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Analysis of institutional authors

Mayoral-Campos CAuthorRedrejo-Rodríguez MCorresponding Author

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A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences

Publicated to:NAR GENOMICS AND BIOINFORMATICS. 5 (3): lqad073-lqad073 - 2023-09-01 5(3), DOI: 10.1093/nargab/lqad073

Authors: Ordonez, Carlos D; Mayoral-Campos, Carmen; Egas, Conceicao; Redrejo-Rodriguez, Modesto

Affiliations

Biocant, Transfer Technology Association, Cantanhede, Portugal. - Author
Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. - Author
Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain. - Author
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain. - Author
Transfer Technol Assoc, Biocant, Cantanhede, Portugal - Author
UAM, Ctr Biol Mol Severo Ochoa, CSIC, Madrid, Spain - Author
UAM, Inst Invest Biomed Sols Morreale CSIC, Madrid, Spain - Author
Univ Autonoma Madrid UAM, Dept Bioquim, Madrid, Spain - Author
Univ Coimbra, Ctr Neurosci & Cell Biol, Coimbra, Portugal - Author
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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.© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

Keywords

biasnumberssamplessingleDisplacement amplification

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal NAR GENOMICS AND BIOINFORMATICS due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2023, it was in position 8/66, thus managing to position itself as a Q1 (Primer Cuartil), in the category Mathematical & Computational Biology.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2025-06-23:

  • WoS: 1
  • Scopus: 1
  • Europe PMC: 1

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-06-23:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 11.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 11 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 17.35.
  • The number of mentions on the social network X (formerly Twitter): 32 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://repositorio.uam.es/handle/10486/708396

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Portugal.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Ordóñez CD) and Last Author (REDREJO RODRIGUEZ, MODESTO).

the author responsible for correspondence tasks has been REDREJO RODRIGUEZ, MODESTO.