Nexus Copy Number™
Accelerating Copy Number Analysis Research
Nexus Copy Number™ software offers simple yet powerful tools for CNV/LOH analysis and visualization from CGH and SNP array as well as next-gen sequencing data. The elegant user-interface and powerful statistical tools designed specifically for the end-user allow detection of chromosomal aberrations and identification of affected pathways with just a few mouse clicks.
Get Started Today with a free trial
To a single solution for various application areas from cytogenetics to large scale population studies…
Flexible
Support for any platform
- Affymetrix
- Agilent
- Illumina
- Roche NimbleGen
- Next-Gen Sequencing
- Other
Support for any organism
Simple addition of custom tracks
Choose/Create custom CNV database
Flexible licensing options
Powerful
Process and visualize thousands of samples.
- Secure, redundant, off-site back up of data
- Validated statistical aberration detection algorithms
- Simple global collaboration support
- Access to publically available data
- Statistical tools for CNV/LOH analysis
- Statistical tools for survival analysis
- Clustering
- Enrichment analysis
- Integration with
Platforms Supported: Windows Win2k/WinXP,OSX
Minimum: 1.0 GHz Pentium or G4, 512 MB RAM
Recommended: 2.0 GHz or faster Core 2 Duo, 1024 or more MB RAM
Compare Editions
Nexus Copy Number follows a modular design to optimally meet the user needs and provide the best possible value. The following packaged configurations are designed to be applicable to most user types. However, any configuration can be custom designed and there is never a cost penalty for changing the license configuration. (click image to enlarge)
Discovery
This multi-sample processing configuration is the flagship product designed to provide all the statistical tools needed to conduct copy number based research with maximum ease and speed. It includes all available computational modules as well as Nexus DB.
Standard
This configuration is designed to be a nice complement to Nexus Solo and for those whose work does not require all the analytical functionality in the Disocovery Edition. The Standard Edition allows multi-sample processing, generation of frequency of aberration plots, detection of minimum common regions of gain or loss, and much more. It can also serve as a local database of samples along with sample annotation that can be viewed within the application as well as by Nexus Solo.
Core
This base component can be used to create any custom multi-sample processing and visualization solution meeting the user’s specific needs. Any of the modules listed in the table below can be added to the Core to create a truly custom solution.
Solo
This configuration is designed to meet the needs of users that need to process and interpret the results of a single sample at a time. This configuration does provide a direct link to Nexus DB so regions of interest can be immediately queried against all samples stored in Nexus DB for which the user has been allowed access. Nexus Solo can display results generated in Nexus Copy Number Standard or Discovery Edition projects.
Reader Clients
All Nexus Copy Number configurations can be licensed as read-only products. This limits the software from processing new samples but all other functions remain fully intact. In fact, with Nexus Copy Number Discovery Edition Reader client you can conduct extensive research by utilizing thousands of already processed samples in Nexus DB without the extra cost of running samples or time spent generating data!
| Solo | Core | Standard | Discovery | |
| Single sample processing, visualization, and interpretation |  |
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| Allele Specific Computation Module – Allelic event processing and visualization for SNP arrays | |
Optional Add-on | |
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| Nexus DB – remote storage, backup, retrieval, sharing, and querying | * |
Optional Add-on | |
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| Multi-sample processing, visualization, and analysis with sample annotations | |
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| Query one or more genes or regions for their genomic alteration status in all samples in a project | |
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| Statistical Comparison Module – Identification of regions with statistically significant differences between a pair of sample populations as well as the Predictive Power tool to identify regions that are highly predictive of a continuous valued factor (such as height) | Optional Add-on | |
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| Survival Analysis Module – Includes Survival Predictive Power computation allowing the user to identify regions that are highly predictive of survival with a given statistical significance and allows generation of Kaplan-Meir plots. | Optional Add-on | |
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| External Data Integration Module –Allows for integration of mRNA, miRNA, and methylation analysis results (e.g. Gene lists) to identify genomic hotspot regions. It calculated for each region a p-value indicated the probability of having so many genes in that regions being part of a list by pure chance. | Optional Add-on | |
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| Enrichment Analysis Module – Performs Annotation enrichment analysis identifying pathways and GO terms that are overrepresented in a gene list | Optional Add-on | |
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| Clustering and Factor Enrichment Module – allows the user to group the samples based on genomic aberrations and perform Factor Enrichment | Optional Add-on | |
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| Nexus Expression Module | Optional Add-on |
Optional Add-on |
Optional Add-on |
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| Nexus Methylation Module | Optional Add-on |
Optional Add-on | Optional Add-on |
*Nexus Solo does not submit samples to Nexus DB but can query and retrieve from the database
What’s New
Addresses complex genomes with sample ploidy estimation as well as extent of normal contamination in mosaic samples. (1)
Employs expanded statistical methods for identification of high frequency aberrations in a population. (2)
Provides complete user control over display and reporting
- Manual calling and classification of calls as benign/malignant/unknown
- New population frequency displays to highlight focal events
- Numerous new filters, color schemes, display tools
- Extensive reporting that is fully customizable by the user
Supports matched paired analysis to easily identify aberrations in the experimental sample only
Complies with new ISCA Consortium color standards for CNV gains and losses
And More…
Try out all the new features in version 6.0 by requesting your free trial of Nexus Copy Number today!
