J.L. et al. Copy number variation: new insights in genome diversity. Genome Res.16, 949–961 (2006). ArticleCAS Google Scholar
Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet.36, 949–951 (2004). ArticleCAS Google Scholar
Khaja, R. et al. Genome assembly comparison identifies structural variants in the human genome. Nat. Genet.38, 1413–1418 (2006). ArticleCAS Google Scholar
Locke, D.P. et al. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet.79, 275–290 (2006). ArticleCAS Google Scholar
Perry, G.H. et al. Hotspots for copy number variation in chimpanzees and humans. Proc. Natl. Acad. Sci. USA103, 8006–8011 (2006). ArticleCAS Google Scholar
Redon, R. et al. Global variation in copy number in the human genome. Nature444, 444–454 (2006). ArticleCAS Google Scholar
Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science305, 525–528 (2004). ArticleCAS Google Scholar
Sharp, A.J., Cheng, Z. & Eichler, E.E. Structural variation of the human genome. Annu. Rev. Genomics Hum. Genet.7, 407–442 (2006). ArticleCAS Google Scholar
Tuzun, E. et al. Fine-scale structural variation of the human genome. Nat. Genet.37, 727–732 (2005). ArticleCAS Google Scholar
Wong, K.K. et al. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet.80, 91–104 (2007). ArticleCAS Google Scholar
Kallioniemi, O.P. et al. Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin. Cancer Biol.4, 41–46 (1993). CASPubMed Google Scholar
Kallioniemi, A., Visakorpi, T., Karhu, R., Pinkel, D. & Kallioniemi, O.P. Gene copy number analysis by fluorescence in situ hybridization and comparative genomic hybridization. Methods9, 113–121 (1996). ArticleCAS Google Scholar
Bentley, D.R. et al. The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X. Nature409, 942–943 (2001). ArticleCAS Google Scholar
Cheung, V.G. et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature409, 953–958 (2001). ArticleCAS Google Scholar
Solinas-Toldo, S. et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosom. Cancer20, 399–407 (1997). ArticleCAS Google Scholar
Pinkel, D. et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet.20, 207–211 (1998). ArticleCAS Google Scholar
Sharp, A.J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet.77, 78–88 (2005). ArticleCAS Google Scholar
Ylstra, B., van den Ijssel, P., Carvalho, B., Brakenhoff, R.H. & Meijer, G.A. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res.34, 445–450 (2006). ArticleCAS Google Scholar
Fiegler, H. et al. Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res.16, 1566–1574 (2006). ArticleCAS Google Scholar
Ishkanian, A.S. et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet.36, 299–303 (2004). ArticleCAS Google Scholar
Kauraniemi, P., Barlund, M., Monni, O. & Kallioniemi, A. New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Res.61, 8235–8240 (2001). CASPubMed Google Scholar
Monni, O. et al. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc. Natl. Acad. Sci. USA98, 5711–5716 (2001). ArticleCAS Google Scholar
Pollack, J.R. et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet.23, 41–46 (1999). ArticleCAS Google Scholar
Porkka, K., Saramaki, O., Tanner, M. & Visakorpi, T. Amplification and overexpression of Elongin C gene discovered in prostate cancer by cDNA microarrays. Lab. Invest.82, 629–637 (2002). ArticleCAS Google Scholar
Squire, J.A. et al. High-resolution mapping of amplifications and deletions in pediatric osteosarcoma by use of CGH analysis of cDNA microarrays. Genes Chromosom. Cancer38, 215–225 (2003). ArticleCAS Google Scholar
Dhami, P. et al. Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome. Am. J. Hum. Genet.76, 750–762 (2005). ArticleCAS Google Scholar
Mantripragada, K.K., Buckley, P.G., Jarbo, C., Menzel, U. & Dumanski, J.P. Development of NF2 gene specific, strictly sequence defined diagnostic microarray for deletion detection. J. Mol. Med.81, 443–451 (2003). ArticleCAS Google Scholar
Carvalho, B., Ouwerkerk, E., Meijer, G.A. & Ylstra, B. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J. Clin. Pathol.57, 644–646 (2004). ArticleCAS Google Scholar
Lucito, R. et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res.13, 2291–2305 (2003). ArticleCAS Google Scholar
Gribble, S.M. et al. Ultra-high resolution array painting facilitates breakpoint sequencing. J. Med. Genet.44, 51–58 (2007). ArticleCAS Google Scholar
International HapMap Consortium. A haplotype map of the human genome. Nature437, 1299–1320 (2005).
Nannya, Y. et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res.65, 6071–6079 (2005). ArticleCAS Google Scholar
Komura, D. et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res.16, 1575–1584 (2006). ArticleCAS Google Scholar
Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E. & Pritchard, J.K. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet.38, 75–81 (2006). ArticleCAS Google Scholar
McCarroll, S.A. et al. Common deletion polymorphisms in the human genome. Nat. Genet.38, 86–92 (2006). ArticleCAS Google Scholar
Vermeesch, J.R. et al. Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis. J. Histochem. Cytochem.53, 413–422 (2005). ArticleCAS Google Scholar
Price, T.S. et al. 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 (2005). ArticleCAS Google Scholar
Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics5, 557–572 (2004). Article Google Scholar
Scherer, S.W. et al. Challenges and standards in integrating surveys of structural variation. Nat. Genet.39, S7–S15 (2007). ArticleCAS Google Scholar
Service, R.F. Gene sequencing: the race for the $1000 genome. Science311, 1544–1546 (2006). ArticleCAS Google Scholar
Shendure, J., Mitra, R.D., Varma, C. & Church, G.M. Advanced sequencing technologies: methods and goals. Nat. Rev. Genet.5, 335–344 (2004). ArticleCAS Google Scholar