Criterion values for multiplex SNP genotyping by the Invader assay

Hiroaki Nakahara, Kazumasa Sekiguchi, Naoya Hosono, Michiaki Kubo, Atsushi Takahashi, Yusuke Nakamura, Kentaro Kasai

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

We have developed a multiplex, single nucleotide polymorphism (SNP) typing system for forensic identification, based on the Invader assay. Using this system, fluorescence data for 21 SNP loci were collected and analyzed. We used endpoint genotyping, commonly used with the Invader assay, and also developed more reliable typing criteria because endpoint typing was occasionally unable to clearly identify the genotype of some loci. Analysis of the fluorescence data identified criteria that had high reproducibility for each genotype. One such criterion is the climbing angle of the curve resulting from two-dimensional plots of the two kinds of fluorescence used for the Invader assay. The climbing angle was observed at the time during the reaction when either or both of the fluorescence intensities increased most significantly. The angles were remarkably associated with homozygous genotypes. On the other hand, all heterozygote endpoint fluorescence ratios were highly reproducible and had very little aberration. These values enabled SNP typing to be more clearly defined compared with typing using only the endpoint fluorescence ratio, which is commonly used with the Invader assay. The values suggested in this study are easily calculated from raw fluorescence data and will be useful for multiplex SNP typing based on the Invader assay.

Original languageEnglish
Pages (from-to)130-136
Number of pages7
JournalForensic Science International: Genetics
Volume4
Issue number2
DOIs
Publication statusPublished - 01-02-2010
Externally publishedYes

Fingerprint

Single Nucleotide Polymorphism
Fluorescence
Genotype
Heterozygote
Information Systems

All Science Journal Classification (ASJC) codes

  • Pathology and Forensic Medicine
  • Genetics

Cite this

Nakahara, H., Sekiguchi, K., Hosono, N., Kubo, M., Takahashi, A., Nakamura, Y., & Kasai, K. (2010). Criterion values for multiplex SNP genotyping by the Invader assay. Forensic Science International: Genetics, 4(2), 130-136. https://doi.org/10.1016/j.fsigen.2009.07.005
Nakahara, Hiroaki ; Sekiguchi, Kazumasa ; Hosono, Naoya ; Kubo, Michiaki ; Takahashi, Atsushi ; Nakamura, Yusuke ; Kasai, Kentaro. / Criterion values for multiplex SNP genotyping by the Invader assay. In: Forensic Science International: Genetics. 2010 ; Vol. 4, No. 2. pp. 130-136.
@article{e8abae720db049c893b40d8ca3f80099,
title = "Criterion values for multiplex SNP genotyping by the Invader assay",
abstract = "We have developed a multiplex, single nucleotide polymorphism (SNP) typing system for forensic identification, based on the Invader assay. Using this system, fluorescence data for 21 SNP loci were collected and analyzed. We used endpoint genotyping, commonly used with the Invader assay, and also developed more reliable typing criteria because endpoint typing was occasionally unable to clearly identify the genotype of some loci. Analysis of the fluorescence data identified criteria that had high reproducibility for each genotype. One such criterion is the climbing angle of the curve resulting from two-dimensional plots of the two kinds of fluorescence used for the Invader assay. The climbing angle was observed at the time during the reaction when either or both of the fluorescence intensities increased most significantly. The angles were remarkably associated with homozygous genotypes. On the other hand, all heterozygote endpoint fluorescence ratios were highly reproducible and had very little aberration. These values enabled SNP typing to be more clearly defined compared with typing using only the endpoint fluorescence ratio, which is commonly used with the Invader assay. The values suggested in this study are easily calculated from raw fluorescence data and will be useful for multiplex SNP typing based on the Invader assay.",
author = "Hiroaki Nakahara and Kazumasa Sekiguchi and Naoya Hosono and Michiaki Kubo and Atsushi Takahashi and Yusuke Nakamura and Kentaro Kasai",
year = "2010",
month = "2",
day = "1",
doi = "10.1016/j.fsigen.2009.07.005",
language = "English",
volume = "4",
pages = "130--136",
journal = "Forensic Science International: Genetics",
issn = "1872-4973",
publisher = "Elsevier Ireland Ltd",
number = "2",