References
1. Van Loo et. al. “Allele-Specific Copy Number Analysis of Tumors”. Proc Natl Acad Sci USA. 2010 Sep 28;107(39):16910-5
2. Beroukhim, R. et. al. “Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma”. Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):20007-12.
Testimonials
“Nexus is light years ahead of the other commercially available software and can be used on multiple platforms”
Dr. Melissa Bondy, The University of Texas, M.D. Anderson Cancer Center
"Nexus Copy Number Software has allowed us to take our OncoScan data to the next level. As the only commercial software platform that has been specifically designed to analyze MIP data, its visualization and analysis algorithms have provided us with rapid and high impact discoveries. The intuitive design and ability to drill down on individual genes with links to the peer-reviewed literature are invaluable for our translational cancer research efforts. Perhaps, though, the biggest strength of Nexus Copy Number is its ease of incorporating clinical datasets and outcome to identify candidate loci for prognostic markers and developmental therapeutics."
Dr. Joshua Schiffman, Medical Director, High Risk Pediatric Cancer Clinic, Division of Pediatric Hematology/Oncology
Huntsman Cancer Institute, University of Utah
NEXUS is impressive. It offers a user-friendly solution for those in need of copy number data analysis. Clearly in active development process and the team is very responsive to our needs. I enjoy the latest version (V6) a lot since it has several exciting features such as running GISTIC within NEXUS."
Dr. Tao Xie, Oncology Unit, Pfizer Inc.
"We have recently switched our platform to utilize BioDiscovery software in our analysis of microarray data from Affymetrix and Agilent platforms. As a leader in this field I have to congratulate your team on their professional attitude towards their customers. Although both ImaGene and Nexus Copy Number are easy to use and utilize, what impressed me most about BioDiscovery is the support you get with your purchase. Mr. Raja Keshavan, Dr. Shams, and Shalini Verma were not only helpful but rather impressive with their support. This "Personal" support played and will play a major role in our success and I am sure in the success of BioDiscovery. I truly congratulate you on this success. We will soon switch fully to BioDiscovery after extensive testing. In the coming year we will install multi-user licenses for Nexus in our Research Core Facility."
Dr. Fahd Al-Mulla, Associate Professor and Head of Molecular Pathology, Kuwait University.
"We have been using Nexus Copy Number software for the past three years and have found it to be very useful in identifying copy number variant (CNV) data from different array platforms."
Dr. Charles Lee, Associate Professor and Clinical Cytogeneticist, Brigham and Women’s Hospital, Harvard Medical School.
"Nexus has made exploration of multiple groups comparisons of large genomic data sets easy and is flexible enough to allow visualization of results from our newly developed algorithms."
Anders Isaksson, Group Leader, and Hanna Göransson Kultima, Bioinformatician, Cancer Pharmacology and Informatics
Uppsala University
"The data exploration modules in Nexus allow us to design straightforward experiments which help clarify the causal nature of genomic alterations in cancer. This has become an invaluable tool for our collaboration with Bio-informatics specialists."
Dr. Lloyd Trotman, Assistant Professor, Cancer Center, Cold Spring Harbor Laboratory
"I feel as though BioDiscovery’s Nexus CGH software puts me back at the bench. It is truly empowering."
Dr. Colin Collins, Director, Microarray Facility, Vancouver Prostate Centre
“Nexus is light years ahead of the other commercially available software and can be used on multiple platforms”
Dr. Melissa Bondy, The University of Texas, M.D. Anderson Cancer Center
"We have been running several different high density genome-wide arrays in our patient samples, and find that Nexus is the most user-friendly and flexible software we have used to be able to integrate and visualize all of our datasets in one place. We are able to quickly and easily identify key regions of interest and jump straight to relevant statistical tests and bioinformatics tools, making the whole process much more efficient."
Dr. Anjene Addington, Child Psychiatry Branch, NIMH, NIH
"Nexus has provided us with a powerful tool for rapidly analyzing genome copy number profiles from large datasets using a variety of different platforms and the ability to incorporate expression data. These analyses are permitting us to link genomic and transcriptomic changes to clinical phenotypes and sub-populations."
