A rapid and cost-effective method for genotyping apolipoprotein e gene polymorphism

Li Zhong; Yong Zhuang Xie; Tian Tian Cao; Zongqi Wang; Tingting Wang; Xinxiu Li; Rui Chi Shen; Huaxi Xu; Guojun Bu; Xiao Fen Chen

doi:10.1186/s13024-016-0069-4

A rapid and cost-effective method for genotyping apolipoprotein e gene polymorphism

Li Zhong, Yong Zhuang Xie, Tian Tian Cao, Zongqi Wang, Tingting Wang, Xinxiu Li, Rui Chi Shen, Huaxi Xu, Guojun Bu, Xiao Fen Chen

Neuroscience

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

Abstract

Background: Apolipoprotein E (ApoE) is a major cholesterol carrier and plays an important role in maintaining lipid homeostasis both in the periphery and brain. Human APOE gene is polymorphic at two single nucleotides (rs429358 and rs7412) resulting in three different alleles (ε2, ε3 and ε4). ApoE isoforms modulate the risk for a variety of vascular and neurodegenerative diseases; thus, APOE genotyping is crucial for predicting disease risk and designing individualized therapy based on APOE genotype. Results: We have developed an APOE genotyping method that is based on allele-specific PCR methodology adapted to Real Time PCR monitored by TaqMan probe. Rather than using TaqMan probes specific for the two polymorphic sites, only one TaqMan probe is used as the polymorphic alleles are recognized by site-specific PCR primers. Each genotyping assay can be completed within 90 minutes and is applicable to high-throughput analysis. Using this protocol, we genotyped a total of 1158 human DNA samples and obtained a 100 % concordance with the APOE genotype determined by sequencing analysis. Conclusion: The APOE genotyping assay we have developed is accurate and cost-effective. In addition, our assay can readily be applied to genotyping large sample numbers. Therefore, our APOE genotyping method can be used for assessing the risk for a variety of vascular and neurodegenerative diseases that have been reported to be associated with APOE polymorphism.

Original language	English (US)
Article number	2
Journal	Molecular neurodegeneration
Volume	11
Issue number	1
DOIs	https://doi.org/10.1186/s13024-016-0069-4
State	Published - Jan 12 2016

Keywords

APOE genotype
Apolipoprotein E
Polymorphism
Real Time PCR
Sequencing
TaqMan

ASJC Scopus subject areas

Molecular Biology
Clinical Neurology
Cellular and Molecular Neuroscience

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10.1186/s13024-016-0069-4

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title = "A rapid and cost-effective method for genotyping apolipoprotein e gene polymorphism",

abstract = "Background: Apolipoprotein E (ApoE) is a major cholesterol carrier and plays an important role in maintaining lipid homeostasis both in the periphery and brain. Human APOE gene is polymorphic at two single nucleotides (rs429358 and rs7412) resulting in three different alleles (ε2, ε3 and ε4). ApoE isoforms modulate the risk for a variety of vascular and neurodegenerative diseases; thus, APOE genotyping is crucial for predicting disease risk and designing individualized therapy based on APOE genotype. Results: We have developed an APOE genotyping method that is based on allele-specific PCR methodology adapted to Real Time PCR monitored by TaqMan probe. Rather than using TaqMan probes specific for the two polymorphic sites, only one TaqMan probe is used as the polymorphic alleles are recognized by site-specific PCR primers. Each genotyping assay can be completed within 90 minutes and is applicable to high-throughput analysis. Using this protocol, we genotyped a total of 1158 human DNA samples and obtained a 100 % concordance with the APOE genotype determined by sequencing analysis. Conclusion: The APOE genotyping assay we have developed is accurate and cost-effective. In addition, our assay can readily be applied to genotyping large sample numbers. Therefore, our APOE genotyping method can be used for assessing the risk for a variety of vascular and neurodegenerative diseases that have been reported to be associated with APOE polymorphism.",

keywords = "APOE genotype, Apolipoprotein E, Polymorphism, Real Time PCR, Sequencing, TaqMan",

author = "Li Zhong and Xie, {Yong Zhuang} and Cao, {Tian Tian} and Zongqi Wang and Tingting Wang and Xinxiu Li and Shen, {Rui Chi} and Huaxi Xu and Guojun Bu and Chen, {Xiao Fen}",

note = "Funding Information: The authors are grateful to all subjects for participation in our study. This study was supported by grants (81370459, 31400914) from the National Natural Science Foundation of China (to X.C.), the Fundamental Research Funds for the Central Universities (20720150051, to X.C.), NIH grants (R01AG027924, R01AG035355, R01AG046205, to G.B.), and grant from Xiamen Science and Technology Bureau (2014S0505, to HX). Publisher Copyright: {\textcopyright} 2016 Zhong et al.",

year = "2016",

month = jan,

day = "12",

doi = "10.1186/s13024-016-0069-4",

language = "English (US)",

volume = "11",

journal = "Molecular Neurodegeneration",

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TY - JOUR

T1 - A rapid and cost-effective method for genotyping apolipoprotein e gene polymorphism

