Detecting sample swaps in diverse NGS data types using linkage disequilibrium
Parallelized analysis in clinical genomics can lead to sample or data mislabelling, and could have serious downstream consequences. Here the authors present a tool to quantify sample genetic relatedness and detect such mistakes, and apply it to thousands of datasets from the ENCODE consortium.
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2020-07-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-020-17453-5 |
| _version_ | 1819200336150134784 |
|---|---|
| author | Nauman Javed Yossi Farjoun Tim J. Fennell Charles B. Epstein Bradley E. Bernstein Noam Shoresh |
| author_facet | Nauman Javed Yossi Farjoun Tim J. Fennell Charles B. Epstein Bradley E. Bernstein Noam Shoresh |
| author_sort | Nauman Javed |
| collection | DOAJ |
| description | Parallelized analysis in clinical genomics can lead to sample or data mislabelling, and could have serious downstream consequences. Here the authors present a tool to quantify sample genetic relatedness and detect such mistakes, and apply it to thousands of datasets from the ENCODE consortium. |
| first_indexed | 2024-12-23T03:30:36Z |
| format | Article |
| id | doaj.art-3aac3ad4af5c44bbbcff502de0819ea0 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-12-23T03:30:36Z |
| publishDate | 2020-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-3aac3ad4af5c44bbbcff502de0819ea02022-12-21T18:01:42ZengNature PortfolioNature Communications2041-17232020-07-011111810.1038/s41467-020-17453-5Detecting sample swaps in diverse NGS data types using linkage disequilibriumNauman Javed0Yossi Farjoun1Tim J. Fennell2Charles B. Epstein3Bradley E. Bernstein4Noam Shoresh5Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical SchoolBroad Institute of MIT and HarvardBroad Institute of MIT and HarvardBroad Institute of MIT and HarvardDepartment of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical SchoolBroad Institute of MIT and HarvardParallelized analysis in clinical genomics can lead to sample or data mislabelling, and could have serious downstream consequences. Here the authors present a tool to quantify sample genetic relatedness and detect such mistakes, and apply it to thousands of datasets from the ENCODE consortium.https://doi.org/10.1038/s41467-020-17453-5 |
| spellingShingle | Nauman Javed Yossi Farjoun Tim J. Fennell Charles B. Epstein Bradley E. Bernstein Noam Shoresh Detecting sample swaps in diverse NGS data types using linkage disequilibrium Nature Communications |
| title | Detecting sample swaps in diverse NGS data types using linkage disequilibrium |
| title_full | Detecting sample swaps in diverse NGS data types using linkage disequilibrium |
| title_fullStr | Detecting sample swaps in diverse NGS data types using linkage disequilibrium |
| title_full_unstemmed | Detecting sample swaps in diverse NGS data types using linkage disequilibrium |
| title_short | Detecting sample swaps in diverse NGS data types using linkage disequilibrium |
| title_sort | detecting sample swaps in diverse ngs data types using linkage disequilibrium |
| url | https://doi.org/10.1038/s41467-020-17453-5 |
| work_keys_str_mv | AT naumanjaved detectingsampleswapsindiversengsdatatypesusinglinkagedisequilibrium AT yossifarjoun detectingsampleswapsindiversengsdatatypesusinglinkagedisequilibrium AT timjfennell detectingsampleswapsindiversengsdatatypesusinglinkagedisequilibrium AT charlesbepstein detectingsampleswapsindiversengsdatatypesusinglinkagedisequilibrium AT bradleyebernstein detectingsampleswapsindiversengsdatatypesusinglinkagedisequilibrium AT noamshoresh detectingsampleswapsindiversengsdatatypesusinglinkagedisequilibrium |