Dr. Simon Gregory, Assistant Professor at Duke Center for Human Genetics
Publications
Genome wide copy number analysis of paediatric Burkitt lymphoma using formalin-fixed tissues reveals a subset with gain of chromosome 13q and corresponding miRNA over expression
Schiffman JD, Lorimer PD, Rodic V, Jahromi MS, Downie JM, Bayerl MG, Sanmann JN, Althof PA, Sanger WG, Barnette P, Perkins SL, Miles RR. Br J Haematol. 2011 Nov;155(4):477-486.
Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics.
Hanemaaijer NM, Sikkema-Raddatz B, van der Vries G, Dijkhuizen T, Hordijk R, van Essen AJ, Veenstra-Knol HE, Kerstjens-Frederikse WS, Herkert JC, Gerkes EH, Leegte LK, Kok K, Sinke RJ, van Ravenswaaij-Arts CM. Eur J Hum Genet. 2011 Sep 21.
Age- and gender-dependent obesity in individuals with 16p11.2 deletion
Yongguo Yua, Haitao Zhua, David T. Millera, James F. Gusellab, Orah S. Platta, Bai-Lin Wu. Journal of Genetics and Genomics, 2011 September;38(9):403-409.
Identification of PHLPP1 as a Tumor Suppressor Reveals the Role of Feedback Activation in PTEN-Mutant Prostate Cancer Progression
Muhan Chen, Christopher P. Pratt, Martha E. Zeeman, Nikolaus Schultz, Barry S. Taylor, Audrey O’Neill, Mireia Castillo-Martin, Dawid G. Nowak, Adam Naguib, Danielle M. Grace, Jernej Murn, Nick Navin, Gurinder S. Atwal, Chris Sander, William L. Gerald, Carlos Cordon-Cardo, Alexandra C. Newton, Brett S. Carver, Lloyd C. Trotman. Cancer Cell; 16 August 2011;20(2):173-186.
A stress response pathway regulates DNA damage through ß2-adrenoreceptors and ß-arrestin-1
Hara MR, Kovacs JJ, Whalen EJ, Rajagopal S, Strachan RT, Grant W, Towers AJ, Williams B, Lam CM, Xiao K, Shenoy SK, Gregory SG, Ahn S, Duckett DR, Lefkowitz RJ. Nature. 2011 Aug 21;477(7364):349-53.
Isolation of a new cell population in the glioblastoma microenvironment
Anne Clavreul, Amandine Etcheverry, Agnès Chassevent, Véronique Quillien, Tony Avril, Marie-Lise Jourdan, Sophie Michalak, Patrick François, Jean-Luc Carré and Jean Mosser, et al. Journal of Neuro-Oncology, 2011 August, online.
The 3q29 microdeletion syndrome: report of three new unrelated patients and in silico “RNA binding” analysis of the 3q29 region
Dasouki MJ, Lushington GH, Hovanes K, Casey J, Gorre M. July 2011. Am J Med Genet Part A 155:1654–1660.
Prostasomal DNA characterization and transfer into human sperm
Ronquist GK, Larsson A, Ronquist G, Isaksson A, Hreinsson J, Carlsson L, Stavreus-Evers A. Mol Reprod Dev. 2011 Jul;78(7):467-76.
Primary central nervous system lymphomas: a validation study of array-based comparative genomic hybridization in formalin-fixed paraffin-embedded tumor specimens
Braggio E, McPhail ER, Macon W, Lopes MB, Schiff D, Law M, Fink S, Sprau D, Giannini C, Dogan A, Fonseca R, O’Neill BP. Clin Cancer Res. 2011 Jul 1;17(13):4245-53.
7 Mb de novo deletion within 8q21 in a patient with distal arthrogryposis type 2B (DA2B)
Hofmann K, Becker J, Heller R, Boute O, Andrieux J, Hoyer J, Ekici AB, Reis A, Rauch A. Eur J Med Genet. 2011 Jun 21..
Structural Chromosome Abnormalities Associated with Obesity: Report of Four New Subjects and Review of Literature
J. Dasouki, Majed; L. Youngs, Erin; Hovanes, Karine. Current Genomics, Volume 12, Number 3, May 2011 , pp. 190-203(14).
Manitoba-oculo-tricho-anal (MOTA) syndrome is caused by mutations in FREM1
Slavotinek AM, Baranzini SE, Schanze D, Labelle-Dumais C, Short KM, Chao R, Yahyavi M, Bijlsma EK, Chu C, Musone S, Wheatley A, Kwok PY, Marles S, Fryns JP, Maga AM, Hassan MG, Gould DB, Madireddy L, Li C, Cox TC, Smyth I, Chudley AE, Zenker M. J Med Genet. 2011 Jun;48(6):375-82. Epub 2011 Apr 20.
High-resolution array CGH identifies common mechanisms that drive embryonal rhabdomyosarcoma pathogenesis
Paulson V, Chandler G, Rakheja D, Galindo RL, Wilson K, Amatruda JF, Cameron S. Genes Chromosomes Cancer. 2011 Jun;50(6):397-408. doi: 10.1002/gcc.20864. Epub 2011 Mar 15.
