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Ordóñez CD, Mayoral-Campos C, Egas C, Redrejo-Rodríguez M. A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences. NAR Genom Bioinform 2023; 5:lqad073. [PMID: 37608803 PMCID: PMC10440786 DOI: 10.1093/nargab/lqad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/03/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023] Open
Abstract
Multiple displacement amplification (MDA) has proven to be a useful technique for obtaining large amounts of DNA from tiny samples in genomics and metagenomics. However, MDA has limitations, such as amplification artifacts and biases that can interfere with subsequent quantitative analysis. To overcome these challenges, alternative methods and engineered DNA polymerase variants have been developed. Here, we present new MDA protocols based on the primer-independent DNA polymerase (piPolB), a replicative-like DNA polymerase endowed with DNA priming and proofreading capacities. These new methods were tested on a genomes mixture containing diverse sequences with high-GC content, followed by deep sequencing. Protocols relying on piPolB as a single enzyme cannot achieve competent amplification due to its limited processivity and the presence of ab initio DNA synthesis. However, an alternative method called piMDA, which combines piPolB with Φ29 DNA polymerase, allows proficient and faithful amplification of the genomes. In addition, the prior denaturation step commonly performed in MDA protocols is dispensable, resulting in a more straightforward protocol. In summary, piMDA outperforms commercial methods in the amplification of genomes and metagenomes containing high GC sequences and exhibits similar profiling, error rate and variant determination as the non-amplified samples.
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Affiliation(s)
- Carlos D Ordóñez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Carmen Mayoral-Campos
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Biocant, Transfer Technology Association, Cantanhede, Portugal
| | - Modesto Redrejo-Rodríguez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:ijms24119331. [PMID: 37298280 DOI: 10.3390/ijms24119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
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Jäger R. New Perspectives for Whole Genome Amplification in Forensic STR Analysis. Int J Mol Sci 2022; 23:ijms23137090. [PMID: 35806097 PMCID: PMC9267064 DOI: 10.3390/ijms23137090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Modern PCR-based analytical techniques have reached sensitivity levels that allow for obtaining complete forensic DNA profiles from even tiny traces containing genomic DNA amounts as small as 125 pg. Yet these techniques have reached their limits when it comes to the analysis of traces such as fingerprints or single cells. One suggestion to overcome these limits has been the usage of whole genome amplification (WGA) methods. These methods aim at increasing the copy number of genomic DNA and by this means generate more template DNA for subsequent analyses. Their application in forensic contexts has so far remained mostly an academic exercise, and results have not shown significant improvements and even have raised additional analytical problems. Until very recently, based on these disappointments, the forensic application of WGA seems to have largely been abandoned. In the meantime, however, novel improved methods are pointing towards a perspective for WGA in specific forensic applications. This review article tries to summarize current knowledge about WGA in forensics and suggests the forensic analysis of single-donor bioparticles and of single cells as promising applications.
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Affiliation(s)
- Richard Jäger
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany;
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Institute of Safety and Security Research, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
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Trinh The S, Trieu Tien S, Vu Van T, Nguyen Ngoc N, Tran Ngoc Thao M, Tran Van K, Vu Nhat D, Do Nhu B. Successful Pregnancy Following Preimplantation Genetic Diagnosis of Adrenoleukodystrophy by Detection of Mutation on the ABCD1 Gene. APPLICATION OF CLINICAL GENETICS 2021; 14:313-319. [PMID: 34285547 PMCID: PMC8286725 DOI: 10.2147/tacg.s318884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/08/2021] [Indexed: 12/31/2022]
Abstract
Background Adrenoleukodystrophy (ALD) is a rare sex-linked recessive disorder that disrupts adrenal gland function and the white matter of the nervous system. According to recent epidemiological statistics, up to this moment, the disease is the most recorded peroxisomal disorder. ABCD1 is a gene related to ALD, with more than 850 unique mutations have been reported. Early diagnosis of the disease would help to consult families with ALD to plan for interventions to prevent passing along the pathogenic mutations to their children. Material and Methods A heterozygous ABCD1 gene mutation related to ALD found in a Vietnamese woman was used to design primers for the polymerase chain reaction (PCR) to amplify the segment spanning the mutation. Then, combining sequencing methods for the PCR products, especially Sanger sequencing and next-generation sequencing (NGS), a protocol was developed to detect mutations on the ABCD1 gene to apply for the DNA samples of in-vitro fertilization (IVF) embryos biopsied at the blastocyst stage to screen for pathogenic alleles. Results The established protocol for PGD of ALD detected mutant alleles in 5/8 embryos (62.5%), while the remaining 3 embryos (37.5%) did not carry any mutation. One of the 3 embryos was transferred, and a healthy female baby was born after a full-term pregnancy. Conclusion The developed protocol was helpful for the preimplantation genetic diagnosis process to help families with the monogenic disease of ALD but wish to have healthy children.
