title: Multiplex PCR-based real-time invader assay (mPCR-RETINA): a novel SNP-based method for detecting allelic asymmetries within copy number variation regions.
abstract: We report the development of a real-time Invader assay combined with multiplex PCR (mPCR-RETINA), an SNP-based approach that can measure the allelic ratio in copy number variation (CNV) regions of a genome. RETINA monitors the real-time fluorescence intensity of each allele during the Invader assay and detects allelic asymmetries caused by genomic duplication/multiplication in heterozygous individuals. By combining mPCR-RETINA and real-time quantitative PCR that detects total copy number, we can estimate the copy number of each allele in CNV regions, which should be useful for investigating the functional significance of allele copy number with disease susceptibilities and drug responses. Also, mPCR-RETINA can efficiently refine the detailed structures of CNV regions. Due to the combination of RETINA with multiplex PCR, mPCR-RETINA requires a very small amount of genomic DNA for analysis (0.1-0.38 ng/locus). Additionally, mPCR-RETINA has clear advantages in its simple protocol and target-specific reaction, even in nonunique regions. We believe mPCR-RETINA will provide a significant contribution to identifying functional alleles in CNV regions.
authors: Laboratory for Genotyping, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan. nhosono@src.riken.jp
authors: Naoya
authors: N
authors: Hosono
authors: Michiaki
authors: M
authors: Kubo
authors: Yumiko
authors: Y
authors: Tsuchiya
authors: Hiroko
authors: H
authors: Sato
authors: Takuya
authors: T
authors: Kitamoto
authors: Susumu
authors: S
authors: Saito
authors: Yozo
authors: Y
authors: Ohnishi
authors: Yusuke
authors: Y
authors: Nakamura
mesh_terms: D000483:Alleles; D018628:Gene Dosage; D020440:Gene Duplication; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D008954:Models, Biological; D008957:Models, Genetic; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D044465:White People