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Noninvasive, low-cost RNA-sequencing enhances discovery potential of transcriptome studies

View ORCID ProfileMolly Martorella, View ORCID ProfileSilva Kasela, Renee Garcia-Flores, View ORCID ProfileAlper Gokden, View ORCID ProfileStephane E. Castel, View ORCID ProfileTuuli Lappalainen
doi: https://doi.org/10.1101/2022.09.06.506813
Molly Martorella
1New York Genome Center, New York, NY, USA
2Department of Systems Biology, Columbia University, New York, NY, USA
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  • ORCID record for Molly Martorella
  • For correspondence: mem2331@cumc.columbia.edu stephanecastel@gmail.com tlappalainen@nygenome.org
Silva Kasela
1New York Genome Center, New York, NY, USA
2Department of Systems Biology, Columbia University, New York, NY, USA
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Renee Garcia-Flores
1New York Genome Center, New York, NY, USA
3Department of Computer Science, Columbia University, New York, NY, USA
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Alper Gokden
1New York Genome Center, New York, NY, USA
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Stephane E. Castel
1New York Genome Center, New York, NY, USA
2Department of Systems Biology, Columbia University, New York, NY, USA
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  • For correspondence: mem2331@cumc.columbia.edu stephanecastel@gmail.com tlappalainen@nygenome.org
Tuuli Lappalainen
1New York Genome Center, New York, NY, USA
2Department of Systems Biology, Columbia University, New York, NY, USA
4Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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  • For correspondence: mem2331@cumc.columbia.edu stephanecastel@gmail.com tlappalainen@nygenome.org
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ABSTRACT

Transcriptomic studies lend insight into the biology of genetic regulation and bear promise in furthering the goals of precision medicine. However, the cost of RNA-sequencing and types of tissues currently assayed pose major limitations to study expansion and disease-relevant discovery. Here, we develop methods for sampling noninvasive biospecimens for transcriptome studies, investigate their technical and biological characteristics, and assess the feasibility of using noninvasive samples in transcriptomic and clinical applications. Of the four tissues we studied (buccal swabs, hair follicles, saliva, and urine cell pellets), we found hair follicles and urine cell pellets to be most promising due to the consistency of sample quality, underlying biology, and capture of disease-relevant signals. We anticipate future use of noninvasive sampling will facilitate discovery by increasing sample sizes in more diverse populations and in tissues with greater cell type diversity and biological relatedness to disease mechanisms. Moreover, the nature of noninvasive samples enables complex study designs with greater ability to capture context-dependent mechanisms of genetic regulation.

Competing Interest Statement

T.L. advises and has equity in Variant Bio, and advises Goldfinch Bio. and GSK. S.E.C. is a cofounder, chief technology officer, and stock owner at Variant Bio.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 06, 2022.
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Noninvasive, low-cost RNA-sequencing enhances discovery potential of transcriptome studies
Molly Martorella, Silva Kasela, Renee Garcia-Flores, Alper Gokden, Stephane E. Castel, Tuuli Lappalainen
bioRxiv 2022.09.06.506813; doi: https://doi.org/10.1101/2022.09.06.506813
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Noninvasive, low-cost RNA-sequencing enhances discovery potential of transcriptome studies
Molly Martorella, Silva Kasela, Renee Garcia-Flores, Alper Gokden, Stephane E. Castel, Tuuli Lappalainen
bioRxiv 2022.09.06.506813; doi: https://doi.org/10.1101/2022.09.06.506813

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