title: Molecular methods for genotyping complex copy number polymorphisms.
abstract: Genome structural variation shows remarkable complexity with respect to copy number, sequence content and distribution. While the discovery of copy number polymorphisms (CNP) has increased exponentially in recent years, the transition from discovery to genotyping has proved challenging, particularly for CNPs embedded in complex regions of the genome. CNPs that are collectively common in the population and possess a dynamic range of copy numbers have proved the most difficult to genotype in association studies. This is in some part due to technical limitations of genotyping assays and the sequence properties of the genomic region being analyzed. Here we describe in detail the basis of a number of molecular techniques used to genotype complex CNPs, compare and contrast these approaches for determination of multi-allelic copy number, and discuss the potential application of these techniques in genetic studies.
authors.affiliation: Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Centre for Reproduction and Development, Monash Institute of Medical Research, Monash University, Melbourne, Victoria, Australia.
authors.forename: Stuart
authors.initials: S
authors.lastname: Cantsilieris
authors.affiliation: Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.
authors.forename: Paul N
authors.initials: PN
authors.lastname: Baird
authors.affiliation: Centre for Reproduction and Development, Monash Institute of Medical Research, Monash University, Melbourne, Victoria, Australia. Electronic address: stefan.white@monash.edu.
authors.forename: Stefan J
authors.initials: SJ
authors.lastname: White
mesh_terms: D015139:Blotting, Southern; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D016521:Electrophoresis, Gel, Pulsed-Field; D060005:Genotyping Techniques; D017404:In Situ Hybridization, Fluorescence; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction