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Whole Genome Amplification
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Whole Genome Amplification

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 April 2023) | Viewed by 31461

Special Issue Editor

Prof. Dr. Richard Jäger

E-Mail Website
Guest Editor
Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany
Interests: forensic genetics; STR analysis; analysis of low copy number DNA; next generation sequencing in forensics

Special Issue Information

Dear Colleagues,

The development of whole-genome amplification (WGA) techniques has opened up new avenues for genetic analysis and genome research, in particular by facilitating the genome-wide analysis of only few or even single cells—eukaryotes or prokaryotes. Applications comprise preimplantation genetic diagnostics (PGD), cell-based non-invasive prenatal testing (NIPT), cytogenetic analysis of single cells derived by liquid biopsy, analysis of genetic heterogeneity in populations of multiple cells (e.g., tumors or microbial communities), the study of meiotic recombination at the level of single sperm cells, and the forensic DNA analysis of limited trace material.

In general aiming at a uniform amplification of the complete genome of interest, the various WGA methods display specific strengths as well as shortcomings, and thus the choice of method requires thorough consideration in terms of suitability for a particular source of genomic DNA and type of downstream analysis.

This Special Issue aims to provide an overview of the various technical principles of WGA and their applications by including review articles as well as original works reflecting the range of analytical applications and current developments, and stimulating future research.

Prof. Dr. Richard Jäger
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • whole-genome amplification (WGA)
  • meiotic recombination
  • microbiome
  • circulating tumor cells (CTCs)
  • liquid biopsy
  • preimplantation genetic diagnostics (PGD)
  • non-invasive prenatal testing (NIPT)
  • copy number variation (CNV)
  • comparative genomic hybridization (CGH)
  • low copy number DNA (LCN DNA)
  • next-generation sequencing (NGS)

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Published Papers (7 papers)

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Editorial

Jump to: Research, Review

3 pages, 179 KiB  
Editorial
Special Issue on Whole Genome Amplification
by Richard Jäger
Int. J. Mol. Sci. 2023, 24(11), 9626; https://doi.org/10.3390/ijms24119626 - 1 Jun 2023
Cited by 1 | Viewed by 1373
Abstract
The development of whole-genome amplification (WGA) techniques has opened up new avenues for genetic analysis and genome research, in particular by facilitating the genome-wide analysis of few or even single copies of genomic DNA, such as from single cells (prokaryotic or eukaryotic) or [...] Read more.
The development of whole-genome amplification (WGA) techniques has opened up new avenues for genetic analysis and genome research, in particular by facilitating the genome-wide analysis of few or even single copies of genomic DNA, such as from single cells (prokaryotic or eukaryotic) or virions [...] Full article
(This article belongs to the Special Issue Whole Genome Amplification)

Research

Jump to: Editorial, Review

21 pages, 4034 KiB  
Article
Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics
by Morgan S. Sobol and Anne-Kristin Kaster
Int. J. Mol. Sci. 2023, 24(5), 4270; https://doi.org/10.3390/ijms24054270 - 21 Feb 2023
Cited by 11 | Viewed by 3631
Abstract
Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary [...] Read more.
Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment. Full article
(This article belongs to the Special Issue Whole Genome Amplification)
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7 pages, 1583 KiB  
Article
Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs
by Ofir Raz, Liming Tao, Tamir Biezuner, Tzipy Marx, Yaara Neumeier, Narek Tumanyan and Ehud Shapiro
Int. J. Mol. Sci. 2022, 23(11), 6161; https://doi.org/10.3390/ijms23116161 - 31 May 2022
Cited by 2 | Viewed by 2296
Abstract
Whole-genome amplification is a crucial first step in nearly all single-cell genomic analyses, with the following steps focused on its products. Bias and variance caused by the whole-genome amplification process add numerous challenges to the world of single-cell genomics. Short tandem repeats are [...] Read more.
Whole-genome amplification is a crucial first step in nearly all single-cell genomic analyses, with the following steps focused on its products. Bias and variance caused by the whole-genome amplification process add numerous challenges to the world of single-cell genomics. Short tandem repeats are sensitive genomic markers used widely in population genetics, forensics, and retrospective lineage tracing. A previous evaluation of common whole-genome amplification targeting ~1000 non-autosomal short tandem repeat loci is extended here to ~12,000 loci across the entire genome via duplex molecular inversion probes. Other than its improved scale and reduced noise, this system detects an abundance of heterogeneous short tandem repeat loci, allowing the allelic balance to be reported. We show here that while the best overall yield is obtained using RepliG-SC, the maximum uniformity between alleles and reproducibility across cells are maximized by Ampli1, rendering it the best candidate for the comparative heterozygous analysis of single-cell genomes. Full article
(This article belongs to the Special Issue Whole Genome Amplification)
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Review

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20 pages, 1656 KiB  
Review
DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions
by Carlos D. Ordóñez and Modesto Redrejo-Rodríguez
Int. J. Mol. Sci. 2023, 24(11), 9331; https://doi.org/10.3390/ijms24119331 - 26 May 2023
Cited by 8 | Viewed by 4232
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Whole Genome Amplification)
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19 pages, 1370 KiB  
Review
Single-Circulating Tumor Cell Whole Genome Amplification to Unravel Cancer Heterogeneity and Actionable Biomarkers
by Tanzila Khan, Therese M. Becker, Joseph W. Po, Wei Chua and Yafeng Ma
Int. J. Mol. Sci. 2022, 23(15), 8386; https://doi.org/10.3390/ijms23158386 - 29 Jul 2022
Cited by 12 | Viewed by 3685
Abstract
The field of single-cell analysis has advanced rapidly in the last decade and is providing new insights into the characterization of intercellular genetic heterogeneity and complexity, especially in human cancer. In this regard, analyzing single circulating tumor cells (CTCs) is becoming particularly attractive [...] Read more.
The field of single-cell analysis has advanced rapidly in the last decade and is providing new insights into the characterization of intercellular genetic heterogeneity and complexity, especially in human cancer. In this regard, analyzing single circulating tumor cells (CTCs) is becoming particularly attractive due to the easy access to CTCs from simple blood samples called “liquid biopsies”. Analysis of multiple single CTCs has the potential to allow the identification and characterization of cancer heterogeneity to guide best therapy and predict therapeutic response. However, single-CTC analysis is restricted by the low amounts of DNA in a single cell genome. Whole genome amplification (WGA) techniques have emerged as a key step, enabling single-cell downstream molecular analysis. Here, we provide an overview of recent advances in WGA and their applications in the genetic analysis of single CTCs, along with prospective views towards clinical applications. First, we focus on the technical challenges of isolating and recovering single CTCs and then explore different WGA methodologies and recent developments which have been utilized to amplify single cell genomes for further downstream analysis. Lastly, we list a portfolio of CTC studies which employ WGA and single-cell analysis for genetic heterogeneity and biomarker detection. Full article
(This article belongs to the Special Issue Whole Genome Amplification)
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15 pages, 900 KiB  
Review
New Perspectives for Whole Genome Amplification in Forensic STR Analysis
by Richard Jäger
Int. J. Mol. Sci. 2022, 23(13), 7090; https://doi.org/10.3390/ijms23137090 - 25 Jun 2022
Cited by 13 | Viewed by 8095
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Whole Genome Amplification)
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24 pages, 2319 KiB  
Review
Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing
by Ludmila Volozonoka, Anna Miskova and Linda Gailite
Int. J. Mol. Sci. 2022, 23(9), 4819; https://doi.org/10.3390/ijms23094819 - 27 Apr 2022
Cited by 20 | Viewed by 5981
Abstract
Successful whole genome amplification (WGA) is a cornerstone of contemporary preimplantation genetic testing (PGT). Choosing the most suitable WGA technique for PGT can be particularly challenging because each WGA technique performs differently in combination with different downstream processing and detection methods. The aim [...] Read more.
Successful whole genome amplification (WGA) is a cornerstone of contemporary preimplantation genetic testing (PGT). Choosing the most suitable WGA technique for PGT can be particularly challenging because each WGA technique performs differently in combination with different downstream processing and detection methods. The aim of this review is to provide insight into the performance and drawbacks of DOP-PCR, MDA and MALBAC, as well as the hybrid WGA techniques most widely used in PGT. As the field of PGT is moving towards a wide adaptation of comprehensive massively parallel sequencing (MPS)-based approaches, we especially focus our review on MPS parameters and detection opportunities of WGA-amplified material, i.e., mappability of reads, uniformity of coverage and its influence on copy number variation analysis, and genomic coverage and its influence on single nucleotide variation calling. The ability of MDA-based WGA solutions to better cover the targeted genome and the ability of PCR-based solutions to provide better uniformity of coverage are highlighted. While numerous comprehensive PGT solutions exploiting different WGA types and adjusted bioinformatic pipelines to detect copy number and single nucleotide changes are available, the ones exploiting MDA appear more advantageous. The opportunity to fully analyse the targeted genome is influenced by the MPS parameters themselves rather than the solely chosen WGA. Full article
(This article belongs to the Special Issue Whole Genome Amplification)
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