BCL6 enables Ph+ acute lymphoblastic leukaemia cells to survive BCR-ABL1 kinase inhibition
Duy C, Hurtz C, Shojaee S, Cerchietti L, Geng H, Swaminathan S, Klemm L, Kweon SM, Nahar R, Braig M, Park E, Kim YM, Hofmann WK, Herzog S, Jumaa H, Koeffler HP, Yu JJ, Heisterkamp N, Graeber TG, Wu H, Ye BH, Melnick A, Müschen M. Nature. 2011 May 19;473(7347):384-8.
Early G1 cyclin-dependent kinases as prognostic markers and potential therapeutic targets in esophageal adenocarcinoma
Amin Ismail*, Santhoshi Bandla, Marie Reveiller, Liana Toia, Zhongren Zhou, William E Gooding, Irina Kalatskaya, Lincoln Stein, Mary D’Souza, Virginia R Litle, Jeffrey H Peters, Arjun Pennathur, James D. Luketich, and Tony E Godfrey. Clin Cancer Res. 2011 May 18. [Epub ahead of print]
Maffucci syndrome: A genome-wide analysis using high resolution single nucleotide polymorphism and expression arrays on four cases.
Pansuriya TC, Oosting J, Verdegaal SH, Flanagan AM, Sciot R, Kindblom LG, Hogendoorn PC, Szuhai K, Bovée JV. Genes Chromosomes Cancer. 2011 May 16. [Epub ahead of print]
Molecular Karyotypes of Hodgkin and Reed-Sternberg Cells at Disease Onset Reveal Distinct Copy Number Alterations in Chemosensitive versus Refractory Hodgkin Lymphoma
Slovak ML, Bedell V, Hsu YH, Estrine DB, Nowak NJ, Delioukina ML, Weiss LM, Smith DD, Forman SJ. Clin Cancer Res. 2011 May 15;17(10):3443-54. Epub 2011 Mar 8.
Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer.
Chen Z, Liu Z, Li W, Qu K, Deng X, Varma MG, Fichera A, Pigazzi A, Garcia-Aguilar J. Genes Chromosomes Cancer. 2011 May 16. [Epub ahead of print]
Array-based genomic screening at diagnosis and follow-up in chronic lymphocytic leukemia
Gunnarsson R, Mansouri L, Isaksson A, Goransson H, Cahill N, Jansson M, Rasmussen M, Lundin J, Norin S, Buhl AM, Ekstrom Smedby K, Hjalgrim H, Karlsson K, Jurlander J, Geisler C, Juliusson G, Rosenquist R.
Haematologica. 2011 May 5. [Epub ahead of print]
Unknown partner for USP6 and unusual SS18 rearrangement detected by fluorescence in situ hybridization in a solid aneurysmal bone cyst.
Geiersbach K, Rector LS, Sederberg M, Hooker A, Randall RL, Schiffman JD, South ST. Cancer Genet. 2011 Apr;204(4):195-202.
Alternative lengthening of telomeres-An enhanced chromosomal instability in aggressive non-MYCN amplified and telomere elongated neuroblastomas
Lundberg G, Sehic D, Länsberg JK, Ora I, Frigyesi A, Castel V, Navarro S, Piqueras M, Martinsson T, Noguera R, Gisselsson D. Genes Chromosomes Cancer. 2011 Apr;50(4):250-62. Epub 2011 Jan 14.
Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP)
Hashemi J, Worrall C, Vasilcanu D, Fryknäs M, Sulaiman L, Karimi M, Weng WH, Lui WO, Rudduck C, Axelson M, Jernberg-Wiklund H, Girnita L, Larsson O, Larsson C. PLoS One. 2011 Mar 14;6(3):e14757.
Recognition of potential predictive markers for diagnosis in Korean serous ovarian cancer patients at stage IIIc using array comparative genomic hybridization with high resolution
Jee Young Kwon, Young Rok Seo and Woong Shick Ahn. Molecular & Cellular Toxicology. 2011 Mar; 7(1):77-86.
Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy.
Norton N, Li D, Rieder MJ, Siegfried JD, Rampersaud E, Züchner S, Mangos S, Gonzalez-Quintana J, Wang L, McGee S, Reiser J, Martin E, Nickerson DA, Hershberger RE. Am J Hum Genet. 2011 Mar 11;88(3):273-82. Epub 2011 Feb 25.
High-resolution genomic screening in mantle cell lymphoma–specific changes correlate with genomic complexity, the proliferation signature and survival
Halldórsdóttir AM, Sander B, Göransson H, Isaksson A, Kimby E, Mansouri M, Rosenquist R, Ehrencrona H. Genes Chromosomes Cancer. 2011 Feb;50(2):113-21
Genome-wide analysis of Ollier disease: Is it all in the genes?
