UNIT 4.14 Application of Nexus Copy Number Software for CNV Detection and Analysis

  1. Katayoon Darvishi

Published Online: 1 APR 2010

DOI: 10.1002/0471142905.hg0414s65

Current Protocols in Human Genetics

Current Protocols in Human Genetics

How to Cite

Darvishi, K. 2010. Application of Nexus Copy Number Software for CNV Detection and Analysis. Current Protocols in Human Genetics. 65:4.14:4.14.1–4.14.28.

Author Information

  1. Harvard Medical School, Boston, Massachusetts

Publication History

  1. Published Online: 1 APR 2010
  2. Published Print: APR 2010


Among human structural genomic variation, copy number variants (CNVs) are the most frequently known component, comprised of gains/losses of DNA segments that are generally 1 kb in length or longer. Array-based comparative genomic hybridization (aCGH) has emerged as a powerful tool for detecting genomic copy number variants (CNVs). With the rapid increase in the density of array technology and with the adaptation of new high-throughput technology, a reliable and computationally scalable method for accurate mapping of recurring DNA copy number aberrations has become a main focus in research. Here we introduce Nexus Copy Number software, a platform-independent tool, to analyze the output files of all types of commercial and custom-made comparative genomic hybridization (CGH) and single-nucleotide polymorphism (SNP) arrays, such as those manufactured by Affymetrix, Agilent Technologies, Illumina, and Roche NimbleGen. It also supports data generated by various array image-analysis software tools such as GenePix, ImaGene, and BlueFuse. Curr. Protoc. Hum. Genet. 65:4.14.1-4.14.28. © 2010 by John Wiley & Sons, Inc.


  • copy number variation;
  • microarrays;
  • comparative genomic hybridization;
  • single-nucleotide polymorphism;
  • Nexus Copy Number;
  • BioDiscovery