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Enabling multiplexed testing of pooled donor cells through whole-genome sequencing
We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleo...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909281/ https://www.ncbi.nlm.nih.gov/pubmed/29673390 http://dx.doi.org/10.1186/s13073-018-0541-6 |
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author | Chan, Yingleong Chan, Ying Kai Goodman, Daniel B. Guo, Xiaoge Chavez, Alejandro Lim, Elaine T. Church, George M. |
author_facet | Chan, Yingleong Chan, Ying Kai Goodman, Daniel B. Guo, Xiaoge Chavez, Alejandro Lim, Elaine T. Church, George M. |
author_sort | Chan, Yingleong |
collection | PubMed |
description | We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the proportions from the sequencing data. By testing using simulated and real data, we showed that our method robustly predicts the individual proportions from a mixed-pool of numerous donors, thus enabling the multiplexed testing of diverse donor cells en masse. More information is available at https://pgpresearch.med.harvard.edu/poolseq/ ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-018-0541-6) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5909281 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-59092812018-04-30 Enabling multiplexed testing of pooled donor cells through whole-genome sequencing Chan, Yingleong Chan, Ying Kai Goodman, Daniel B. Guo, Xiaoge Chavez, Alejandro Lim, Elaine T. Church, George M. Genome Med Method We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the proportions from the sequencing data. By testing using simulated and real data, we showed that our method robustly predicts the individual proportions from a mixed-pool of numerous donors, thus enabling the multiplexed testing of diverse donor cells en masse. More information is available at https://pgpresearch.med.harvard.edu/poolseq/ ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-018-0541-6) contains supplementary material, which is available to authorized users. BioMed Central 2018-04-19 /pmc/articles/PMC5909281/ /pubmed/29673390 http://dx.doi.org/10.1186/s13073-018-0541-6 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Method Chan, Yingleong Chan, Ying Kai Goodman, Daniel B. Guo, Xiaoge Chavez, Alejandro Lim, Elaine T. Church, George M. Enabling multiplexed testing of pooled donor cells through whole-genome sequencing |
title | Enabling multiplexed testing of pooled donor cells through whole-genome sequencing |
title_full | Enabling multiplexed testing of pooled donor cells through whole-genome sequencing |
title_fullStr | Enabling multiplexed testing of pooled donor cells through whole-genome sequencing |
title_full_unstemmed | Enabling multiplexed testing of pooled donor cells through whole-genome sequencing |
title_short | Enabling multiplexed testing of pooled donor cells through whole-genome sequencing |
title_sort | enabling multiplexed testing of pooled donor cells through whole-genome sequencing |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909281/ https://www.ncbi.nlm.nih.gov/pubmed/29673390 http://dx.doi.org/10.1186/s13073-018-0541-6 |
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