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Comparison of whole genome amplification techniques for human single cell exome sequencing
BACKGROUND: Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. RESULTS: The largest difference betw...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313163/ https://www.ncbi.nlm.nih.gov/pubmed/28207771 http://dx.doi.org/10.1371/journal.pone.0171566 |
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author | Borgström, Erik Paterlini, Marta Mold, Jeff E. Frisen, Jonas Lundeberg, Joakim |
author_facet | Borgström, Erik Paterlini, Marta Mold, Jeff E. Frisen, Jonas Lundeberg, Joakim |
author_sort | Borgström, Erik |
collection | PubMed |
description | BACKGROUND: Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. RESULTS: The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells. DISCUSSION: In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling. |
format | Online Article Text |
id | pubmed-5313163 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-53131632017-03-03 Comparison of whole genome amplification techniques for human single cell exome sequencing Borgström, Erik Paterlini, Marta Mold, Jeff E. Frisen, Jonas Lundeberg, Joakim PLoS One Research Article BACKGROUND: Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. RESULTS: The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells. DISCUSSION: In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling. Public Library of Science 2017-02-16 /pmc/articles/PMC5313163/ /pubmed/28207771 http://dx.doi.org/10.1371/journal.pone.0171566 Text en © 2017 Borgström et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Borgström, Erik Paterlini, Marta Mold, Jeff E. Frisen, Jonas Lundeberg, Joakim Comparison of whole genome amplification techniques for human single cell exome sequencing |
title | Comparison of whole genome amplification techniques for human single cell exome sequencing |
title_full | Comparison of whole genome amplification techniques for human single cell exome sequencing |
title_fullStr | Comparison of whole genome amplification techniques for human single cell exome sequencing |
title_full_unstemmed | Comparison of whole genome amplification techniques for human single cell exome sequencing |
title_short | Comparison of whole genome amplification techniques for human single cell exome sequencing |
title_sort | comparison of whole genome amplification techniques for human single cell exome sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313163/ https://www.ncbi.nlm.nih.gov/pubmed/28207771 http://dx.doi.org/10.1371/journal.pone.0171566 |
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