Multiplex PCR-based Real-Time Invader Assay (mPCR-RETINA)

A novel SNP-based method for detecting allelic asymmetries within copy number variation regions

Naoya Hosono, Michiaki Kubo, Yumiko Tsuchiya, Hiroko Sato, Takuya Kitamoto, Susumu Saito, Yozo Ohnishi, Yusuke Nakamura

Research output: Contribution to journalArticle

24 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)182-189
Number of pages8
JournalHuman Mutation
Volume29
Issue number1
DOIs
Publication statusPublished - 01-01-2008
Externally publishedYes

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Multiplex Polymerase Chain Reaction
Single Nucleotide Polymorphism
Alleles
Disease Susceptibility
Real-Time Polymerase Chain Reaction
Fluorescence
Genome
DNA
Pharmaceutical Preparations

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Hosono, Naoya ; Kubo, Michiaki ; Tsuchiya, Yumiko ; Sato, Hiroko ; Kitamoto, Takuya ; Saito, Susumu ; Ohnishi, Yozo ; Nakamura, Yusuke. / Multiplex PCR-based Real-Time Invader Assay (mPCR-RETINA) : A novel SNP-based method for detecting allelic asymmetries within copy number variation regions. In: Human Mutation. 2008 ; Vol. 29, No. 1. pp. 182-189.
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Multiplex PCR-based Real-Time Invader Assay (mPCR-RETINA) : A novel SNP-based method for detecting allelic asymmetries within copy number variation regions. / Hosono, Naoya; Kubo, Michiaki; Tsuchiya, Yumiko; Sato, Hiroko; Kitamoto, Takuya; Saito, Susumu; Ohnishi, Yozo; Nakamura, Yusuke.

In: Human Mutation, Vol. 29, No. 1, 01.01.2008, p. 182-189.

Research output: Contribution to journalArticle

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AU - Hosono, Naoya

AU - Kubo, Michiaki

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AU - Sato, Hiroko

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AU - Nakamura, Yusuke

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