Pansuriya TC, Oosting J, Krenács T, Taminiau AH, Verdegaal SH, Sangiorgi L, Sciot R, Hogendoorn PC, Szuhai K, Bovée JV. Orphanet J Rare Dis. 2011 Jan 14;6(1):2.
Accuracy of CNV Detection from GWAS Data
Zhang D, Qian Y, Akula N, Alliey-Rodriguez N, Tang J; Bipolar Genome Study, Gershon ES, Liu C. PLoS One. 2011 Jan 13;6(1):e14511.
A new 17p13.3 microduplication including the PAFAH1B1 and YWHAE genes resulting from an unbalanced X;17 translocation
Hyon C, Marlin S, Chantot-Bastaraud S, Mabboux P, Beaujard MP, Al Ageeli E, Vazquez MP, Picard A, Siffroi JP, Portnoï MF. Eur J Med Genet. 2010 Dec 31. [Epub ahead of print]
Small Molecule Inhibition of GDC-0449 Refractory Smoothened Mutants and Downstream Mechanisms of Drug Resistance
Dijkgraaf GJ, Alicke B, Weinmann L, Januario T, West K, Modrusan Z, Burdick D, Goldsmith R, Robarge K, Sutherlin D, Scales SJ, Gould SE, Yauch RL, de Sauvage FJ. Cancer Res. 2011 Jan 15;71(2):435-44. Epub 2010 Dec 1
Molecular characterization of putative chordoma cell lines
Brüderlein S, Sommer JB, Meltzer PS, Li S, Osada T, Ng D, Möller P, Alcorta DA, Kelley MJ. Sarcoma. 2010; Epub 2010 Dec 30.
Comparable low-level mosaicism in affected and non affected tissue of a complex CDH patient
Veenma D, Beurskens N, Douben H, Eussen B, Noomen P, Govaerts L, Grijseels E, Lequin M, de Krijger R, Tibboel D, de Klein A, Van Opstal D. PLoS One. 2010 Dec 21;5(12).
Common pathogenetic mechanism involving human chromosome 18 in familial and sporadic ileal carcinoid tumors
Janet L. Cunningham, Teresita Díaz de Ståhl, Tobias Sjöblom, Gunnar Westin, Jan P. Dumanski, Eva T. Janson. 2010 Nov. Genes, Chromosomes and Cancer.
Targeted resequencing of candidate genes using selector probes
H. Johansson, M. Isaksson, E. Falk Sörqvist, F. Roos, J. Stenberg, T. Sjöblom, J. Botling, P. Micke, K. Edlund, S. Fredriksson, H. Göransson Kultima, Olle Ericsson, and Mats Nilsson. 2010 Nov. Nucleic Acids Research.
Gene copy number variation in male breast cancer by aCGH
Stefania Tommasi, Anita Mangia, Giuseppina Iannelli, Patrizia Chiarappa, Elena Rossi, Laura Ottini, Marcella Mottolese, Wainer Zoli, Orsetta Zuffardi, Angelo Paradiso. 2010 Nov. Analytical Cellular Pathology / Cellular Oncology.
Archival Fine-Needle Aspiration Cytopathology (FNAC) Samples
Untapped Resource for Clinical Molecular Profiling
J. Keith Killian, Robert L. Walker, Miia Suuriniemi, Laura Jones, Stephanie Scurci, Parvati Singh, Robert Cornelison, Shannon Harmon, Nichole Boisvert, Jack Zhu, Yonghong Wang, Sven Bilke, Sean Davis, Giuseppe Giaccone , William I. Smith, Jr and Paul S. Meltzer. J Mol Diagn. Nov 2010; 12: 739-745
Genomic, immunophenotypic, and NPM1/FLT3 mutational studies on 17 patients with normal karyotype acute myeloid leukemia (AML) followed by aberrant karyotype AML at relapse.
Wang ES, Sait SN, Gold D, Mashtare T, Starostik P, Ford LA, Wetzler M, Nowak NJ, Deeb G. Cancer Genet Cytogenet. 2010 Oct 15;202(2):101-7.
No Haploinsufficiency but Loss of Heterozygosity for EXT in Multiple Osteochondromas
Reijnders CM, Waaijer CJ, Hamilton A, Buddingh EP, Dijkstra SP, Ham J, Bakker E, Szuhai K, Karperien M, Hogendoorn PC, Stringer SE, Bovée JV. Am J Pathol. 2010 Oct;177(4):1946-57. Epub 2010 Sep 2.
