Current analysis platforms and methods for detecting copy number variation

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works

Mean shift: a robust approach toward feature space analysis

Comaniciu, D., & Meer, P. (2002) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/34.1000236 · Cited by 11,417 · see citing works

<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool

Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works

Genome sequencing in microfabricated high-density picolitre reactors

Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693 · see citing works

Sampling-based approaches to calculating marginal densities

Gelfand, A. E., & Smith, A. F. M. (1990) · Journal of the American Statistical Association · doi:10.1080/01621459.1990.10476213 · Cited by 6,606 · see citing works

Accurate whole human genome sequencing using reversible terminator chemistry

Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684 · see citing works

De novo assembly of human genomes with massively parallel short read sequencing

Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · see citing works

Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

MAGIC, Speliotes, E. K., on behalf of Procardis Consortium, Willer, C. J., Berndt, S. I., Monda, K. L., Thorleifsson, G., Jackson, A. U., Allen, H. L., Lindgren, C. M., et al. (2010) · Nature Genetics · doi:10.1038/ng.686 · Cited by 2,912 · see citing works

Mapping short DNA sequencing reads and calling variants using mapping quality scores

Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638 · see citing works

Circular binary segmentation for the analysis of array-based DNA copy number data

Olshen, A. B., Venkatraman, E. S., Lucito, R., & Wigler, M. H. (2004) · Biostatistics · doi:10.1093/biostatistics/kxh008 · Cited by 2,256 · see citing works

PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S. F. A., Hakonarson, H., & Bucan, M. (2007) · Genome Research · doi:10.1101/gr.6861907 · Cited by 1,792 · see citing works

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011) · Genome Research · doi:10.1101/gr.114876.110 · Cited by 1,658 · see citing works

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Burton, J. N., Walker, B. J., Sharpe, T., Hall, G., Shea, T., Sykes, S. M., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017351108 · Cited by 1,510 · see citing works

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q., Locke, D. P., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1363 · Cited by 1,463 · see citing works

A copy number variation morbidity map of developmental delay

Cooper, G. M., Coe, B. P., Girirajan, S., Rosenfeld, J. A., Vu, T. H., Baker, C., Williams, C., Stalker, H., Hamid, R., Hannig, V., et al. (2011) · Nature Genetics · doi:10.1038/ng.909 · Cited by 1,351 · see citing works

DNA duplication associated with Charcot-Marie-Tooth disease type 1A

Lupski, J. R., Montes‐de‐Oca‐Luna, R., Slaugenhaupt, S., Pentao, L., Guzzetta, V., Trask, B. J., Cárdenas, O. S., Barker, D. F., Killian, J. M., Garcia, C. A., et al. (1991) · Cell · doi:10.1016/0092-8674(91)90613-4 · Cited by 1,327 · see citing works

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayır, A., Bakkaloğlu, A., Özen, S., Sanjad, S. A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910672106 · Cited by 1,327 · see citing works

APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy

Rovelet‐Lecrux, A., Hannequin, D., Raux, G., Meur, N. L., Laquerrière, A., Vital, A., Dumanchin‐Njock, C., Feuillette, S., Brice, A., Vercelletto, M., et al. (2005) · Nature Genetics · doi:10.1038/ng1718 · Cited by 1,249 · see citing works

Structural Variation in the Human Genome and its Role in Disease

Stankiewicz, P., & Lupski, J. R. (2010) · Annual Review of Medicine · doi:10.1146/annurev-med-100708-204735 · Cited by 1,201 · see citing works

Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome

Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., Kim, P. M., Palejev, D., Carriero, N. J., Du, L., et al. (2007) · Science · doi:10.1126/science.1149504 · Cited by 1,163 · see citing works

Mapping copy number variation by population-scale genome sequencing

1000 Genomes Project, Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., et al. (2011) · Nature · doi:10.1038/nature09708 · Cited by 1,140 · see citing works

Mapping and sequencing of structural variation from eight human genomes

Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., et al. (2008) · Nature · doi:10.1038/nature06862 · Cited by 1,119 · see citing works

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

Boeva, V., Popova, T. G., Kevin Bleakley, A., Chiche, P., Cappo, J., Schleiermacher, G., Janoueix‐Lerosey, I., Delattre, O., & Barillot, E. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr670 · Cited by 1,012 · see citing works

A faster circular binary segmentation algorithm for the analysis of array CGH data

