A quantitative comparison of single-cell whole genome amplification methods.
Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA) is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-ce...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4138190?pdf=render |
| _version_ | 1818197399848353792 |
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| author | Charles F A de Bourcy Iwijn De Vlaminck Jad N Kanbar Jianbin Wang Charles Gawad Stephen R Quake |
| author_facet | Charles F A de Bourcy Iwijn De Vlaminck Jad N Kanbar Jianbin Wang Charles Gawad Stephen R Quake |
| author_sort | Charles F A de Bourcy |
| collection | DOAJ |
| description | Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA) is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment. |
| first_indexed | 2024-12-12T01:49:22Z |
| format | Article |
| id | doaj.art-75f6a03e3eee4559a014eb2188ba230e |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T01:49:22Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-75f6a03e3eee4559a014eb2188ba230e2022-12-22T00:42:31ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0198e10558510.1371/journal.pone.0105585A quantitative comparison of single-cell whole genome amplification methods.Charles F A de BourcyIwijn De VlaminckJad N KanbarJianbin WangCharles GawadStephen R QuakeSingle-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA) is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment.http://europepmc.org/articles/PMC4138190?pdf=render |
| spellingShingle | Charles F A de Bourcy Iwijn De Vlaminck Jad N Kanbar Jianbin Wang Charles Gawad Stephen R Quake A quantitative comparison of single-cell whole genome amplification methods. PLoS ONE |
| title | A quantitative comparison of single-cell whole genome amplification methods. |
| title_full | A quantitative comparison of single-cell whole genome amplification methods. |
| title_fullStr | A quantitative comparison of single-cell whole genome amplification methods. |
| title_full_unstemmed | A quantitative comparison of single-cell whole genome amplification methods. |
| title_short | A quantitative comparison of single-cell whole genome amplification methods. |
| title_sort | quantitative comparison of single cell whole genome amplification methods |
| url | http://europepmc.org/articles/PMC4138190?pdf=render |
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