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Wen WC, Lin YH, Duh TH, Chen CH, Feng CH, Chen YL. Fluorescence detection of apolipoprotein E gene polymorphisms based on oligonucleotide ligation and magnetic separation. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4710-4717. [PMID: 37680175 DOI: 10.1039/d3ay01245j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Alzheimer's disease is a progressive neurodegenerative condition that causes brain cell death and is the leading cause of dementia. Most patients with Alzheimer's disease are diagnosed with late-onset Alzheimer's disease (LOAD), with apolipoprotein E (APOE) genotypes being highly associated with the frequency of LOAD risk. A fluorescence detection system coupled with oligonucleotide ligation and magnetic separation was developed to identify two single-nucleotide polymorphisms (SNPs) for the APOE gene and recognize APOE alleles for LOAD. The system utilized a fluorescence probe with one base-discriminating nucleoside for SNP (F probe) and a perfectly complementary biotin-modified sequence against the target DNA (P probe). When the F and P probes matched the target DNA sequences, DNA ligation occurred, and ligation products were produced. Streptavidin magnetic beads were subsequently employed to remove the ligation products, and a decrease in fluorescence intensity was observed in the supernatant compared to when there was no target DNA. This system detected two SNPs of APOE alleles, namely rs429358 and rs7412. The results indicated that the R-values ((F0 - F1)/F0) for rs429358 were 0.92 ± 0.002 for the T/T target, 0.47 ± 0.004 for the T/C target and 0.11 ± 0.004 for the C/C target, respectively. The R-values for rs7412 were 0.73 ± 0.009 for the C/C target, 0.42 ± 0.001 for the C/T target and 0.16 ± 0.007 for the T/T target, respectively. F0 and F1 represent the fluorescence intensity of the F probe without and with target DNA, respectively. Based on fluorescence intensity, the fluorescence detection system was able to identify the genotypes of the APOE gene accurately to evaluate the risk of Alzheimer's disease.
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Affiliation(s)
- Wan-Chen Wen
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
| | - Yi-Hui Lin
- School of Pharmacy, College of Pharmacy, China Medical University, Taichung 406040, Taiwan
| | - Tsai-Hui Duh
- Department of Medicinal and Applied Chemistry, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chun-Hsien Chen
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chia-Hsien Feng
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
- College of Professional Studies, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
| | - Yen-Ling Chen
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 621301, Taiwan.
- Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 621301, Taiwan
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Electrochemiluminescent assay for detection of extremely rare mutations based on ligase reaction and bead enrichment. Anal Biochem 2013; 434:34-8. [DOI: 10.1016/j.ab.2012.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 01/05/2023]
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Asari M, Omura T, Oka K, Maseda C, Tasaki Y, Shiono H, Matsubara K, Matsuda M, Shimizu K. Multiplex PCR-based Alu insertion polymorphisms genotyping for identifying individuals of Japanese ethnicity. Genomics 2012; 99:227-32. [PMID: 22293435 DOI: 10.1016/j.ygeno.2012.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Revised: 12/21/2011] [Accepted: 01/10/2012] [Indexed: 01/06/2023]
Abstract
Discrimination of Alu insertions is a useful tool for geographic ancestry analysis, and is usually performed by Alu element amplification and agarose gel electrophoresis. Here, we have developed a new fluorescence-based method for multiple Alu genotyping in forensic identification. Allele frequencies were determined in 70 Japanese individuals, and we selected 30 polymorphic Alu insertions. Three primers were designed for each Alu locus to discriminate alleles using the 3-6 bp differences in amplicon sizes. Furthermore, we classified the amplification primers for the 30 loci into three different sets, and PCR using each set of primers provided 10 loci fragments ranging from 50 to 137 bp. Based on population data, the probability of incorrectly assigning a match was 3.7×10(-13). Three independent amplifications and subsequent capillary electrophoresis enabled the sensitive genotyping of small amounts of DNA, indicating that this method is suitable for identifying individuals of Japanese ethnicity.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, 2-1-1-1 Midorigaoka-Higashi, Asahikawa 078-8510, Japan.
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