Distinctive Phenotypic Abnormalities Associated with Submicroscopic 21q22 Deletion Including DYRK1A
R. Oegemaa, A. de Kleina, A.J. Verkerkb, R. Schota, B. Dumeeb, H. Doubena, B. Eussena, L. Dubbela, P.J. Poddighea, I. van der Laara, W.B. Dobynsc, P.J. van der Spekb, M.H. Lequind, I.F.M. de Cooe, M.-C.Y. de Wite, M.W. Wesselsa, G.M.S. Mancinia. Mol Syndromol 2010 Sept; 1:113-120.
Molecular diversity in ductal carcinoma in situ (DCIS) and early invasive breast cancer
Muggerud AA, Hallett M, Johnsen H, Kleivi K, Zhou W, Tahmasebpoor S, Amini RM, Botling J, Børresen-Dale AL, Sørlie T, Wärnberg F. Mol Oncol. 2010 Aug;4(4):357-68.
Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours
Kresse SH, Szuhai K, Barragan-Polania AH, Rydbeck H, Cleton-Jansen AM, Myklebost O, Meza-Zepeda LA. BMC Res Notes. 2010 Aug 8;3:223.
A de novo duplication of Xp11.22-p11.4 in a girl with intellectual disability, structural brain anomalies, and preferential inactivation of the normal X chromosome.
Holden ST, Clarkson A, Thomas NS, Abbott K, James MR, Willatt L. Am J Med Genet A. 2010 Jul;152A(7):1735-40.
Loss of p15/Ink4b accompanies tumorigenesis triggered by complex DNA double-strand breaks
Camacho CV, Mukherjee B, McEllin B, Ding LH, Hu B, Habib A, Xie XJ, Nirodi C, Saha D, Story M, Balajee A, Bachoo RM, Boothman DA, Burma S. Carcinogenesis. 2010 Jul 26. [Epub ahead of print]
Application of Nexus Copy Number Software for CNV Detection and Analysis.
Bert Eussen and Annelies de Klein. European Cytogeneticists Association Newsletter. July 2010.
A novel mutation of GATA4 in a familial atrial septal defect
Chen Y, Mao J, Sun Y, Zhang Q, Cheng HB, Yan WH, Choy KW, Li H. Clin Chim Acta. 2010 Jul 24. [Epub ahead of print]
NF1 Is a Tumor Suppressor in Neuroblastoma that Determines Retinoic Acid Response and Disease Outcome
Michael Hölzel, Sidong Huang, Jan Koster, Ingrid Øra, Arjan Lakeman, Huib Caron, Wouter Nijkamp, Jing Xie, Tom Callens, Shahab Asgharzadeh, Robert C. Seeger, Ludwine Messiaen, Rogier Versteeg, René Bernards. Cell – 23 July 2010
Array comparative genomic hybridization-based characterization of genetic alterations in pulmonary neuroendocrine tumors
Voortman J, Lee JH, Killian JK, Suuriniemi M, Wang Y, Lucchi M, Smith WI Jr, Meltzer P, Wang Y, Giaccone G. Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13040-5.
Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array–comparative genomic hybridization
Isinger-Ekstrand A, Johansson J, Ohlsson M, Francis P, Staaf J, Jönsson M, Borg A, Nilbert M. Cancer Genet Cytogenet. 2010 Jul 15;200(2):120-6.
Patterns and incidence of chromosomal instability and their prognostic relevance in breast cancer subtypes
Smid M, Hoes M, Sieuwerts AM, Sleijfer S, Zhang Y, Wang Y, Foekens JA, Martens JW. Breast Cancer Res Treat. 2010 Jul 15. [Epub ahead of print]
Low grade mosaic for a complex supernumerary ring chromosome 18 in an adult patient with multiple congenital anomalies
van der Veken LT, Dieleman MM, Douben H, van de Brug JC, van de Graaf R, Hoogeboom AJ, Poddighe PJ, de Klein A. Mol Cytogenet. 2010 Jul 9;3:13.
Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma.
Parris TZ, Danielsson A, Nemes S, Kovács A, Delle U, Fallenius G, Möllerström E, Karlsson P, Helou K. Clin Cancer Res. 2010 Jun 15.
HDMX regulates p53 activity and confers chemoresistance to 3-Bis (2-chloroethyl)-1-nitrosoureaG
Jin G, Cook S, Cui B, Chen WC, Keir ST, Killela P, Di C, Payne CA, Gregory SG, McLendon R, Bigner DD, Yan H. Neuro Oncol. 2010 May 14. [Epub ahead of print]
Tourette disorder spectrum maps to chromosome 14q31. 1 in an Italian kindred
Breedveld GJ, Fabbrini G, Oostra BA, Berardelli A, Bonifati V. Neurogenetics. 2010 May 2. [Epub ahead of print]
High-density screening reveals a different spectrum of genomic aberrations in chronic lymphocytic leukemia patients with “stereotyped” IGHV3-21 and IGHV4-34 B cell receptors
Marincevic M, Cahill N, Gunnarsson R, Isaksson A, Mansouri M, Göransson H, Rasmusson M, Jansson M, Ryan F, Karlsson K, Adami HO, Davi F, Jurlander J, Juliusson G, Stamatopoulus K, Rosenquist R. Haematologica. 2010 Apr 26. [Epub ahead of print]
Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis.
Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, May GD, Woodward JE, Caillier SJ, McElroy JP, Gomez R, Pando MJ, Clendenen LE, Ganusova EE, Schilkey FD, Ramaraj T, Khan OA, Huntley JJ, Luo S, Kwok PY, Wu TD, Schroth GP, Oksenberg JR, Hauser SL, Kingsmore SF. Nature. 2010 Apr 29;464(7293):1351-6.
A pathway-based classification of human breast cancer.
Gatza ML, Lucas JE, Barry WT, Kim JW, Wang Q, Crawford MD, Datto MB, Kelley M, Mathey-Prevot B, Potti A, Nevins JR. Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6994-9. Epub 2010 Mar 24.
Analysis of Segmental Duplications, Mouse Genome Synteny and Recurrent Cancer-Associated Amplicons in Human Chromosome 6p21–p12
J.W. Martin, M. Yoshimoto, O. Ludkovski, P.S. Thorner, M. Zielenska, J.A. Squire, P.A.S. Nuin. Cytogenet Genome Res 2010;128:199-213
Oligonucleotide-based array CGH analysis of diffuse large B-cell lymphomas identifies gain of 7q22 as the most common genomic alteration
Edward A. Medina, Aswani R Bolla, Rajya L Bandi and Ryan S Robetorye. FASEB J. 2010 24:954.11.
Application of Nexus Copy Number Software for CNV Detection and Analysis.
Darvishi K. Curr Protoc Hum Genet. 2010 Apr;Chapter 4:Unit4.14.
In-depth investigation of the molecular pathogenesis of bladder cancer in a unique 26-year old patient with extensive multifocal disease: a case report.
Zuiverloon TC, Abas CS, van der Keur KA, Vermeij M, Tjin SS, van Tilborg AG, Busstra M, Zwarthoff EC.BMC Urol. 2010 Feb 26;10:5.
Unfavorable prognosis of CRTC1-MAML2 positive mucoepidermoid tumors with CDKN2A deletions.
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Genomic alterations in histopathologically normal breast tissue from BRCA1 mutation carriers may be caused by BRCA1 haploinsufficiency.
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Frequent genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression.
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Genetics of uveal melanoma
Hanneke W Mensink, Dion Paridaens, Annelies de Klein Expert Review of Ophthalmology, December 2009, Vol. 4, No. 6, Pages 607-616.
Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.
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Detailed cytogenetic and array analysis of pediatric primitive sarcomas reveals a recurrent CIC-DUX4 fusion gene event.
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Genomic Landscape of Meningiomas.
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Glioblastoma Proto-oncogene SEC61-gamma Is Required for Tumor Cell Survival and Response to Endoplasmic Reticulum Stress.
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Integrative genomics reveals mechanisms of copy number alterations responsible for transcriptional deregulation in colorectal cancer
Camps J, Nguyen QT, Padilla-Nash HM, Knutsen T, McNeil NE, Wangsa D, Hummon AB, Grade M, Ried T, Difilippantonio MJ. Genes Chromosomes Cancer. 2009 Nov;48(11):1002-17.
CNTNAP2 and NRXN1 are mutated in autosomal-recessive Pitt-Hopkins-like mental retardation and determine the level of a common synaptic protein in Drosophila.
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Microarray based analysis of 3p25-p26 deletions (3p- syndrome).
Shuib S, McMullan D, Rattenberry E, Barber RM, Rahman F, Zatyka M, Chapman C, Macdonald F, Latif F, Davison V, Maher ER. Am J Med Genet A. 2009 Oct;149A(10):2099-105.
Genomic and epigenetic evidence for oxytocin receptor deficiency in autism.
Gregory SG, Connelly JJ, Towers AJ, Johnson J, Biscocho D, Markunas CA, Lintas C, Abramson RK, Wright HH, Ellis P, Langford CF, Worley G, Delong GR, Murphy SK, Cuccaro ML, Persico A, Pericak-Vance MA.
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Disruption of ST5 is associated with mental-retardation and multiple congenital anomalies.
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Identification of chromosome 7 inversion breakpoints in an autistic family narrows candidate region for autism susceptibility.
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Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients.
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Array-CGH analysis indicates a high prevalence of genomic rearrangements in holoprosencephaly: an updated map of candidate loci.
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A highly annotated whole-genome sequence of a Korean individual.
Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS. Nature. 2009 Jul 8.
Gene copy number and malaria biology.
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DNA copy number variation and gene expression analyses reveal the implication of specific oncogenes and genes in GBM.