AU - Zhong, Li

AU - Xie, Yong Zhuang

AU - Cao, Tian Tian

AU - Wang, Zongqi

AU - Wang, Tingting

AU - Li, Xinxiu

AU - Shen, Rui Chi

AU - Xu, Huaxi

AU - Bu, Guojun

AU - Chen, Xiao Fen

N1 - Funding Information: The authors are grateful to all subjects for participation in our study. This study was supported by grants (81370459, 31400914) from the National Natural Science Foundation of China (to X.C.), the Fundamental Research Funds for the Central Universities (20720150051, to X.C.), NIH grants (R01AG027924, R01AG035355, R01AG046205, to G.B.), and grant from Xiamen Science and Technology Bureau (2014S0505, to HX). Publisher Copyright: © 2016 Zhong et al.

PY - 2016/1/12

Y1 - 2016/1/12

N2 - Background: Apolipoprotein E (ApoE) is a major cholesterol carrier and plays an important role in maintaining lipid homeostasis both in the periphery and brain. Human APOE gene is polymorphic at two single nucleotides (rs429358 and rs7412) resulting in three different alleles (ε2, ε3 and ε4). ApoE isoforms modulate the risk for a variety of vascular and neurodegenerative diseases; thus, APOE genotyping is crucial for predicting disease risk and designing individualized therapy based on APOE genotype. Results: We have developed an APOE genotyping method that is based on allele-specific PCR methodology adapted to Real Time PCR monitored by TaqMan probe. Rather than using TaqMan probes specific for the two polymorphic sites, only one TaqMan probe is used as the polymorphic alleles are recognized by site-specific PCR primers. Each genotyping assay can be completed within 90 minutes and is applicable to high-throughput analysis. Using this protocol, we genotyped a total of 1158 human DNA samples and obtained a 100 % concordance with the APOE genotype determined by sequencing analysis. Conclusion: The APOE genotyping assay we have developed is accurate and cost-effective. In addition, our assay can readily be applied to genotyping large sample numbers. Therefore, our APOE genotyping method can be used for assessing the risk for a variety of vascular and neurodegenerative diseases that have been reported to be associated with APOE polymorphism.

AB - Background: Apolipoprotein E (ApoE) is a major cholesterol carrier and plays an important role in maintaining lipid homeostasis both in the periphery and brain. Human APOE gene is polymorphic at two single nucleotides (rs429358 and rs7412) resulting in three different alleles (ε2, ε3 and ε4). ApoE isoforms modulate the risk for a variety of vascular and neurodegenerative diseases; thus, APOE genotyping is crucial for predicting disease risk and designing individualized therapy based on APOE genotype. Results: We have developed an APOE genotyping method that is based on allele-specific PCR methodology adapted to Real Time PCR monitored by TaqMan probe. Rather than using TaqMan probes specific for the two polymorphic sites, only one TaqMan probe is used as the polymorphic alleles are recognized by site-specific PCR primers. Each genotyping assay can be completed within 90 minutes and is applicable to high-throughput analysis. Using this protocol, we genotyped a total of 1158 human DNA samples and obtained a 100 % concordance with the APOE genotype determined by sequencing analysis. Conclusion: The APOE genotyping assay we have developed is accurate and cost-effective. In addition, our assay can readily be applied to genotyping large sample numbers. Therefore, our APOE genotyping method can be used for assessing the risk for a variety of vascular and neurodegenerative diseases that have been reported to be associated with APOE polymorphism.

KW - APOE genotype

KW - Apolipoprotein E

KW - Polymorphism

KW - Real Time PCR

KW - Sequencing

KW - TaqMan

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U2 - 10.1186/s13024-016-0069-4

DO - 10.1186/s13024-016-0069-4

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AN - SCOPUS:84954161379

SN - 1750-1326

VL - 11

JO - Molecular Neurodegeneration

JF - Molecular Neurodegeneration

IS - 1

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ER -

A rapid and cost-effective method for genotyping apolipoprotein e gene polymorphism

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Keywords

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