Application of Nexus copy number software for CNV detection and analysis

Curr Protoc Hum Genet. 2010 Apr;Chapter 4:Unit 4.14.1-28. doi: 10.1002/0471142905.hg0414s65.

Abstract

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.

MeSH terms

  • Comparative Genomic Hybridization / methods*
  • DNA Copy Number Variations / genetics*
  • Genome, Human / genetics*
  • Humans
  • Microarray Analysis / methods*
  • Polymorphism, Single Nucleotide / genetics*
  • Software*