Venkatraman, E. S., & Olshen, A. B. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btl646 · Cited by 963 · see citing works

Chromosome instability is common in human cleavage-stage embryos

Vanneste, E., Voet, T., Le Caignec, C., Ampe, M., Konings, P., Melotte, C., Debrock, S., Amyere, M., Vikkula, M., Schuit, F., et al. (2009) · Nature Medicine · doi:10.1038/nm.1924 · Cited by 880 · see citing works

De novo truncating mutations in E6-AP ubiquitin-protein ligase gene (UBE3A) in Angelman syndrome

Matsuura, T., Sutcliffe, J. S., Fang, P., Galjaard, R. H., Jiang, Y., Benton, C. S., Rommens, J. M., & Beaudet, A. L. (1997) · Nature Genetics · doi:10.1038/ng0197-74 · Cited by 858 · see citing works

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

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) · Nature Genetics · doi:10.1038/ng.237 · Cited by 783 · see citing works

An initial map of insertion and deletion (INDEL) variation in the human genome

Mills, R. E., Luttig, C. T., Larkins, C. E., Beauchamp, A., Tsui, C., Pittard, W. S., & Devine, S. E. (2006) · Genome Research · doi:10.1101/gr.4565806 · Cited by 673 · see citing works

Psoriasis is associated with increased β-defensin genomic copy number

Hollox, E. J., Hüffmeier, U., Zeeuwen, P. L. J. M., Raquel, P., Lascorz, J., Rodijk‐Olthuis, D., van de Kerkhof, P. C. M., Traupe, H., de Jongh, G. J., den Heijer, M., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.48 · Cited by 630 · see citing works

Sensitive and accurate detection of copy number variants using read depth of coveragePreprint

Yoon, S. C., Xuan, Z., Makarov, V., Ye, K. Q., & Sebat, J. L. (2009) · Genome Research · doi:10.1101/gr.092981.109 · Cited by 619 · see citing works

QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data

Colella, S., Yau, C., Taylor, J. M., Mirza, G., Butler, H., Clouston, P., Bassett, A. S., Seller, A., Holmes, C. C., & Ragoussis, J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm076 · Cited by 616 · see citing works

Genomic Disorders: Molecular Mechanisms for Rearrangements and Conveyed Phenotypes

Lupski, J. R., & Stankiewicz, P. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010049 · Cited by 582 · see citing works

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

Xie, C., & Tammi, M. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-80 · Cited by 582 · see citing works

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encodingPreprint

McKernan, K. J., Peckham, H. E., Costa, G. L., McLaughlin, S. F., Fu, Y., Tsung, E. F., Clouser, C. R., Duncan, C., Ichikawa, J. K., Lee, C. C., et al. (2009) · Genome Research · doi:10.1101/gr.091868.109 · Cited by 529 · see citing works

Analysis of array CGH data: from signal ratio to gain and loss of DNA regions

Hupé, P., Stransky, N., Thiery, J. P., Radvanyi, F., & Barillot, E. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth418 · Cited by 521 · see citing works

High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotypingPreprint

Peiffer, D. A., Le, J. M., Steemers, F. J., Chang, W., Jenniges, T., Garcia, F., Haden, K., Li, J., Shaw, C. A., Belmont, J. W., et al. (2006) · Genome Research · doi:10.1101/gr.5402306 · Cited by 519 · see citing works

High-resolution mapping of copy-number alterations with massively parallel sequencing

Chiang, D. Y., Getz, G. A., Jaffe, D. B., O'Kelly, M., Zhao, X., Carter, S. L., Russ, C., Nusbaum, C., Meyerson, M. M., & Lander, E. S. (2008) · Nature Methods · doi:10.1038/nmeth.1276 · Cited by 510 · see citing works

Genomic rearrangements and sporadic disease

Lupski, J. R. (2007) · Nature Genetics · doi:10.1038/ng2084 · Cited by 424 · see citing works

Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data

Lai, W. R., Johnson, M. D., Kucherlapati, R., & Park, P. J. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti611 · Cited by 402 · see citing works

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

Sathirapongsasuti, J. F., Lee, H., Horst, B. A. J., Brunner, G., Cochran, A. J., Binder, S. W., Quackenbush, J. F., & Nelson, S. F. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr462 · Cited by 374 · see citing works

