Coms 363 Assignments Discovery

Iafrate, A. J.et al.Detection of large-scale variation in the human genome. Nature Genet.36, 949–951 (2004). The first report of CNVs in the human genome using array CGH.

Redon, R.et al.Global variation in copy number in the human genome. Nature444, 444–454 (2006).

Tuzun, E.et al.Fine-scale structural variation of the human genome. Nature Genet.37, 727–732 (2005). The first study to implement a paired-end sequencing approach to study structural variation.

Kidd, J. M.et al.Mapping and sequencing of structural variation from eight human genomes. Nature453, 56–64 (2008).

Conrad, D. F.et al.Origins and functional impact of copy number variation in the human genome. Nature464, 704–712 (2010). This study represents the first application of an ultra-high-density CGH array.

Sebat, J.et al.Large-scale copy number polymorphism in the human genome. Science305, 525–528 (2004).

Feuk, L., Carson, A. R. & Scherer, S. W.Structural variation in the human genome. Nature Rev. Genet.7, 85–97 (2006).

The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature467, 1061–1073 (2010). A milestone paper describing the pilot phase of the 1000 Genomes Project, the most extensive study on genomic variation in human genomes to date.

Sebat, J.et al.Strong association of de novo copy number mutations with autism. Science316, 445–449 (2007). The first study to report CNVs in a common complex neuropsychiatric disease.

Sharp, A. J.et al.Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nature Genet.38, 1038–1042 (2006).

de Vries, B. B.et al.Diagnostic genome profiling in mental retardation. Am. J. Hum. Genet.77, 606–616 (2005).

Stankiewicz, P. & Lupski, J. R.Genomic architecture, rearrangements and genomic disorders. Trends Genet.18, 74–82 (2002).

Fellermann, K.et al.A chromosome 8 gene-cluster polymorphism with low human b-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am. J. Hum. Genet.79, 439–448 (2006).

Aitman, T. J.et al.Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature439, 851–855 (2006).

Locke, D. P.et al.BAC microarray analysis of 15q11–q13 rearrangements and the impact of segmental duplications. J. Med. Genet.41, 175–182 (2004).

Itsara, A.et al.Population analysis of large copy number variants and hotspots of human genetic disease. Am. J. Hum. Genet.84, 148–161 (2009).

Snijders, A. M.et al.Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genet.29, 263–264 (2001).

Pinkel, D.et al.High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genet.20, 207–211 (1998).

Park, H.et al.Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nature Genet.42, 400–405 (2010).

McCarroll, S. A.et al.Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genet.40, 1166–1174 (2008).

Perry, G. H.et al.The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet.82, 685–695 (2008).

Miller, D. T.et al.Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am. J. Hum. Genet.86, 749–764 (2010).

Cooper, G. M., Zerr, T., Kidd, J. M., Eichler, E. E. & Nickerson, D. A.Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nature Genet.40, 1199–1203 (2008).

Peiffer, D. A.et al.High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res.16, 1136–1148 (2006).

Coe, B. P.et al.Resolving the resolution of array CGH. Genomics89, 647–653 (2007).

Greshock, J.et al.A comparison of DNA copy number profiling platforms. Cancer Res.67, 10173–10180 (2007).

Curtis, C.et al.The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics10, 588 (2009).

Jakobsson, M.et al.Genotype, haplotype and copy-number variation in worldwide human populations. Nature451, 998–1003 (2008).

Gusev, A.et al.Whole population, genome-wide mapping of hidden relatedness. Genome Res.19, 318–326 (2009).

Winchester, L., Yau, C. & Ragoussis, J.Comparing CNV detection methods for SNP arrays. Brief. Funct. Genomic. Proteomic.8, 353–366 (2009).

Kidd, J. M.et al.Characterization of missing human genome sequences and copy-number polymorphic insertions. Nature Methods7, 365–371 (2010).

Wellcome Trust Case Control Consortium. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature464, 713–720 (2010).

Paris, P. L.et al.High resolution oligonucleotide CGH using DNA from archived prostate tissue. The Prostate67, 1447–1455 (2007).

Hehir-Kwa, J. Y.et al.Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis. DNA Res.14, 1–11 (2007).

Wicker, N.et al.A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics8, 84 (2007).

van de Wiel, M. A.et al.CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics (Oxford, England)23, 892–894 (2007).

van Wieringen, W. N., van de Wiel, M. A. & Ylstra, B.Normalized, segmented or called aCGH data?Cancer Inform.3, 321–327 (2007).

Wang, K.et al.PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res.17, 1665–1674 (2007).

Korn, J. M.et al.Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nature Genet.40, 1253–1260 (2008).

Coe, B. P., Chari, R., MacAulay, C. & Lam, W. L.FACADE: a fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data. Nucleic Acids Res.38, e157 (2010).