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Lara-Hernandez F, Cortez J, Garcia-Sorribes S, Blesa S, Olivares MD, Alic AS, Garcia-Garcia AB, Chaves FJ, Ivorra C. EOSAL-CNV for Easy and Rapid Detection of CNVs by Fragment Analysis : EOSAL: A Fast and Reliable New Method for CNV Detection. Methods Mol Biol 2023; 2621:241-253. [PMID: 37041448 DOI: 10.1007/978-1-0716-2950-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Copy number variations (CNVs) are a type of genetic variation involving from 50 base pairs (bps) to millions of bps and, in a general point of view, can include alterations of complete chromosomes. As CNVs mean the gain or loss of DNA sequences, their detection requires specific techniques and analysis. We have developed Easy One-Step Amplification and Labeling for CNV Detection (EOSAL-CNV) by fragment analysis in a DNA sequencer. The procedure is based on a single PCR reaction for amplification and labeling of all fragments included. The protocol includes specific primers for the amplification of the regions of interest with a tail in each of the primers (one for forward and another for the reverse primers) together with primers for tail amplification. One of the primers for tail amplification is labeled with a fluorophore, allowing the amplification and labeling in the same reaction. Combination of several tail pairs and labels allows the detection of DNA fragment by different fluorophores and increases the number of fragments that can be analyzed in one reaction. PCR products can be analyzed without any purification on a DNA sequencer for fragment detection and quantification. Finally, simple and easy calculations allow the detection of fragments with deletions or extra copies. The use of EOSAL-CNV allows simplifying and reducing costs in sample analysis for CNV detection.
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Affiliation(s)
| | - Jessica Cortez
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
| | | | - Sebastian Blesa
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain
| | | | - Andy S Alic
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
| | - Ana-Barbara Garcia-Garcia
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain.
- CIBERDEM, ISCIII, Madrid, Spain.
| | - F Javier Chaves
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
- CIBERDEM, ISCIII, Madrid, Spain
| | - Carmen Ivorra
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
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Blesa S, Olivares MD, Alic AS, Serrano A, Lendinez V, González-Albert V, Olivares L, Martínez-Hervás S, Juanes JM, Marín P, Real JT, Navarro B, García-García AB, Chaves FJ, Ivorra C. Easy One-Step Amplification and Labeling Procedure for Copy Number Variation Detection. Clin Chem 2020; 66:463-473. [PMID: 32068788 DOI: 10.1093/clinchem/hvaa002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/21/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The specific characteristics of copy number variations (CNVs) require specific methods of detection and characterization. We developed the Easy One-Step Amplification and Labeling procedure for CNV detection (EOSAL-CNV), a new method based on proportional amplification and labeling of amplicons in 1 PCR. METHODS We used tailed primers for specific amplification and a pair of labeling probes (only 1 labeled) for amplification and labeling of all amplicons in just 1 reaction. Products were loaded directly onto a capillary DNA sequencer for fragment sizing and quantification. Data obtained could be analyzed by Microsoft Excel spreadsheet or EOSAL-CNV analysis software. We developed the protocol using the LDLR (low density lipoprotein receptor) gene including 23 samples with 8 different CNVs. After optimizing the protocol, it was used for genes in the following multiplexes: BRCA1 (BRCA1 DNA repair associated), BRCA2 (BRCA2 DNA repair associated), CHEK2 (checkpoint kinase 2), MLH1 (mutL homolog 1) plus MSH6 (mutS homolog 6), MSH2 (mutS homolog 2) plus EPCAM (epithelial cell adhesion molecule) and chromosome 17 (especially the TP53 [tumor protein 53] gene). We compared our procedure with multiplex ligation-dependent probe amplification (MLPA). RESULTS The simple procedure for CNV detection required 150 min, with <10 min of handwork. After analyzing >240 samples, EOSAL-CNV excluded the presence of CNVs in all controls, and in all cases, results were identical using MLPA and EOSAL-CNV. Analysis of the 17p region in tumor samples showed 100% similarity between fluorescent in situ hybridization and EOSAL-CNV. CONCLUSIONS EOSAL-CNV allowed reliable, fast, easy detection and characterization of CNVs. It provides an alternative to targeted analysis methods such as MLPA.
