Predesigned TaqMan™ Copy Number Assays are ideal for analysis of copy number variation (CNV) and smaller regions in human and mouse genomes. CNV is an important polymorphism associated with diseases such as cancer, immune diseases and neurological disorders as well as drug metabolism.

  • Simplest method available to study copy number variation
  • Assays available for common vector market and reporter genes
  • Measure distinct copy number changes quantitatively with high specificity and reproducibility

The human assay collection includes over 1.6 million assays targeting gene exons and introns, extragenic regions, and CNV sequences from the Database of Genomic Variants (DGV). The mouse collection includes over 180,000 assays targeting gene exons. Assays to common vector marker and reporter genes are also available for transgenic studies.

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Pre-formulated Assay
  • 2 unlabeled PCR primers (small and medium scale 18 µM concentration, large scale is 54 µM)
  • 1 FAM™ dye-labeled TaqMan® MGB™ probe (small and medium scale is 5 µM concentration, large scale is 15 µM)
Documentation Available to download at :
  • Assay Information File (AIF)
  • TaqMan® Copy Number Assays Protocol (PDF)
  • TaqMan® Copy Number Assays Quick Reference Card (PDF)
  • CopyCaller™ Software User Guide (PDF)
  • CopyCaller™ Software Quick Reference Card (PDF)
  • Product Insert (PDF)
  • Data Sheet (PDF)
  • Safety Data Sheet (PDF)
  • Understanding Your Shipment Document (PDF)
Assay Information File (AIF) Predesigned Assay AIF includes: sales order number, ship date, part number, product type, assay ID, lot number, assay mix concentration, primer & probe concentrations, reporter dye & quencher, context sequence (includes probe region), gene ID (if applicable), DGV ID (if applicable), species, cytogenetic band, location on NCBI reference genome assembly (middle of context sequence), assembly build version, and other information. Assay sequences are not provided.
Reactions Sufficient for 360, 750, or 2,900 20-uL reactions in a 96-well plate, or 720, 1,500 or 5,800 10-uL reactions in a 384-well plate (depending on scale ordered)
  • 2D barcode laser-etched on the bottom of each assay tube
  • 1D barcode printed on each rack of tubes
Expiration Date 5 years from date of manufacture.
Shipping and Storage

Shipped at ambient temperature.
Store at –15ºC to –25ºC.

White Paper: Ambient Temperature Shipping Reduces Environmental Impact and Retains Quality and Stability

Catalog # Size # of 20 µL Reactions (96-well) # of 10 µL Reactions (384-well)
4400291 S: 20X concentration 360 720
4400292 M: 20X concentration 750 1,500
4400293 L: 60X concentration 2,900 5,800
  1. Low copy number of the salivary amylase gene predisposes to obesity. 
    VOLUME 46. NUMBER 5. MAY 2014 Nature Genetics. Mario Falchi et. al.

