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Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale

Whole-exome sequencing has become a popular technique in research and clinical settings, assisting in disease diagnosis and increasing the understanding of disease pathogenesis. In this study, we aimed to compare common enrichment capture solutions available in the market. Peripheral blood-purified...

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Autores principales: Díaz-de Usera, Ana, Lorenzo-Salazar, Jose M., Rubio-Rodríguez, Luis A., Muñoz-Barrera, Adrián, Guillen-Guio, Beatriz, Marcelino-Rodríguez, Itahisa, García-Olivares, Víctor, Mendoza-Alvarez, Alejandro, Corrales, Almudena, Íñigo-Campos, Antonio, González-Montelongo, Rafaela, Flores, Carlos
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7696786/
https://www.ncbi.nlm.nih.gov/pubmed/33202991
http://dx.doi.org/10.3390/jcm9113656
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author Díaz-de Usera, Ana
Lorenzo-Salazar, Jose M.
Rubio-Rodríguez, Luis A.
Muñoz-Barrera, Adrián
Guillen-Guio, Beatriz
Marcelino-Rodríguez, Itahisa
García-Olivares, Víctor
Mendoza-Alvarez, Alejandro
Corrales, Almudena
Íñigo-Campos, Antonio
González-Montelongo, Rafaela
Flores, Carlos
author_facet Díaz-de Usera, Ana
Lorenzo-Salazar, Jose M.
Rubio-Rodríguez, Luis A.
Muñoz-Barrera, Adrián
Guillen-Guio, Beatriz
Marcelino-Rodríguez, Itahisa
García-Olivares, Víctor
Mendoza-Alvarez, Alejandro
Corrales, Almudena
Íñigo-Campos, Antonio
González-Montelongo, Rafaela
Flores, Carlos
author_sort Díaz-de Usera, Ana
collection PubMed
description Whole-exome sequencing has become a popular technique in research and clinical settings, assisting in disease diagnosis and increasing the understanding of disease pathogenesis. In this study, we aimed to compare common enrichment capture solutions available in the market. Peripheral blood-purified DNA samples were enriched with SureSelect(QXT) V6 (Agilent) and various Illumina solutions: TruSeq DNA Nano, TruSeq DNA Exome, Nextera DNA Exome, and Illumina DNA Prep with Enrichment, and sequenced on a HiSeq 4000. We found that their percentage of duplicate reads was as much as 2 times higher than previously reported values for the previous HiSeq series. SureSelect(QXT) and Illumina DNA Prep with Enrichment showed the best average on-target coverage, which improved when off-target regions were included. At high coverage levels and in shared bases, these two solutions and TruSeq DNA Exome provided three of the best performances. With respect to the number of small variants detected, SureSelect(QXT) presented the lowest number of detected variants in target regions. When off-target regions were considered, its ability equalized to other solutions. Our results show SureSelect(QXT) and Illumina DNA Prep with Enrichment to be the best enrichment capture solutions.
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spelling pubmed-76967862020-11-29 Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale Díaz-de Usera, Ana Lorenzo-Salazar, Jose M. Rubio-Rodríguez, Luis A. Muñoz-Barrera, Adrián Guillen-Guio, Beatriz Marcelino-Rodríguez, Itahisa García-Olivares, Víctor Mendoza-Alvarez, Alejandro Corrales, Almudena Íñigo-Campos, Antonio González-Montelongo, Rafaela Flores, Carlos J Clin Med Article Whole-exome sequencing has become a popular technique in research and clinical settings, assisting in disease diagnosis and increasing the understanding of disease pathogenesis. In this study, we aimed to compare common enrichment capture solutions available in the market. Peripheral blood-purified DNA samples were enriched with SureSelect(QXT) V6 (Agilent) and various Illumina solutions: TruSeq DNA Nano, TruSeq DNA Exome, Nextera DNA Exome, and Illumina DNA Prep with Enrichment, and sequenced on a HiSeq 4000. We found that their percentage of duplicate reads was as much as 2 times higher than previously reported values for the previous HiSeq series. SureSelect(QXT) and Illumina DNA Prep with Enrichment showed the best average on-target coverage, which improved when off-target regions were included. At high coverage levels and in shared bases, these two solutions and TruSeq DNA Exome provided three of the best performances. With respect to the number of small variants detected, SureSelect(QXT) presented the lowest number of detected variants in target regions. When off-target regions were considered, its ability equalized to other solutions. Our results show SureSelect(QXT) and Illumina DNA Prep with Enrichment to be the best enrichment capture solutions. MDPI 2020-11-13 /pmc/articles/PMC7696786/ /pubmed/33202991 http://dx.doi.org/10.3390/jcm9113656 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Díaz-de Usera, Ana
Lorenzo-Salazar, Jose M.
Rubio-Rodríguez, Luis A.
Muñoz-Barrera, Adrián
Guillen-Guio, Beatriz
Marcelino-Rodríguez, Itahisa
García-Olivares, Víctor
Mendoza-Alvarez, Alejandro
Corrales, Almudena
Íñigo-Campos, Antonio
González-Montelongo, Rafaela
Flores, Carlos
Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale
title Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale
title_full Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale
title_fullStr Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale
title_full_unstemmed Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale
title_short Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale
title_sort evaluation of whole-exome enrichment solutions: lessons from the high-end of the short-read sequencing scale
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7696786/
https://www.ncbi.nlm.nih.gov/pubmed/33202991
http://dx.doi.org/10.3390/jcm9113656
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