Enabling multiplexed testing of pooled donor cells through whole-genome sequencing
Abstract 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 sing...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-04-01
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| Series: | Genome Medicine |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13073-018-0541-6 |
| _version_ | 1811325118764285952 |
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| author | Yingleong Chan Ying Kai Chan Daniel B. Goodman Xiaoge Guo Alejandro Chavez Elaine T. Lim George M. Church |
| author_facet | Yingleong Chan Ying Kai Chan Daniel B. Goodman Xiaoge Guo Alejandro Chavez Elaine T. Lim George M. Church |
| author_sort | Yingleong Chan |
| collection | DOAJ |
| description | Abstract 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/ |
| first_indexed | 2024-04-13T14:27:28Z |
| format | Article |
| id | doaj.art-91ce078fac0a446897ce139106322d9d |
| institution | Directory Open Access Journal |
| issn | 1756-994X |
| language | English |
| last_indexed | 2024-04-13T14:27:28Z |
| publishDate | 2018-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Medicine |
| spelling | doaj.art-91ce078fac0a446897ce139106322d9d2022-12-22T02:43:16ZengBMCGenome Medicine1756-994X2018-04-0110111110.1186/s13073-018-0541-6Enabling multiplexed testing of pooled donor cells through whole-genome sequencingYingleong Chan0Ying Kai Chan1Daniel B. Goodman2Xiaoge Guo3Alejandro Chavez4Elaine T. Lim5George M. Church6Wyss Institute for Biologically Inspired Engineering, Harvard UniversityWyss Institute for Biologically Inspired Engineering, Harvard UniversityWyss Institute for Biologically Inspired Engineering, Harvard UniversityWyss Institute for Biologically Inspired Engineering, Harvard UniversityDepartment of Pathology and Cell Biology, Columbia University College of Physicians and SurgeonsWyss Institute for Biologically Inspired Engineering, Harvard UniversityWyss Institute for Biologically Inspired Engineering, Harvard UniversityAbstract 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/http://link.springer.com/article/10.1186/s13073-018-0541-6Multiplexed testingBarcode free methodSingle nucleotide polymorphismsExpectation maximization algorithmNext-generation sequencingPersonal Genome Project |
| spellingShingle | Yingleong Chan Ying Kai Chan Daniel B. Goodman Xiaoge Guo Alejandro Chavez Elaine T. Lim George M. Church Enabling multiplexed testing of pooled donor cells through whole-genome sequencing Genome Medicine Multiplexed testing Barcode free method Single nucleotide polymorphisms Expectation maximization algorithm Next-generation sequencing Personal Genome Project |
| 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 | Multiplexed testing Barcode free method Single nucleotide polymorphisms Expectation maximization algorithm Next-generation sequencing Personal Genome Project |
| url | http://link.springer.com/article/10.1186/s13073-018-0541-6 |
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