Barcoding bias in high-throughput multiplex sequencing of miRNA
Second-generation sequencing is gradually becoming the method of choice for miRNA detection and expression profiling. Given the relatively small number of miRNAs and improvements in DNA sequencing technology, studying miRNA expression profiles of multiple samples in a single flow cell lane becomes f...
| Main Authors: | , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Cold Spring Harbor Laboratory Press
2013
|
| Online Access: | http://hdl.handle.net/1721.1/76787 |
| _version_ | 1826210469930598400 |
|---|---|
| author | Alon, Shahar Vigneault, Francois Eminaga, Seda Christodoulou, Danos C. Seidman, Jonathan G. Church, George M. Eisenberg, Eli |
| author2 | Ragon Institute of MGH, MIT and Harvard |
| author_facet | Ragon Institute of MGH, MIT and Harvard Alon, Shahar Vigneault, Francois Eminaga, Seda Christodoulou, Danos C. Seidman, Jonathan G. Church, George M. Eisenberg, Eli |
| author_sort | Alon, Shahar |
| collection | MIT |
| description | Second-generation sequencing is gradually becoming the method of choice for miRNA detection and expression profiling. Given the relatively small number of miRNAs and improvements in DNA sequencing technology, studying miRNA expression profiles of multiple samples in a single flow cell lane becomes feasible. Multiplexing strategies require marking each miRNA library with a DNA barcode. Here we report that barcodes introduced through adapter ligation confer significant bias on miRNA expression profiles. This bias is much higher than the expected Poisson noise and masks significant expression differences between miRNA libraries. This bias can be eliminated by adding barcodes during PCR amplification of libraries. The accuracy of miRNA expression measurement in multiplexed experiments becomes a function of sample number. |
| first_indexed | 2024-09-23T14:50:23Z |
| format | Article |
| id | mit-1721.1/76787 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:50:23Z |
| publishDate | 2013 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | mit-1721.1/767872022-09-29T10:52:27Z Barcoding bias in high-throughput multiplex sequencing of miRNA Alon, Shahar Vigneault, Francois Eminaga, Seda Christodoulou, Danos C. Seidman, Jonathan G. Church, George M. Eisenberg, Eli Ragon Institute of MGH, MIT and Harvard Vigneault, Francois Second-generation sequencing is gradually becoming the method of choice for miRNA detection and expression profiling. Given the relatively small number of miRNAs and improvements in DNA sequencing technology, studying miRNA expression profiles of multiple samples in a single flow cell lane becomes feasible. Multiplexing strategies require marking each miRNA library with a DNA barcode. Here we report that barcodes introduced through adapter ligation confer significant bias on miRNA expression profiles. This bias is much higher than the expected Poisson noise and masks significant expression differences between miRNA libraries. This bias can be eliminated by adding barcodes during PCR amplification of libraries. The accuracy of miRNA expression measurement in multiplexed experiments becomes a function of sample number. National Human Genome Research Institute (U.S.) (Center for Excellence in Genome Sciences grant) Canadian Institutes of Health Research National Heart, Lung, and Blood Institute National Institutes of Health (U.S.) (SysCODE Consortium) United States-Israel Binational Science Foundation (grant no. 2009290) Ragon Institute of MGH, MIT and Harvard (Fellowship) Leducq Foundation 2013-02-12T21:57:48Z 2013-02-12T21:57:48Z 2011-07 2011-02 Article http://purl.org/eprint/type/JournalArticle 1088-9051 http://hdl.handle.net/1721.1/76787 Alon, S. et al. “Barcoding Bias in High-throughput Multiplex Sequencing of miRNA.” Genome Research 21.9 (2011): 1506–1511. Web. en_US http://dx.doi.org/10.1101/gr.121715.111 Genome Research Creative Commons Attribution Non-Commercial http://creativecommons.org/licenses/by-nc/3.0 application/pdf Cold Spring Harbor Laboratory Press Genome Research |
| spellingShingle | Alon, Shahar Vigneault, Francois Eminaga, Seda Christodoulou, Danos C. Seidman, Jonathan G. Church, George M. Eisenberg, Eli Barcoding bias in high-throughput multiplex sequencing of miRNA |
| title | Barcoding bias in high-throughput multiplex sequencing of miRNA |
| title_full | Barcoding bias in high-throughput multiplex sequencing of miRNA |
| title_fullStr | Barcoding bias in high-throughput multiplex sequencing of miRNA |
| title_full_unstemmed | Barcoding bias in high-throughput multiplex sequencing of miRNA |
| title_short | Barcoding bias in high-throughput multiplex sequencing of miRNA |
| title_sort | barcoding bias in high throughput multiplex sequencing of mirna |
| url | http://hdl.handle.net/1721.1/76787 |
| work_keys_str_mv | AT alonshahar barcodingbiasinhighthroughputmultiplexsequencingofmirna AT vigneaultfrancois barcodingbiasinhighthroughputmultiplexsequencingofmirna AT eminagaseda barcodingbiasinhighthroughputmultiplexsequencingofmirna AT christodouloudanosc barcodingbiasinhighthroughputmultiplexsequencingofmirna AT seidmanjonathang barcodingbiasinhighthroughputmultiplexsequencingofmirna AT churchgeorgem barcodingbiasinhighthroughputmultiplexsequencingofmirna AT eisenbergeli barcodingbiasinhighthroughputmultiplexsequencingofmirna |