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Special Issues
Clinical Application of Personalized Genomic Medicine
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Clinical Application of Personalized Genomic Medicine

A special issue of Journal of Personalized Medicine (ISSN 2075-4426). This special issue belongs to the section "Omics/Informatics".

Deadline for manuscript submissions: closed (15 April 2021) | Viewed by 7520

Special Issue Editor

Dr. Matthew Lebo

E-Mail Website
Guest Editor
Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
Interests: genomics; human genetics; next generation sequencing; genetic analysis; molecular genetics; computational biology; NGS data analysis; DNA sequencing; bioinformatics and computational biology; sequencing

Special Issue Information

Dear Colleagues,

With the dramatic reduced costs of genome and exome sequencing, there are now large datasets to determine the full scope and impact of genomics in personalized medicine. Furthermore, in combination with standardization and data sharing efforts, a wealth of data is now emerging on the impact of these technologies in clinical care. As more and more information is being gleamed from a genome, understanding how best to incorporate this data into the clinical environment is now critical.

The aim of this Special Issue is to present current best practices, emerging areas of development, and informatics approaches in applying personalized genomic medicine into the clinical environment.

We are inviting the submission of original articles and reviews for this Special Issue. Articles may be focused on (though not limited to) the clinical application of: bioinformatics, phenotype-based approaches to diagnostic sequencing, genomic screening, polygenic risk scores, risk alleles and low penetrance variants, genomic-based blood typing, integrative reporting, and return of genomic results, including applications and methods communicating with the HER.

Dr. Matthew Lebo
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. Journal of Personalized Medicine is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • Genomics
  • Genome and exome sequencing
  • Pharmacogenomics
  • Genome screening
  • Polygenic risk scores
  • Phenotype-driven analyses
  • Integrated reporting
  • Return of genomic results
  • Clinical bioinformatics

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

8 pages, 1058 KiB  
Article
Middle Eastern Genetic Variation Improves Clinical Annotation of the Human Genome
by Sathishkumar Ramaswamy, Ruchi Jain, Maha El Naofal, Nour Halabi, Sawsan Yaslam, Alan Taylor and Ahmad Abou Tayoun
J. Pers. Med. 2022, 12(3), 423; https://doi.org/10.3390/jpm12030423 - 9 Mar 2022
Cited by 5 | Viewed by 3169
Abstract
Genetic variation in populations of Middle Eastern origin remains highly underrepresented in most comprehensive genomic databases. This underrepresentation hampers the functional annotation of the human genome and challenges accurate clinical variant interpretation. To highlight the importance of capturing genetic variation in the Middle [...] Read more.
Genetic variation in populations of Middle Eastern origin remains highly underrepresented in most comprehensive genomic databases. This underrepresentation hampers the functional annotation of the human genome and challenges accurate clinical variant interpretation. To highlight the importance of capturing genetic variation in the Middle East, we aggregated whole exome and genome sequencing data from 2116 individuals in the Middle East and established the Middle East Variation (MEV) database. Of the high-impact coding (missense and loss of function) variants in this database, 53% were absent from the most comprehensive Genome Aggregation Database (gnomAD), thus representing a unique Middle Eastern variation dataset which might directly impact clinical variant interpretation. We highlight 39 variants with minor allele frequency >1% in the MEV database that were previously reported as rare disease variants in ClinVar and the Human Gene Mutation Database (HGMD). Furthermore, the MEV database consisted of 281 putative homozygous loss of function (LoF) variants, or complete knockouts, of which 31.7% (89/281) were absent from gnomAD. This set represents either complete knockouts of 83 unique genes in reportedly healthy individuals, with implications regarding disease penetrance and expressivity, or might affect dispensable exons, thus refining the clinical annotation of those regions. Intriguingly, 24 of those genes have several clinically significant variants reported in ClinVar and/or HGMD. Our study shows that genetic variation in the Middle East improves functional annotation and clinical interpretation of the genome and emphasizes the need for expanding sequencing studies in the Middle East and other underrepresented populations. Full article
(This article belongs to the Special Issue Clinical Application of Personalized Genomic Medicine)
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15 pages, 1587 KiB  
Article
Helpful Criteria When Implementing NGS Panels in Childhood Lymphoblastic Leukemia
by Nerea Vega-Garcia, Rocío Benito, Elena Esperanza-Cebollada, Marta Llop, Cristina Robledo, Clara Vicente-Garcés, Javier Alonso, Eva Barragán, Guerau Fernández, Jesús M. Hernández-Sánchez, Marta Martín-Izquierdo, Joan Maynou, Alfredo Minguela, Adrián Montaño, Margarita Ortega, Montserrat Torrebadell, José Cervera, Joaquín Sánchez, Antonio Jiménez-Velasco, Susana Riesco, Jesús M. Hernández-Rivas, Álvaro Lassaletta, José María Fernández, Susana Rives, José Luis Dapena, Manuel Ramírez, Mireia Camós and on behalf of the Group of Leukemia of the Spanish Society of Pediatric Hematology and Oncology (SEHOP)add Show full author list remove Hide full author list
J. Pers. Med. 2020, 10(4), 244; https://doi.org/10.3390/jpm10040244 - 26 Nov 2020
Cited by 1 | Viewed by 3751
Abstract
The development of Next-Generation Sequencing (NGS) has provided useful diagnostic, prognostic, and therapeutic strategies for individualized management of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Consequently, NGS is rapidly being established in clinical practice. However, the technology’s complexity, bioinformatics analysis, and the different [...] Read more.
The development of Next-Generation Sequencing (NGS) has provided useful diagnostic, prognostic, and therapeutic strategies for individualized management of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Consequently, NGS is rapidly being established in clinical practice. However, the technology’s complexity, bioinformatics analysis, and the different available options difficult a broad consensus between different laboratories in its daily routine introduction. This collaborative study among Spanish centers was aimed to assess the feasibility, pros, and cons of our customized panel and other commercial alternatives of NGS-targeted approaches. The custom panel was tested in three different sequencing centers. We used the same samples to assess other commercial panels (OncomineTM Childhood Cancer Research Assay; Archer®FusionPlex® ALL, and Human Comprehensive Cancer Panel GeneRead Panel v2®). Overall, the panels showed a good performance in different centers and platforms, but each NGS approach presented some issues, as well as pros and cons. Moreover, a previous consensus on the analysis and reporting following international guidelines would be preferable to improve the concordance in results among centers. Our study shows the challenges posed by NGS methodology and the need to consider several aspects of the chosen NGS-targeted approach and reach a consensus before implementing it in daily practice. Full article
(This article belongs to the Special Issue Clinical Application of Personalized Genomic Medicine)
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