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Affiliation(s)
- Son Trinh The
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, 12108, Vietnam
| | - Sang Trieu Tien
- Department of Biology and Genetics, Vietnam Military Medical University, Hanoi, 12108, Vietnam
| | - Tam Vu Van
- Director Office, Hai Phong Hospital of Obstetrics and Gynecology, Haiphong, 40000, Vietnam.,Obstetrics and Gynecology Department of Haiphong University of Medicine and Pharmacy, Haiphong, 40000, Vietnam
| | - Nhat Nguyen Ngoc
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, 12108, Vietnam
| | - My Tran Ngoc Thao
- Département de formation Biologie moléculaire et cellulaire, Sorbonne University, Paris, 75006, France
| | - Khoa Tran Van
- Department of Biology and Genetics, Vietnam Military Medical University, Hanoi, 12108, Vietnam
| | - Dinh Vu Nhat
- Director Office, Military Hospital 103, Hanoi, 12108, Vietnam.,Department of Trauma and Orthopedic Surgery, Vietnam Military Medical University, Hanoi, 121-08, Vietnam
| | - Binh Do Nhu
- Division of Military Science, Military Hospital 103, Hanoi, 12108, Vietnam.,Department of Infectious Disease, Vietnam Military Medical University, Hanoi, 12108, Vietnam
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Weisz F, Lalle M, Nohynkova E, Sannella AR, Dluhošová J, Cacciò SM. Testing the impact of Whole Genome Amplification on genome comparison using the polyploid flagellated Giardia duodenalis as a model. Exp Parasitol 2019; 207:107776. [PMID: 31628895 DOI: 10.1016/j.exppara.2019.107776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/03/2019] [Accepted: 10/13/2019] [Indexed: 11/27/2022]
Abstract
The availability of high quality genomic DNA in sufficient amounts to perform Next Generation Sequencing (NGS) experiments is challenging for pathogens that cannot be cultivated in vitro, as is the case for many parasites. Therefore, Whole Genome Amplification (WGA) of genomic DNA is used to overcome this limitation. In this study, we evaluated the effect of WGA using the intestinal flagellated protozoan Giardia duodenalis as a model, due to its genome compactness (12 Mb), the presence of two diploid nuclei with variable levels of allelic sequence heterogeneity (ASH), and the availability of reference genomes. We selected one isolate (ZX15) belonging to the same genetic group of the reference isolate WB, namely Assemblage A, sub-Assemblage AI. Genomic DNA from the ZX15 isolate (GEN dataset) and that obtained by WGA of 1 ng of the same genomic DNA (WGA dataset) were sequenced on a HiSeq Illumina platform. Trimmed reads from the GEN and WGA experiments were mapped against the WB reference genome, showing the presence of a very small number of mutations (846 and 752, respectively). The difference in the number of mutations is largely accounted by local variation in coverage and not by bias introduced by WGA. No significant difference were observed in the distribution of mutations in coding and non-coding regions, in the proportion of heterozygous mutations (ASH), or in the transition/transversion ratio of Single Nucleotide Variants within coding sequences. We conclude that the quantitative and qualitative impact of WGA on the identification of mutations is limited, and that this technique can be used to conduct comparative genomics studies.
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Affiliation(s)
- Filip Weisz
- Institute of Immunology and Microbiology, First Faculty of Medicine and General University Hospital, Charles University in Prague, Czech Republic; Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Lalle
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Eva Nohynkova
- Institute of Immunology and Microbiology, First Faculty of Medicine and General University Hospital, Charles University in Prague, Czech Republic
| | - Anna Rosa Sannella
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Jana Dluhošová
- Institute of Immunology and Microbiology, First Faculty of Medicine and General University Hospital, Charles University in Prague, Czech Republic
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
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A Talip B, Snelling WJ, Sleator RD, Lowery C, Dooley JSG. A rapid and sensitive system for recovery of nucleic acids from Mycobacteria sp. on archived glass slides. BMC Microbiol 2018; 18:196. [PMID: 30477427 PMCID: PMC6260770 DOI: 10.1186/s12866-018-1335-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/12/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes. There are significant challenges faced when examining archived samples in order that an adequate amount of amplifiable DNA can be obtained. Herein, we describe a model system to detect low numbers of bacterial cells isolated from glass slides using (laser capture microscopy) LCM coupled with PCR amplification of a suitable target. RESULTS Mycobacterium smegmatis was used as a model organism to provide a proof of principle for a method to recover bacteria from a stained sample on a glass slide using a laser capture system. Ziehl-Neelsen (ZN) stained cells were excised and catapulted into tubes. Recovered cells were subjected to DNA extraction and pre-amplified with multiple displacement amplification (MDA). This system allowed a minimum of 30 catapulted cells to be detected following a nested real-time PCR assay, using rpoB specific primers. The combination of MDA and nested real-time PCR resulted in a 30-fold increase in sensitivity for the detection of low numbers of cells isolated using LCM. CONCLUSIONS This study highlights the potential of LCM coupled with MDA as a tool to improve the recovery of amplifiable nucleic acids from archived glass slides. The inclusion of the MDA step was essential to enable downstream amplification. This platform should be broadly applicable to a variety of diagnostic applications and we have used it as a proof of principle with a Mycobacterium sp. model system.
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Affiliation(s)
- Balkis A Talip
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, 84000 Pagoh, Muar, Johor, Malaysia
| | - William J Snelling
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland
| | - Roy D Sleator
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Colm Lowery
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland
| | - James S G Dooley
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland.
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Warris S, Schijlen E, van de Geest H, Vegesna R, Hesselink T, Te Lintel Hekkert B, Sanchez Perez G, Medvedev P, Makova KD, de Ridder D. Correcting palindromes in long reads after whole-genome amplification. BMC Genomics 2018; 19:798. [PMID: 30400848 PMCID: PMC6218980 DOI: 10.1186/s12864-018-5164-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/15/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long sequencing reads. RESULTS Here, we present Pacasus, a tool for correcting such errors. Two datasets show that it markedly improves read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. CONCLUSIONS With Pacasus long-read technologies become available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.
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Affiliation(s)
- Sven Warris
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.
| | - Elio Schijlen
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.,Present address Genetwister Technologies BV, Wageningen, The Netherlands
| | - Rahulsimham Vegesna
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Computation, Bioinformatics, Statistics Graduate Training Program, Pennsylvania State University, University Park, State College, PA, 16802, USA.,The Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thamara Hesselink
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Bas Te Lintel Hekkert
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.,Present address Genetwister Technologies BV, Wageningen, The Netherlands
| | - Paul Medvedev
- The Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Computer Science and Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.,The Center for Medical Genomics, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Kateryna D Makova
- The Center for Medical Genomics, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
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Systematic assessment of the performance of whole-genome amplification for SNP/CNV detection and β-thalassemia genotyping. J Hum Genet 2018; 63:407-416. [PMID: 29440707 DOI: 10.1038/s10038-018-0411-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 11/08/2022]
Abstract
In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods. Through Sanger sequencing at the single-cell and five-cell levels, we showed that both the amplification rate and ADO rate of MDA were better than those using MALBAC, and the sensitivity and positive predictive value obtained from MDA were higher than those from MALBAC for β-thalassemia genotyping. Using next-generation sequencing (NGS) at the single-cell level, we confirmed that MDA has better properties than MALBAC for SNP detection. However, MALBAC was more stable and homogeneous than MDA using low-depth NGS at the single-cell level for CNV detection. We conclude that MALBAC is the better option for CNV detection, while MDA is better suited for SNV detection.
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