Human Copy Number Variation and Complex Genetic Disease

Girirajan, S., Campbell, C. D., & Eichler, E. E. (2011) · Annual Review of Genetics · doi:10.1146/annurev-genet-102209-163544 · Cited by 367 · see citing works

The Fine-Scale and Complex Architecture of Human Copy-Number Variation

Perry, G. H., Ben‐Dor, A., Tsalenko, A., Sampas, N., Rodríguez‐Revenga, L., Tran, C. W., Scheffer-Wong, A., Steinfeld, I., Tsang, P. W. K., Yamada, N. A., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.12.010 · Cited by 346 · see citing works

De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome

Rivière, J., van Bon, B. W. M., Hoischen, A., Kholmanskikh, S. S., O’Roak, B. J., Gilissen, C., Gijsen, S. J., Sullivan, C. T., Christian, S. L., Abdul-Rahman, O. A., et al. (2012) · Nature Genetics · doi:10.1038/ng.1091 · Cited by 303 · see citing works

mrsFAST: a cache-oblivious algorithm for short-read mapping

Hach, F., Hormozdiari, F., Alkan, C., Hormozdiari, F., Birol, İ., Eichler, E. E., & Şahinalp, S. C. (2010) · Nature Methods · doi:10.1038/nmeth0810-576 · Cited by 274 · see citing works

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

Korbel, J. O., Abyzov, A. S., Mu, X. J., Carriero, N. J., Cayting, P. D., Zhang, Z., Snyder, M. P., & Gerstein, M. (2009) · Genome biology · doi:10.1186/gb-2009-10-2-r23 · Cited by 272 · see citing works

Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors.

Kallioniemi, O., Kallioniemi, A. H., Sudar, D., Rutovitz, D., Gray, J. W., Waldman, F., & Pinkel, D. (1993) · PubMed · Cited by 227 · see citing works

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

Xi, R., Hadjipanayis, A. G., Luquette, L. J., Kim, T., Lee, E., Zhang, J., Johnson, M. D., Muzny, D. M., Wheeler, D. A., Gibbs, R. A., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110574108 · Cited by 217 · see citing works

Comparing CNV detection methods for SNP arrays

Winchester, L. M., Yau, C., & Ragoussis, J. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp017 · Cited by 216 · see citing works

Single-cell chromosomal imbalances detection by array CGH

Caignec, C. L., Spits, C., Sermon, K., Rycke, M. D., Thienpont, B., Debrock, S., Staessen, C., Moreau, Y., Fryns, J. P., Steirteghem, A. V., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl336 · Cited by 203 · see citing works

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

Lam, H. Y. K., Mu, X. J., Stütz, A. M., Andrea Tanzer, A., Cayting, P. D., Snyder, M. P., Kim, P. M., Korbel, J. O., & Gerstein, M. (2009) · Nature Biotechnology · doi:10.1038/nbt.1600 · Cited by 189 · see citing works

Detecting copy number variation with mated short readsPreprint

Medvedev, P., Fiume, M., Dzamba, M., Smith, T. P. L., & Brudno, M. (2010) · Genome Research · doi:10.1101/gr.106344.110 · Cited by 177 · see citing works

A portrait of copy-number polymorphism in Drosophila melanogaster

Dopman, E. B., & Hartl, D. L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709888104 · Cited by 136 · see citing works

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

Wong, K., Keane, T., Stalker, J. W., & Adams, D. J. (2010) · Genome biology · doi:10.1186/gb-2010-11-12-r128 · Cited by 133 · see citing works

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

Lee, S., Hormozdiari, F., Alkan, C., & Brudno, M. (2009) · Nature Methods · doi:10.1038/nmeth.f.256 · Cited by 132 · see citing works

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

Li, Y., Zheng, H., Luo, R., Wu, H., Zhu, H., Li, R., Cao, H., Wu, B., Huang, S., Shao, H., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1904 · Cited by 131 · see citing works

Sparse representation and Bayesian detection of genome copy number alterations from microarray data

Piqué-Regi, R., Monso-Varona, J., Ortega, A., Seeger, R. C., Triche, T. J., & Asgharzadeh, S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm601 · Cited by 128 · see citing works

Association of Higher DEFB4 Genomic Copy Number With Crohn's Disease

Bentley, R. W., Pearson, J. F., Gearry, R. B., Barclay, M. L., McKinney, C., Merriman, T. R., & Roberts, R. L. (2009) · The American Journal of Gastroenterology · doi:10.1038/ajg.2009.582 · Cited by 127 · see citing works