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High resolution array analysis: diagnosing pregnancies with abnormal ultrasound findings.
Tyreman M, Abbott KM, Willatt LR, Nash R, Lees C, Whittaker J, Simonic I. J Med Genet. 2009 Aug;46(8):531-41. Epub 2009 May 17.
Copy Number Variation in African Americans.
Joseph P. McElroy, Matthew R. Nelson, Stacy J. Caillier, Jorge, R. Oksenberg. BMC Genetics 2009, 10:15.
Genomic aberrations in squamous cell lung carcinoma related to lymph node or distant metastasis.
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Customized oligonucleotide array-based comparative genomic hybridization as a clinical assay for genomic profiling of chronic lymphocytic leukemia
Sargent R, Jones D, Abruzzo LV, Yao H, Bonderover J, Cisneros M, Wierda WG, Keating MJ, Luthra R. J Mol Diagn. 2009 Jan;11(1):25-34. Epub 2008 Dec 12.
6.7 Mb interstitial duplication in chromosome band 11q24.2q25 associated with infertility, minor dysmorphic features and normal psychomotor development
Göhring Ina; Blümlein Hans-Martin; Hoyer Juliane; Ekici Arif B; Trautmann Udo; Rauch Anita. Eur J Med Genet. 2008 Nov-Dec;51(6):666-71. Epub 2008 Aug 12. [PubMed]
Multiple sub-microscopic genomic lesions are a universal feature of chronic myeloid leukaemia at diagnosis
Khorashad JS, De Melo VA, Fiegler H, Gerrard G, Marin D, Apperley JF, Goldman JM, Foroni L, Reid AG. Leukemia. 2008 Sep;22(9):1806-7. Epub 2008 Jul 31. [Abstract] [PubMed]
3.8 MB Deletion of Chromosome 5q in a Newborn Tracheal Agenesis Patient
Elisabeth de Jong, Hannie Douben, Bert Eussen, Dick Tibboel and Annelies de Klein. Poster presentation at ASHG 2008, Philadelphia, PA [Poster]
DNA Copy Number Stratification of Breast Cancer Samples Identifies Distinct Biological Mechanisms
S. Shams, R. Davis, B. Poirier, J. Gregg. Poster presentation at AACR Translational Cancer Medicine Conference, July 2008, San Diego, CA. [Poster]
Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431)
Moore SR, Persons DL, Sosman JA, Bobadilla D, Bedell V, Smith DD, Wolman SR, Tuthill RJ, Moon J, Sondak VK, Slovak ML. Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431). Clin Cancer Res. 2008 May 15;14(10):2927-35. [PubMed]
A de-novo 7.6 Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay
Thiel CT, Dörr HG, Trautmann U, Hoyer J, Hofmann K, Kraus C, Ekici AB, Reis A, Rauch A. A de novo 7.6Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay. Eur J Med Genet. 2008 Jul-Aug; 51(4):362-7. Epub 2008 Mar 20. [PubMed]
Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia
Tom Walsh, Jon M. McClellan, Shane E. McCarthy, Anjene M. Addington, Sarah B. Pierce, Greg M. Cooper, Alex S. Nord, Mary Kusenda, Dheeraj Malhotra, Abishek Bhandari, Sunday M. Stray, Caitlin F. Rippey, Patricia Roccanova, Vlad Makarov, B. Lakshmi, Robert L. Findling, Linmarie Sikich, Thomas Stromberg , Barry Merriman, Nitin Gogtay, Philip Butler, Kristen Eckstrand, Laila Noory, Peter Gochman, Robert Long, Zugen Chen, Sean Davis, Carl Baker, Evan E. Eichler, Paul S. Meltzer, Stanley F. Nelson, Andrew B. Singleton, Ming K. Lee, Judith L. Rapoport, Mary-Claire King, Jonathan Sebat. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science, 27 March 2008. (10.1126/science.1155174). [Abstract]
Challenges In Array CGH For the Analysis Of Cancer Samples
Nowak NJ, Miecznikowski J, Moore SR, Gaile D, Bobadilla D, Smith DD, Kernstine K, Forman SJ, Mwahech-Fauceglia P, Reid M, Stoler D, Loree T, Rigual N, Sullivan M, Weiss LM, Hicks D, Slovak ML. Challenges In Array CGH For the Analysis Of Cancer Samples. Genetics in Medicine, 9(9): 585-595, 2007. [PubMed]
Whitepapers
• Copy Number Analysis of Head and Neck cancer
• Cancer Survival and Copy Number Variations
• Copy Number Analysis of Parkinson’s Samples Using Roche NimbleGen Microarrays White Paper
• Locating Significantly Different CNV Regions between Two Groups
• Integrated Analysis of Copy Number and Gene Expression
• Simplifying Data Interpretation with Nexus Copy Number