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Affiliation(s)
- Sebastián Blesa
- Genomic and Genetic Diagnosis Unit, INCLIVA Biomedical Research Institute (UGDG, INCLIVA), Valencia, Valencian Community, Spain
| | - María D Olivares
- I+D+I Department, Sequencing Multiplex SL (I+d+I, Seqplexing), Serra, Valencian Community, Spain
| | - Andy S Alic
- I+D+I Department, Sequencing Multiplex SL (I+d+I, Seqplexing), Serra, Valencian Community, Spain
| | - Alicia Serrano
- Hematology Department, Clinical University Hospital of Valencia (HCUV), Valencia, Valencian Community, Spain.,Physiology Department, University of Valencia (FD, UV), Valencia, Valencian Community, Spain
| | - Verónica Lendinez
- Genomic and Genetic Diagnosis Unit, INCLIVA Biomedical Research Institute (UGDG, INCLIVA), Valencia, Valencian Community, Spain
| | - Verónica González-Albert
- Genomic and Genetic Diagnosis Unit, INCLIVA Biomedical Research Institute (UGDG, INCLIVA), Valencia, Valencian Community, Spain
| | - Laura Olivares
- Genomic and Genetic Diagnosis Unit, INCLIVA Biomedical Research Institute (UGDG, INCLIVA), Valencia, Valencian Community, Spain
| | - Sergio Martínez-Hervás
- Endocrinology Service, Clinical University Hospital of Valencia (HCUV), Valencia, Valencian Community, Spain
| | - José M Juanes
- Genomic and Genetic Diagnosis Unit, INCLIVA Biomedical Research Institute (UGDG, INCLIVA), Valencia, Valencian Community, Spain
| | - Pablo Marín
- Computational and Clinical Genomics Department, Kanteron Systems SLU (CCGD, Kanteron), Valencia, Valencian Community, Spain
| | - Jose T Real
- Endocrinology Service, Clinical University Hospital of Valencia (HCUV), Valencia, Valencian Community, Spain.,Department of Medicine, University of Valencia (DM; UV), Valencia, Valencian Community, Spain
| | - Blanca Navarro
- Hematology Department, Clinical University Hospital of Valencia (HCUV), Valencia, Valencian Community, Spain.,Physiology Department, University of Valencia (FD, UV), Valencia, Valencian Community, Spain
| | - Ana B García-García
- Genomic and Genetic Diagnosis Unit, INCLIVA Biomedical Research Institute (UGDG, INCLIVA), Valencia, Valencian Community, Spain.,CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Autonomous Community of Madrid, Spain
| | - Felipe J Chaves
- Genomic and Genetic Diagnosis Unit, INCLIVA Biomedical Research Institute (UGDG, INCLIVA), Valencia, Valencian Community, Spain.,I+D+I Department, Sequencing Multiplex SL (I+d+I, Seqplexing), Serra, Valencian Community, Spain.,CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Autonomous Community of Madrid, Spain
| | - Carmen Ivorra
- I+D+I Department, Sequencing Multiplex SL (I+d+I, Seqplexing), Serra, Valencian Community, Spain
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Zhou Y, Nie J, Yu S, Hu Z, Wang B. Multiplex Ligation-Dependent Probe Amplification for Simultaneous Identification of Bungarus multicinctus and Its Common Adulterants in a Single Assay. Front Pharmacol 2020; 11:501. [PMID: 32372964 PMCID: PMC7186403 DOI: 10.3389/fphar.2020.00501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/30/2020] [Indexed: 11/13/2022] Open
Abstract
Bungarus multicinctus, an important traditional Chinese medicine, possesses remarkable medicinal activities, while lots of adulterants from other species were misused as B. multicinctus for its large demand and resource starvation. In order to accurately identify B. multicinctus and its common adulterants such as Sinonatrix annularis, Xenochrophis flavipunctatus, Deinagkistrodon acutus, and Naja atra, a simultaneous identification method was designed with multiplex ligation-dependent probe amplification (MLPA) analysis. Five species-specific MLPA probe-couples for B. multicinctus and its common adulterants were designed based on the universal primer amplified COI sequences, which can specifically detect the five species with no mutual interference, and sensitivity analysis showed as less as 5% B. multicinctus or 8.75% adulterants in the mixed samples can be identified in a MLPA assay, especially, the relative quantity of the adulterants can be also inferred based on the MLPA peak area values. Moreover, the results of the present study confirmed the effectiveness of this technique in terms of simultaneous identification of B. multicinctus and its common adulterants in an assay, which has great potential for ensuring the safety of this commercially valuable snake species.
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Affiliation(s)
- Yuxin Zhou
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Jing Nie
- Chinese Medicine Testing and Research Center, Hubei Institute for Drug Control, Wuhan, China
| | - Shiqi Yu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Bo Wang
- Chinese Medicine Testing and Research Center, Hubei Institute for Drug Control, Wuhan, China
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Agirbasli D, Hyatt T, Agirbasli M. Familial hypercholesterolemia with extensive coronary artery disease and tuberous and tendinous xanthomas: A case report and mutation analysis. J Clin Lipidol 2018; 12:863-867. [PMID: 29784571 DOI: 10.1016/j.jacl.2018.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/03/2018] [Accepted: 04/17/2018] [Indexed: 11/18/2022]
Abstract
This is a case report of a 38-year-old Syrian refugee male with early-onset extensive atherosclerosis. The physical and laboratory examination were remarkable with severe xanthomas in the upper and lower extremities and with low-density lipoprotein cholesterol (LDL-C) 417 mg/dL, total cholesterol 495 mg/dL, high-density lipoprotein cholesterol 30 mg/dL, and triglycerides 242 mg/dL. LDL-C level responded poorly to the high-dose statin treatment. The genetic analysis indicated that the patient had a large homozygous deletion in LDL receptor gene including the exons 7-14. A 12-kb deletion had occurred between the 2 Alu repetitive sequences that were oriented in opposite directions, one in intron 6 and the other in intron 14. This deletion eliminated exons 7-14, which exactly corresponded to the entire exon sequence coding the epidermal growth factor precursor homology domain. This deletion in LDL receptor was previously reported. This rare case of homozygous familial hypercholesterolemia presenting with multiple large and widely distributed xanthomas implicates the need for novel treatment options in familial hypercholesterolemia patients. The case is a Syrian refugee and emphasizes the urgent need to address orphan disease in refugee populations throughout the world.
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Affiliation(s)
- Deniz Agirbasli
- Acıbadem Mehmet Ali Aydınlar University School of Medicine, Department of Medical Biology, İstanbul, Turkey
| | - Tommy Hyatt
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mehmet Agirbasli
- Medeniyet University Medical Center, Department of Cardiology, İstanbul, Turkey.
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