Integrated study of copy number states and genotype calls using high-density SNP arrays

Sun, W., Wright, F., Tang, Z., Nordgard, S. H., van Loo, P., Yu, T.-W., Kristensen, V., & Perou, C. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp493 · Cited by 125 · see citing works

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions

Schuster‐Böckler, B., Conrad, D. F., & Bateman, A. G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009474 · Cited by 97 · see citing works

Happy mapping: linkage mapping using a physical analogue of meiosis

Dear, P. H., & Cook, P. R. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.1.13 · Cited by 97 · see citing works

Copy Number Alterations that Predict Metastatic Capability of Human Breast Cancer

Zhang, Y., Martens, J. W. M., Yu, J. X., Jiang, J., Sieuwerts, A. M., Smid, M., Klijn, J. G. M., Wang, Y., & Foekens, J. A. (2009) · Cancer Research · doi:10.1158/0008-5472.can-08-4596 · Cited by 93 · see citing works

Catching Change-points with Lasso

Lévy‐Leduc, C., & Harchaoui, Z. (2007) · neural information processing systems · Cited by 90 · see citing works

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

Abyzov, A. S., & Gerstein, M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq713 · Cited by 87 · see citing works

Analysis of Copy Number Variation in Alzheimer’s Disease: The NIALOAD/ NCRAD Family Study

Swaminathan, S., Shen, L., Kim, S., Inlow, M. H., West, J. D., Faber, K. M., Foroud, T., Mayeux, R. P., & Saykin, A. J. (2012) · Current Alzheimer Research · doi:10.2174/156720512802455331 · Cited by 84 · see citing works

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

Qi, J., & Zhao, F. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr506 · Cited by 79 · see citing works

Identification of genomic indels and structural variations using split reads

Zhang, Z. D., Du, J., Lam, H. Y. K., Abyzov, A. S., Urban, A. E., Snyder, M. P., & Gerstein, M. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-375 · Cited by 79 · see citing works

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS

Emde, A., Schulz, M. H., Weese, D., Sun, R., Vingron, M., Kalscheuer, V. M., Haas, S. A., & Reinert, K. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts019 · Cited by 77 · see citing works

Accuracy of CNV Detection from GWAS Data

Zhang, D., Qian, Y., Akula, N., Alliey‐Rodriguez, N., Tang, J., Study, T. B. G., Gershon, E. S., & Liu, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014511 · Cited by 73 · see citing works

A Comparison of DNA Copy Number Profiling Platforms

Greshock, J. D., Feng, B., Nogueira, C., Ivanova, E. V., Perna, I., Nathanson, K. L., Protopopov, A. I., Weber, B., & Chin, L. (2007) · Cancer Research · doi:10.1158/0008-5472.can-07-2102 · Cited by 72 · see citing works

Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms

Haraksingh, R., Abyzov, A. S., Gerstein, M., Urban, A. E., & Snyder, M. P. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027859 · Cited by 67 · see citing works

Large Copy-Number Variations Are Enriched in Cases With Moderate to Extreme Obesity

Wang, K., Li, W., Glessner, J., Grant, S. F. A., Hakonarson, H. H., & Price, R. A. (2010) · Diabetes · doi:10.2337/db10-0192 · Cited by 67 · see citing works

Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity

Waszak, S. M., Hasin-Brumshtein, Y., Zichner, T., Olender, T., Keydar, I., Khen, M., Stütz, A. M., Schlattl, A., Lancet, D., & Korbel, J. O. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000988 · Cited by 62 · see citing works

Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform

Eckel‐Passow, J. E., Atkinson, E. J., Maharjan, S., Kardia, S. L. R., & de Andrade, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-220 · Cited by 56 · see citing works

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data

Baross, Á., Delaney, A. D., Li, H. I., Nayar, T., Flibotte, S., Qian, H., Chan, S. Y., Asano, J. K., Ally, A., Cao, M., et al. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-368 · Cited by 55 · see citing works

R-Gada: a fast and flexible pipeline for copy number analysis in association studies

Piqué-Regi, R., Cáceres, A., & González, J. R. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-380 · Cited by 54 · see citing works

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics

Gai, X., Perin, J. C., Murphy, K., O'Hara, R., D’Arcy, M. E., Wenocur, A. S., Xie, H. M., Rappaport, E. F., Shaikh, T. H., & White, P. S. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-74 · Cited by 50 · see citing works

