SSCP screening of the dihydropyrimidine dehydrogenase gene polymorphisms of the Japanese population using a semi-automated electrophoresis unit

Yoshihiro Okamoto, Akihito Ueta, Satoshi Sumi, Tetsuya Ito, Yumiko Okubo, Yuki Jose, Akiko Ninomiya, Hajime Togari, Mikio Nishida

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The single-strand conformation polymorphism (SSCP) procedure has been applied in routine testing for hereditary diseases. Temperature, running buffer, gel composition, and fragment length can influence its sensitivity. Mutation detection in the clinical setting depends on the development of automated technology, especially for large genes, such as the dihydropyrimidine dehydrogenase (DPYD) gene, which codes the initial, rate-limiting enzyme in the catabolism of 5-fluorouracil (5FU). The authors have optimized the condition of SSCP with an automated system (GenePhor system, GE Healthcare UK Ltd.) to screen genetic polymorphisms in the DPYD gene. The efficiency of the method was evaluated using 21 positive controls (DNA samples with polymorphisms in the DPYD gene, previously characterized) and DNA samples from 35 Japanese. Results showed that the use of three different running buffers (pH 7.4, 8.3, and 9.0) in combination with other optimized conditions (10% polyacrylamide gel, 60-90 min at constant 900 V at 5°C) resulted in a high polymorphism detection rate (95.3%), which was considered appropriate for routine screening. Therefore, this strategy could be useful for pharmacogenetic studies on 5FU.

Original languageEnglish
Pages (from-to)713-724
Number of pages12
JournalBiochemical Genetics
Volume45
Issue number9-10
DOIs
Publication statusPublished - 01-10-2007
Externally publishedYes

Fingerprint

Dihydrouracil Dehydrogenase (NADP)
single-stranded conformational polymorphism
Electrophoresis
Polymorphism
electrophoresis
Conformations
electrokinesis
Screening
polymorphism
Genes
genetic polymorphism
screening
fluorouracil
gene
Fluorouracil
Population
Buffers
genes
buffers
gels

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Okamoto, Yoshihiro ; Ueta, Akihito ; Sumi, Satoshi ; Ito, Tetsuya ; Okubo, Yumiko ; Jose, Yuki ; Ninomiya, Akiko ; Togari, Hajime ; Nishida, Mikio. / SSCP screening of the dihydropyrimidine dehydrogenase gene polymorphisms of the Japanese population using a semi-automated electrophoresis unit. In: Biochemical Genetics. 2007 ; Vol. 45, No. 9-10. pp. 713-724.
@article{b4df30b6254f4f5881a0dd0c1f67c9b4,
title = "SSCP screening of the dihydropyrimidine dehydrogenase gene polymorphisms of the Japanese population using a semi-automated electrophoresis unit",
abstract = "The single-strand conformation polymorphism (SSCP) procedure has been applied in routine testing for hereditary diseases. Temperature, running buffer, gel composition, and fragment length can influence its sensitivity. Mutation detection in the clinical setting depends on the development of automated technology, especially for large genes, such as the dihydropyrimidine dehydrogenase (DPYD) gene, which codes the initial, rate-limiting enzyme in the catabolism of 5-fluorouracil (5FU). The authors have optimized the condition of SSCP with an automated system (GenePhor system, GE Healthcare UK Ltd.) to screen genetic polymorphisms in the DPYD gene. The efficiency of the method was evaluated using 21 positive controls (DNA samples with polymorphisms in the DPYD gene, previously characterized) and DNA samples from 35 Japanese. Results showed that the use of three different running buffers (pH 7.4, 8.3, and 9.0) in combination with other optimized conditions (10{\%} polyacrylamide gel, 60-90 min at constant 900 V at 5°C) resulted in a high polymorphism detection rate (95.3{\%}), which was considered appropriate for routine screening. Therefore, this strategy could be useful for pharmacogenetic studies on 5FU.",
author = "Yoshihiro Okamoto and Akihito Ueta and Satoshi Sumi and Tetsuya Ito and Yumiko Okubo and Yuki Jose and Akiko Ninomiya and Hajime Togari and Mikio Nishida",
year = "2007",
month = "10",
day = "1",
doi = "10.1007/s10528-007-9109-7",
language = "English",
volume = "45",
pages = "713--724",
journal = "Biochemical Genetics",
issn = "0006-2928",
publisher = "Springer New York",
number = "9-10",