}

Nakahara, H, Sekiguchi, K, Hosono, N, Kubo, M, Takahashi, A, Nakamura, Y & Kasai, K 2010, 'Criterion values for multiplex SNP genotyping by the Invader assay', Forensic Science International: Genetics, vol. 4, no. 2, pp. 130-136. https://doi.org/10.1016/j.fsigen.2009.07.005

Criterion values for multiplex SNP genotyping by the Invader assay. / Nakahara, Hiroaki; Sekiguchi, Kazumasa; Hosono, Naoya; Kubo, Michiaki; Takahashi, Atsushi; Nakamura, Yusuke; Kasai, Kentaro.

In: Forensic Science International: Genetics, Vol. 4, No. 2, 01.02.2010, p. 130-136.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Criterion values for multiplex SNP genotyping by the Invader assay

AU - Nakahara, Hiroaki

AU - Sekiguchi, Kazumasa

AU - Hosono, Naoya

AU - Kubo, Michiaki

AU - Takahashi, Atsushi

AU - Nakamura, Yusuke

AU - Kasai, Kentaro

PY - 2010/2/1

Y1 - 2010/2/1

N2 - We have developed a multiplex, single nucleotide polymorphism (SNP) typing system for forensic identification, based on the Invader assay. Using this system, fluorescence data for 21 SNP loci were collected and analyzed. We used endpoint genotyping, commonly used with the Invader assay, and also developed more reliable typing criteria because endpoint typing was occasionally unable to clearly identify the genotype of some loci. Analysis of the fluorescence data identified criteria that had high reproducibility for each genotype. One such criterion is the climbing angle of the curve resulting from two-dimensional plots of the two kinds of fluorescence used for the Invader assay. The climbing angle was observed at the time during the reaction when either or both of the fluorescence intensities increased most significantly. The angles were remarkably associated with homozygous genotypes. On the other hand, all heterozygote endpoint fluorescence ratios were highly reproducible and had very little aberration. These values enabled SNP typing to be more clearly defined compared with typing using only the endpoint fluorescence ratio, which is commonly used with the Invader assay. The values suggested in this study are easily calculated from raw fluorescence data and will be useful for multiplex SNP typing based on the Invader assay.

AB - We have developed a multiplex, single nucleotide polymorphism (SNP) typing system for forensic identification, based on the Invader assay. Using this system, fluorescence data for 21 SNP loci were collected and analyzed. We used endpoint genotyping, commonly used with the Invader assay, and also developed more reliable typing criteria because endpoint typing was occasionally unable to clearly identify the genotype of some loci. Analysis of the fluorescence data identified criteria that had high reproducibility for each genotype. One such criterion is the climbing angle of the curve resulting from two-dimensional plots of the two kinds of fluorescence used for the Invader assay. The climbing angle was observed at the time during the reaction when either or both of the fluorescence intensities increased most significantly. The angles were remarkably associated with homozygous genotypes. On the other hand, all heterozygote endpoint fluorescence ratios were highly reproducible and had very little aberration. These values enabled SNP typing to be more clearly defined compared with typing using only the endpoint fluorescence ratio, which is commonly used with the Invader assay. The values suggested in this study are easily calculated from raw fluorescence data and will be useful for multiplex SNP typing based on the Invader assay.

UR - http://www.scopus.com/inward/record.url?scp=73249148468&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=73249148468&partnerID=8YFLogxK

U2 - 10.1016/j.fsigen.2009.07.005

DO - 10.1016/j.fsigen.2009.07.005

M3 - Article

VL - 4

SP - 130

EP - 136

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

SN - 1872-4973

IS - 2

ER -