A multilevel model to address batch effects in copy number estimation using SNP arrays

Scharpf, R. B., Ruczinski, I., Carvalho, B. S., Doan, B. Q., Chakravarti, A., & Irizarry, R. A. (2010) · Biostatistics · doi:10.1093/biostatistics/kxq043 · Cited by 46 · see citing works

Targeted Screening and Validation of Copy Number Variations

Ceulemans, S., van der Ven, K., & Del‐Favero, J. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-507-7_15 · Cited by 41 · see citing works

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

Deng, X. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-267 · Cited by 41 · see citing works

Interrogation of genomes by molecular copy-number counting (MCC)

Daser, A., Thangavelu, M., Pannell, R., Forster, A. M., Sparrow, L., Chung, G., Dear, P. H., & Rabbitts, T. H. (2006) · Nature Methods · doi:10.1038/nmeth880 · Cited by 40 · see citing works

Accuracy in Copy Number Calling by qPCR and PRT: A Matter of DNA

Fernández‐Jiménez, N., Castellanos–Rubio, A., Plaza‐Izurieta, L., Gutierrez, G., Irastorza, I., Castaño, L. A., Vitoria, J. C., & Bilbao, J. R. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028910 · Cited by 35 · see citing works

MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal Cells

Liu, Z. Z., Li, A., Schulz, V., Chen, M., & Tuck, D. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010909 · Cited by 33 · see citing works

Copy Number Variation Detection via High-Density SNP GenotypingPreprint

sprotocols, & Bucan, M. (2008) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top46 · Cited by 30 · see citing works

Application of Nexus Copy Number Software for CNV Detection and Analysis

Darvishi, K. (2010) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg0414s65 · Cited by 29 · see citing works

Microarray analysis of copy number variation in single cells

Könings, P., Vanneste, E., Jackmaert, S., Ampe, M., Verbeke, G. N., Moreau, Y., Vermeesch, J. R., & Voet, T. (2012) · Nature Protocols · doi:10.1038/nprot.2011.426 · Cited by 29 · see citing works

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays

Rigaill, G. J., Hupé, P., Almeida, A., Rosa, P. L., Meyniel, J.-P., Decraene, C., & Barillot, E. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn048 · Cited by 29 · see citing works

A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data

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Whole genome sequencing–based copy number variations reveal novel pathways and targets in Alzheimer's disease

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Copy number alteration profiling facilitates differential diagnosis between ossifying fibroma and fibrous dysplasia of the jaws

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Copy number variation analysis in the context of electronic medical records and large-scale genomics consortium efforts

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Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application

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Comprehensive Analysis of Genome Rearrangements in Eight Human Malignant Tumor Tissues

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CRISPR-based functional evaluation of schizophrenia risk variants

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The clinical impact of copy number variants in inherited bone marrow failure syndromes

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Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis )

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Genome-wide copy number variation-, validation- and screening study implicates a new copy number polymorphism associated with suicide attempts in major depressive disorder

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Digital PCR for the Analysis of MYC Copy Number Variation in Lung Cancer

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Numerical analysis of intensity signals resulting from genotyping pooled DNA samples in beef cattle and broiler chicken1

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Estimation of theRNU2macrosatellite mutation rate byBRCA1mutation tracing

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Role of Rare Germline Copy Number Variation in Melanoma-Prone Patients

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CNV and Structural Variation in Plants: Prospects of NGS Approaches

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Copy number variation related disease genes

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CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer

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Application of exome sequencing in the search for genetic causes of rare disorders of copper metabolism

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Copy number variant analysis and expression profiling of the olfactory receptor-rich 11q11 region in obesity predisposition

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Perspective: DNA Copy Number Variations in Cardiovascular Diseases

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Copy Number Variations Detection: Unravelling the Problem in Tangible Aspects

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Validation of quantitative PCR-based assays for detection of gene copy number aberrations in formalin-fixed, paraffin embedded solid tumor samples

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Methods for Copy Number Aberration Detection from Single-cell DNA Sequencing DataPreprint

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Whole genome sequencing analysis of small and large colony mutants from the mouse lymphoma assay

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Population-level gene copy number variations reveal distinct genetic properties of different Malus species

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NeuroArray : A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders

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Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing

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Laboratory Techniques in Cellular and Molecular Medicine

