Whole-Genome Single Nucleotide Polymorphism Microarray for Copy Number and Loss of Heterozygosity Analysis in Tumors

Methods Mol Biol. 2019:1908:89-111. doi: 10.1007/978-1-4939-9004-7_7.


The basis of cancer biology is built upon two fundamental processes that result in uncontrolled cell proliferation and tumor formation: loss of tumor suppressor gene function and gain of oncogene function. Somatic DNA copy number variants (CNVs), which generally range in size from kilobases to entire chromosomes, facilitate gains and losses of chromosomal material incorporating oncogenes and tumor suppressor genes, respectively. In fact, many cancer types are characterized by DNA copy number changes and relatively few single nucleotide mutations (Ciriello et al. Nat Genet 45:1127-1133, 2013). Currently, the optimal method to detect such somatic copy number changes across the cancer genome is whole-genome single nucleotide polymorphism (SNP) microarray analysis.

Keywords: B-allele frequency; Copy number; Cytogenomics; Loss of heterozygosity; SNP microarray.

MeSH terms

  • DNA Copy Number Variations*
  • Genomics / methods
  • Humans
  • Loss of Heterozygosity*
  • Mutation
  • Neoplasms / genetics*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Paraffin Embedding
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA / methods*
  • Tissue Fixation