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

Ross Rowsey; Iya Znoyko; Daynna J Wolff

doi:10.1007/978-1-4939-9004-7_7

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.

Authors

Ross Rowsey¹, Iya Znoyko², Daynna J Wolff³

Affiliations

¹ Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
² Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA.
³ Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA. wolffd@musc.edu.

PMID: 30649723
DOI: 10.1007/978-1-4939-9004-7_7

Abstract

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