High-throughput genotyping of copy number variation in glutathione S-transferases M1 and T1 using real-time PCR in 20,687 individuals

Marianne S Nørskov; Ruth Frikke-Schmidt; Steffen Loft; Anne Tybjaerg-Hansen

doi:10.1016/j.clinbiochem.2008.10.020

High-throughput genotyping of copy number variation in glutathione S-transferases M1 and T1 using real-time PCR in 20,687 individuals

Marianne S Nørskov, Ruth Frikke-Schmidt, Steffen Loft, Anne Tybjaerg-Hansen

23 Citations (Scopus)

Abstract

OBJECTIVES: Characteristic for the genes encoding glutathione S-transferase (GST) M1 and GSTT1 is a null allele, suggested to increase susceptibility to chronic diseases. We report an optimized method for the determination of copy number variation (CNV) in GST genes.

DESIGN AND METHODS: Real-time multiplex PCR reactions were optimized for quantification of GSTM1 and GSTT1 CNV using the DeltaCt method, a fixed volume of diluted DNA, a total volume of 10 microL, 384-well formats, and single determinations of each sample.

RESULTS: Consistent genotyping was obtained using DNA in a range of 0.41 ng to 100 ng. In a general population sample of 20,687 individuals the genotype frequencies were concordant with other methods used as standards. Throughput was 4600 genotypes per day at a reagent price of 0.5 euros per sample.

CONCLUSIONS: This high-throughput, low cost method accurately determines CNV in the GST genes enabling reliable estimates of disease prediction in large epidemiological samples.

Original language	English
Journal	Clinical Biochemistry
Volume	42
Issue number	3
Pages (from-to)	201-9
Number of pages	9
ISSN	0009-9120
DOIs	https://doi.org/10.1016/j.clinbiochem.2008.10.020
Publication status	Published - Feb 2009
Externally published	Yes

Keywords

Gene Dosage
Gene Frequency
Genotype
Glutathione Transferase/genetics
Humans
Mass Screening
Molecular Epidemiology/methods
Polymerase Chain Reaction/methods

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10.1016/j.clinbiochem.2008.10.020

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title = "High-throughput genotyping of copy number variation in glutathione S-transferases M1 and T1 using real-time PCR in 20,687 individuals",

abstract = "OBJECTIVES: Characteristic for the genes encoding glutathione S-transferase (GST) M1 and GSTT1 is a null allele, suggested to increase susceptibility to chronic diseases. We report an optimized method for the determination of copy number variation (CNV) in GST genes.DESIGN AND METHODS: Real-time multiplex PCR reactions were optimized for quantification of GSTM1 and GSTT1 CNV using the DeltaCt method, a fixed volume of diluted DNA, a total volume of 10 microL, 384-well formats, and single determinations of each sample.RESULTS: Consistent genotyping was obtained using DNA in a range of 0.41 ng to 100 ng. In a general population sample of 20,687 individuals the genotype frequencies were concordant with other methods used as standards. Throughput was 4600 genotypes per day at a reagent price of 0.5 euros per sample.CONCLUSIONS: This high-throughput, low cost method accurately determines CNV in the GST genes enabling reliable estimates of disease prediction in large epidemiological samples.",

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doi = "10.1016/j.clinbiochem.2008.10.020",

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T1 - High-throughput genotyping of copy number variation in glutathione S-transferases M1 and T1 using real-time PCR in 20,687 individuals

AU - Nørskov, Marianne S

AU - Frikke-Schmidt, Ruth

AU - Loft, Steffen

AU - Tybjaerg-Hansen, Anne

PY - 2009/2

Y1 - 2009/2

N2 - OBJECTIVES: Characteristic for the genes encoding glutathione S-transferase (GST) M1 and GSTT1 is a null allele, suggested to increase susceptibility to chronic diseases. We report an optimized method for the determination of copy number variation (CNV) in GST genes.DESIGN AND METHODS: Real-time multiplex PCR reactions were optimized for quantification of GSTM1 and GSTT1 CNV using the DeltaCt method, a fixed volume of diluted DNA, a total volume of 10 microL, 384-well formats, and single determinations of each sample.RESULTS: Consistent genotyping was obtained using DNA in a range of 0.41 ng to 100 ng. In a general population sample of 20,687 individuals the genotype frequencies were concordant with other methods used as standards. Throughput was 4600 genotypes per day at a reagent price of 0.5 euros per sample.CONCLUSIONS: This high-throughput, low cost method accurately determines CNV in the GST genes enabling reliable estimates of disease prediction in large epidemiological samples.

AB - OBJECTIVES: Characteristic for the genes encoding glutathione S-transferase (GST) M1 and GSTT1 is a null allele, suggested to increase susceptibility to chronic diseases. We report an optimized method for the determination of copy number variation (CNV) in GST genes.DESIGN AND METHODS: Real-time multiplex PCR reactions were optimized for quantification of GSTM1 and GSTT1 CNV using the DeltaCt method, a fixed volume of diluted DNA, a total volume of 10 microL, 384-well formats, and single determinations of each sample.RESULTS: Consistent genotyping was obtained using DNA in a range of 0.41 ng to 100 ng. In a general population sample of 20,687 individuals the genotype frequencies were concordant with other methods used as standards. Throughput was 4600 genotypes per day at a reagent price of 0.5 euros per sample.CONCLUSIONS: This high-throughput, low cost method accurately determines CNV in the GST genes enabling reliable estimates of disease prediction in large epidemiological samples.

KW - Gene Dosage

KW - Gene Frequency

KW - Genotype

KW - Glutathione Transferase/genetics

KW - Humans

KW - Mass Screening

KW - Molecular Epidemiology/methods

KW - Polymerase Chain Reaction/methods

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DO - 10.1016/j.clinbiochem.2008.10.020

M3 - Journal article

C2 - 19026998

SN - 0009-9120

VL - 42

SP - 201

EP - 209

JO - Clinical Biochemistry

JF - Clinical Biochemistry

IS - 3

ER -

High-throughput genotyping of copy number variation in glutathione S-transferases M1 and T1 using real-time PCR in 20,687 individuals

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Keywords

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