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Optical genome mapping reveals novel structural variations in an autism spectrum disorder cohort

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Copy number variations at the Rhg1 locus and their relationship with resistance to soybean cyst nematode (Heterodera glycines)

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Copy number variants associated with epilepsy from gene expression microarrays

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Association of melanoma with intraepithelial neoplasia of the pancreas in three patients

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A Prospective Screening of Gene Copy Number Variation in Brazilian Admixed Population Sample

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An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays

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Genome-wide association study of copy number variations in Parkinson’s disease

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Analytical Validation and Performance Evaluation of Amplicon-Based Next-Generation Sequencing Assays for Detecting ERBB2 and Other Gene Amplifications in Solid Tumors

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Formalin-fixed cells as an internal standard approach for the detection and quantitative assessment of Shiga toxin-producing Escherichia coli (STEC)

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Copy number variations (CNVs) in Brazilian patients with autism spectrum disorder (ASD)

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Prioritization of driver genes in cancer-associated copy number alterations identifies B4GALT5 as a glycooncogenePreprint

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Analysis of copy number variation in the NEDD4L gene potentially implicated in body height in the Japanese population

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Molecular Diagnostics in Cancer: A Fundamental Component of Precision Oncology

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Tandem Duplications, Segmental Duplications and Deletions, and Their Applications

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Correcting estimates of DNA CNAs using improved confidence masks tuned to gold standard

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Copy Number Analysis of Cancer

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Association of complex traits with common genetic variation across genomic regions containing pathogenic copy number variationsPreprint

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Genomics approaches to study music perception and performance

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Copy Number Variation in the Porcine Genome Detected from Whole-Genome Sequence

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Inherited copy number variation in the chicken genome and association with breast muscle traits

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Structural variants in the great tit genome and their effect on seasonal timing

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IIIB: Characterization of Penile Cancers with Comprehensive Genomic Profiling

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Copy Number Variation Analysis from SNP Genotyping Microarrays in Large Cohorts of Neurological Disorders

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Clinical case of distal arthrogryposis in combination with epilepsy due to an unbalanced translocation

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Genomic instability as a predictive biomarker for the application of DNA-damaging therapies in gynecological cancer patients

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Connecting genes to physiology: the first 25 years of Physiological Genomics

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Critical Role of Genomics for Directed Therapeutic Management of Lung Cancer

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Evaluation of Pork-Specific DNA Primers for Halal Authentication in Processed Meats

Salsabila, A., & Wahyudi, D. (2025) · Halal Science · doi:10.58920/halal0101364

MLDeCNV: A machine learning approach for predicting copy number variation types in plant genomes

Das, P., Saha, B., Sharma, N. K., Iquebal, M. A., Papanicolaou, A., Angadi, U. B., Kumar, D., & Jaiswal, S. (2025) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2025.111394

Classification pangénomique des adénomes hypophysaires

Néou, M. (2019) · doi:10.70675/e47bc827zd61ez4faeza49ezffa79ee52797

Impasses dans le diagnostic moléculaire des maladies rares : apport d'une meilleure caractérisation fonctionnelle des variants dans le cadre des myopathies et des lipodystrophies héréditaires

Cérino, M. (2021) · doi:10.70675/8245c7bez1129z48daz9349zdb6a6dbe4f59

Identification of case-specific copy number variants reveals novel genetic insights into familial hemiplegic migraine pathogenesis

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Methods and strategies for analyzing copy number variation using DNA microarrays

Carter, N. P. (2007) · Nature Genetics · doi:10.1038/ng2028 · Cited by 510 · see citing works

Computational strategies for copy number variation detection, disease association, and beyond

Saeidian, A. H., Sabaie, H., Akbarzadeh, M., Vahidnezhad, H., Youssefian, L., Saadattalab, T., Du, H., Luo, X., Owen, N. M., Zhao, X., et al. (2026) · Genome biology · doi:10.1186/s13059-026-04189-6

Copy Number Variation in the Human Genome

Ferreira, E. N., & Quaio, C. R. D. C. (2021) · Springer eBooks · doi:10.1007/978-3-030-73151-9_9

Copy Number Variations in the Human Genome and Strategies for Analysis

Vucic, E. A., Thu, K. L., Williams, A. C., Lam, W. L., & Coe, B. P. (2010) · Methods in molecular biology · doi:10.1007/978-1-60327-367-1_6 · Cited by 5 · see citing works

Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis

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