}

SSCP screening of the dihydropyrimidine dehydrogenase gene polymorphisms of the Japanese population using a semi-automated electrophoresis unit. / Okamoto, Yoshihiro; Ueta, Akihito; Sumi, Satoshi; Ito, Tetsuya; Okubo, Yumiko; Jose, Yuki; Ninomiya, Akiko; Togari, Hajime; Nishida, Mikio.

In: Biochemical Genetics, Vol. 45, No. 9-10, 01.10.2007, p. 713-724.

Research output: Contribution to journalArticle

TY - JOUR

T1 - SSCP screening of the dihydropyrimidine dehydrogenase gene polymorphisms of the Japanese population using a semi-automated electrophoresis unit

AU - Okamoto, Yoshihiro

AU - Ueta, Akihito

AU - Sumi, Satoshi

AU - Ito, Tetsuya

AU - Okubo, Yumiko

AU - Jose, Yuki

AU - Ninomiya, Akiko

AU - Togari, Hajime

AU - Nishida, Mikio

PY - 2007/10/1

Y1 - 2007/10/1

N2 - The single-strand conformation polymorphism (SSCP) procedure has been applied in routine testing for hereditary diseases. Temperature, running buffer, gel composition, and fragment length can influence its sensitivity. Mutation detection in the clinical setting depends on the development of automated technology, especially for large genes, such as the dihydropyrimidine dehydrogenase (DPYD) gene, which codes the initial, rate-limiting enzyme in the catabolism of 5-fluorouracil (5FU). The authors have optimized the condition of SSCP with an automated system (GenePhor system, GE Healthcare UK Ltd.) to screen genetic polymorphisms in the DPYD gene. The efficiency of the method was evaluated using 21 positive controls (DNA samples with polymorphisms in the DPYD gene, previously characterized) and DNA samples from 35 Japanese. Results showed that the use of three different running buffers (pH 7.4, 8.3, and 9.0) in combination with other optimized conditions (10% polyacrylamide gel, 60-90 min at constant 900 V at 5°C) resulted in a high polymorphism detection rate (95.3%), which was considered appropriate for routine screening. Therefore, this strategy could be useful for pharmacogenetic studies on 5FU.

AB - The single-strand conformation polymorphism (SSCP) procedure has been applied in routine testing for hereditary diseases. Temperature, running buffer, gel composition, and fragment length can influence its sensitivity. Mutation detection in the clinical setting depends on the development of automated technology, especially for large genes, such as the dihydropyrimidine dehydrogenase (DPYD) gene, which codes the initial, rate-limiting enzyme in the catabolism of 5-fluorouracil (5FU). The authors have optimized the condition of SSCP with an automated system (GenePhor system, GE Healthcare UK Ltd.) to screen genetic polymorphisms in the DPYD gene. The efficiency of the method was evaluated using 21 positive controls (DNA samples with polymorphisms in the DPYD gene, previously characterized) and DNA samples from 35 Japanese. Results showed that the use of three different running buffers (pH 7.4, 8.3, and 9.0) in combination with other optimized conditions (10% polyacrylamide gel, 60-90 min at constant 900 V at 5°C) resulted in a high polymorphism detection rate (95.3%), which was considered appropriate for routine screening. Therefore, this strategy could be useful for pharmacogenetic studies on 5FU.

UR - http://www.scopus.com/inward/record.url?scp=35449005887&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=35449005887&partnerID=8YFLogxK

U2 - 10.1007/s10528-007-9109-7

DO - 10.1007/s10528-007-9109-7

M3 - Article

C2 - 17876700

AN - SCOPUS:35449005887

VL - 45

SP - 713

EP - 724

JO - Biochemical Genetics

JF - Biochemical Genetics

SN - 0006-2928

IS - 9-10

ER -