  2. A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures 
    Publication: VOLUME 40 [ NUMBER 3 [ MARCH 2008 NATURE GENETICS 322-328 
    Authors: Andrew J Sharp1,15, Heather C Mefford1, Kelly Li2, Carl Baker1, Cindy Skinner3, Roger E Stevenson3, Richard J Schroer3, Francesca Novara4, Manuela De Gregori4, Roberto Ciccone4, Adam Broomer2, Iris Casuga2, Yu Wang2, Chunlin Xiao2, Catalin Barbacioru2, Giorgio Gimelli5, Bernardo Dalla Bernardina6, Claudia Torniero6, Roberto Giorda7, Regina Regan8, Victoria Murday9, Sahar Mansour10, Marco Fichera11, Lucia Castiglia11, Pinella Failla11, Mario Ventura12, Zhaoshi Jiang1, Gregory M Cooper1, Samantha J L Knight8, Corrado Romano11, Orsetta Zuffardi4,13, Caifu Chen2, Charles E Schwartz3 & Evan E Eichler1,14 
    See also:
  3. Recurrent Rearrangements of Chromosome 1q21.1 and Variable Pediatric Phenotypes 
    Publication: N Engl J Med 2008;359. n engl j med 10.1056/nejmoa0805384 
    Authors: H. Mefford, A. Sharp, C. Baker, A. Itsara, Z. Jiang, K. Buysse, S. Huang, V. Maloney, J. Crolla, D. Baralle, A. Collins, C. Mercer, K. Norga, T. de Ravel, K. Devriendt, E. Bongers, N. de Leeuw, W. Reardon, S. Gimelli, F. Bena, R. Hennekam, A. Male, L. Gaunt, J. Clayton-Smith, I. Simonic, S. Park, S. Mehta, S. Nik-Zainal, C. Woods, H. Firth, G. Parkin, M. Fichera, S. Reitano, M. Lo Giudice, K. Li, I. Casuga, A. Broomer, B. Conrad, M. Schwerzmann, L. Räber, S. Gallati, P. Striano, A. Coppola, J. Tolmie, E. Tobias, C. Lilley, L. Armengol, Y. Spysschaert, P. Verloo, A. De Coene, L. Goossens, G. Mortier, F. Speleman, E. van Binsbergen, M. Nelen, R. Hochstenbach, M. Poot, L. Gallagher, M. Gill, J. McClellan, M.-C. King, R. Regan, C. Skinner, R. Stevenson, S. Antonarakis, C. Chen, X. Estivill, B. Menten, G. Gimelli, S. Gribble, S. Schwartz, 
    J. Sutcliffe, T. Walsh, S. Knight, J. Sebat, C. Romano, C. Schwartz, J. Veltman, B. de Vries, J. Vermeesch, J. Barber, L. Willatt, M. Tassabehji, and E. Eichler* 
    See also:
  4. Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays 
    Publication: Anal Biochem. 2009 Mar 15;386(2):288-90. 
    Authors: Holly N. Cukier, Margaret A. Pericak-Vance, John R. Gilbert, Dale J. Hedges * 
    See also:
  5. Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: precedent for disorders with complex inheritance 
    Publication: Human Molecular Genetics, 2009, Vol. 18, No. 19 3626–3631 doi:10.1093/hmg/ddp311 
    Authors: Leanne M. Dibbens1,2,_, Saul Mullen4, Ingo Helbig5,9, Heather C. Mefford6,7, Marta A. Bayly1, 
    Susannah Bellows4, Costin Leu8,9, Holger Trucks8,9, Tanja Obermeier5,9, Michael Wittig5,9, Andre Franke5,9, Hande Caglayan9,10, Zuhal Yapici9,11, EPICURE Consortium9{Thomas Sander8,9, Evan E. Eichler6,7, Ingrid E. Scheffer4,12, John C. Mulley1,3 and Samuel F. Berkovic4 
    See also:
  6. Dissection of Chromosome 16p12 Linkage Peak Suggests a Possible Role for CACNG3 Variants in Age-Related Macular Degeneration Susceptibility. 
    Publication: Invest Ophthalmol Vis Sci. 2010 Dec 17. [Epub ahead of print] 
    Authors: Spencer KL, Olson LM, Schnetz-Boutaud N, Gallins P, Wang G, Scott WK, Agarwal A, Jakobsdottir J, Conley Y, Weeks DE, Gorin MB, Pericak-Vance MA, Haines JL. 
    See also:
  7. A Rare Novel Deletion of the Tyrosine Hydroxylase Gene in Parkinson Disease 
    Publication: HUMAN MUTATION Mutation in Brief 31: E1767-E1771 (2010) Online 
    Authors: Güney Bademci1, Todd L. Edwards2, Andre L. Torres1, William K. Scott1,3, Stephan Züchner1,3, Eden R. Martin1,3, Jeffery M. Vance1,3, and Liyong Wang1,3* 
    See also:
  8. Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture 
    Publication: Cell Stem Cell 8, 106–118, January 7, 2011 ª2011 Elsevier Inc. 
    Authors: Louise C. Laurent,1,3,4,* Igor Ulitsky,6,7 Ileana Slavin,3,4 Ha Tran,3,4 Andrew Schork,2 Robert Morey,1,3,4 Candace Lynch,3,4, Julie V. Harness,8 Sunray Lee,9 Maria J. Barrero,10,11 Sherman Ku,5 Marina Martynova,12 Ruslan Semechkin,12, Vasiliy Galat,13,14 Joel Gottesfeld,5 Juan Carlos Izpisua Belmonte,10,11 Chuck Murry,15 Hans S. Keirstead,8, Hyun-Sook Park,9 Uli Schmidt,16 Andrew L. Laslett,17,18,19 Franz-Josef Muller,3,4 Caroline M. Nievergelt,2 Ron Shamir,7, and Jeanne F. Loring3,4 
    See also:
  9. CNV Analysis Using TaqMan Copy Number Assays 
    Publication: Current Protocols in Human Genetics 2.13.1-2.13.10, October 2010 
    Authors: Ping Mayo,1 Toinette Hartshorne,2 Kelly Li,2 Chara McMunn-Gibson,1Kylee Spencer,1 and Nathalie Schnetz-Boutaud1 
    See also:;jsessionid=A422A349D5A55C71489F098AE6BBA306.d03t01
  10. Differential quantification of CYP2D6 gene copy number by four different quantitative real-time PCR assays 
    Publication: Pharmacogenetics and Genomics 2010, Vol 20 No 7 452-454 
    Authors: Anuradha Ramamoorthya,b, David A. Flockharta,b, Naoya Hosonoc, Michiaki Kuboc, Yusuke Nakamurac,d and Todd C. Skaara
  11. Population-specific GSTM1 copy number variation 
    Publication: Human Molecular Genetics, 2009, Vol. 18, No. 2 366–372 
    Authors: R. Stephanie Huang1, Peixian Chen2, Steve Wisel1, Shiwei Duan1, Wei Zhang1, Edwin H. Cook4, 
    Soma Das2, Nancy J. Cox3 and M. Eileen Dolan1 
    See also:
  12. Analysis of Immune Regulatory Genes' Copy Number Variants in Graves' Disease 
    Publication: Thyroid. January 2011, 21(1): 69-74. doi:10.1089/thy.2010.0262. 
    Authors: Amanda K. Huber, Erlinda S. Concepcion, Alisha Gandhi, Francesca Menconi, Eric P. Smith, Mehdi Keddache, Yaron Tomer. 
    See also:


  13. Copy Number Variants of GSTM1 and GSTT1 in Relation to Lung Cancer Risk in a Prospective Cohort Study 
    Publication: Ann Epidemiol. 2009 Aug;19(8):546-52. Epub 2009 Apr 25. 
    See also:


  14. Effects of GSTM1 in Rheumatoid Arthritis; Results from the Swedish EIRA study. 
    Publication: PLoS ONE 6(3): e17880. doi:10.1371/journal.pone.0017880 (2011) 
    Authors: Emeli Lundström1*, Toinette Hartshorne2, Kelly Li2, Staffan Lindblad1, Marius C. Wick1,3, Camilla Bengtsson4, Lars Alfredsson4, Lars Klareskog1, Leonid Padyukov1 
    See also:
  15. Origins and functional effect of copy number variation in the human genome 
    Publication: Nature. 2010 Apr 1;464(7289):704-12. Epub 2009 Oct 7. 
    Authors: Donald F. Conrad1*, Dalila Pinto2*, Richard Redon1,3, Lars Feuk2,4, Omer Gokumen5, Yujun Zhang1, Jan Aerts1, T. Daniel Andrews1, Chris Barnes1, Peter Campbell1, Tomas Fitzgerald1, Min Hu1, Chun HwaIhm5, Kati Kristiansson1, Daniel G. MacArthur1, Jeffrey R. MacDonald2, Ifejinelo Onyiah1, Andy Wing Chun Pang2, Sam Robson1, Kathy Stirrups1, Armand Valsesia1, Klaudia Walter1, John Wei2, Wellcome Trust Case Control Consortium, Chris Tyler-Smith1, Nigel P. Carter1, Charles Lee5, Stephen W. Scherer2,6 & Matthew E. Hurles1
  16. Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies. 
    Publication: Brain. 2010 Jan;133(Pt 1):23-32. Epub 2009 Oct 20. 
    Authors: de Kovel CG, Trucks H, Helbig I, Mefford HC, Baker C, Leu C, Kluck C, Muhle H, von Spiczak S, Ostertag P, Obermeier T, Kleefuss-Lie AA, Hallmann K, Steffens M, Gaus V, Klein KM, Hamer HM, Rosenow F, Brilstra EH, Trenité DK, Swinkels ME, Weber YG, Unterberger I, Zimprich F, Urak L, Feucht M, Fuchs K, Møller RS, Hjalgrim H, De Jonghe P, Suls A, Rückert IM, Wichmann HE, Franke A, Schreiber S, Nürnberg P, Elger CE, Lerche H, Stephani U, Koeleman BP, Lindhout D, Eichler EE, Sander T. 
    See also:
  17. Identification of de novo copy number variants associated with human disorders of sexual development. 
    Publication: PLoS One. 2010 Oct 26;5(10):e15392. 
    Authors: Tannour-Louet M, Han S, Corbett ST, Louet JF, Yatsenko S, Meyers L, Shaw CA, Kang SH, Cheung SW, Lamb DJ. 
    See also:
  18. Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. 
    Publication: PLoS One. 2010 Feb 19;5(2):e9317. 
    Authors: Tuch BB, Laborde RR, Xu X, Gu J, Chung CB, Monighetti CK, Stanley SJ, Olsen KD, Kasperbauer JL, Moore EJ, Broomer AJ, Tan R, Brzoska PM, Muller MW, Siddiqui AS, Asmann YW, Sun Y, Kuersten S, Barker MA, De La Vega FM, Smith DI. 
    See also:


  19. New Addition:
  20. Identification of Rare Recurrent Copy Number Variants in High-Risk Autism Families and Their Prevalence in a Large ASD Population.
    Publication: PLoS One. 2013 Jan; 8(1); e52239 
    Authors: Nori Matsunami, Dexter Hadley, Charles H. Hensel, G. Bryce Christensen, Cecilia Kim, Edward Frackelton, Kelly Thomas, Renata Pellegrino da Silva, Jeff Stevens, Lisa Baird, Brith Otterud, Karen Ho, Tena Varvil, Tami Leppert, Christophe G. Lambert, Mark Leppert, Hakon Hakonarson. 
  21. Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient. 
    Publication: BMC Research Notes 2011, 4:476 
    Authors: Håkan Thonberg, Marie Fallström, Jenny Björkström, Jacqueline Schoumans, Inger Nennesmo and Caroline Graff.