miRTrace reveals the organismal origins of microRNA sequencing data
Abstract We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurat...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-12-01
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| Series: | Genome Biology |
| Online Access: | http://link.springer.com/article/10.1186/s13059-018-1588-9 |
| _version_ | 1818036724621639680 |
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| author | Wenjing Kang Yrin Eldfjell Bastian Fromm Xavier Estivill Inna Biryukova Marc R. Friedländer |
| author_facet | Wenjing Kang Yrin Eldfjell Bastian Fromm Xavier Estivill Inna Biryukova Marc R. Friedländer |
| author_sort | Wenjing Kang |
| collection | DOAJ |
| description | Abstract We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately (> 99%) assigns real and simulated data to 14 important animal and plant groups, sensitively detects parasitic infection in mammals, and discovers the primate origin of single cells. Applying our algorithm to over 700 public datasets, we find evidence that over 7% are cross-contaminated and present a novel solution to clean these computationally, even after sequencing has occurred. miRTrace is freely available at https://github.com/friedlanderlab/mirtrace. |
| first_indexed | 2024-12-10T07:15:30Z |
| format | Article |
| id | doaj.art-47f900a9cfb6434682d1d9fd0af9ed9e |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-10T07:15:30Z |
| publishDate | 2018-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-47f900a9cfb6434682d1d9fd0af9ed9e2022-12-22T01:57:57ZengBMCGenome Biology1474-760X2018-12-0119111510.1186/s13059-018-1588-9miRTrace reveals the organismal origins of microRNA sequencing dataWenjing Kang0Yrin Eldfjell1Bastian Fromm2Xavier Estivill3Inna Biryukova4Marc R. Friedländer5Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityScience for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityScience for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityGenetics and Genomics Department, Sidra MedicineScience for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityScience for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityAbstract We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately (> 99%) assigns real and simulated data to 14 important animal and plant groups, sensitively detects parasitic infection in mammals, and discovers the primate origin of single cells. Applying our algorithm to over 700 public datasets, we find evidence that over 7% are cross-contaminated and present a novel solution to clean these computationally, even after sequencing has occurred. miRTrace is freely available at https://github.com/friedlanderlab/mirtrace.http://link.springer.com/article/10.1186/s13059-018-1588-9 |
| spellingShingle | Wenjing Kang Yrin Eldfjell Bastian Fromm Xavier Estivill Inna Biryukova Marc R. Friedländer miRTrace reveals the organismal origins of microRNA sequencing data Genome Biology |
| title | miRTrace reveals the organismal origins of microRNA sequencing data |
| title_full | miRTrace reveals the organismal origins of microRNA sequencing data |
| title_fullStr | miRTrace reveals the organismal origins of microRNA sequencing data |
| title_full_unstemmed | miRTrace reveals the organismal origins of microRNA sequencing data |
| title_short | miRTrace reveals the organismal origins of microRNA sequencing data |
| title_sort | mirtrace reveals the organismal origins of microrna sequencing data |
| url | http://link.springer.com/article/10.1186/s13059-018-1588-9 |
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