| SMIRNOVA, Anastasia O, Anna M MIROSHNICHENKOVA, Yulia V OLSHANSKAYA, Michael A MASCHAN, Yuri B LEBEDEV, Dmitriy CHUDAKOV, Ilgar Z MAMEDOV and Alexander KOMKOV. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. elife. CAMBRIDGE: ELIFE SCIENCES PUBLICATIONS LTD, 2023, vol. 12, Jan, p. 1-17. ISSN 2050-084X. Available from: https://dx.doi.org/10.7554/eLife.69157. |
Other formats:
BibTeX
LaTeX
RIS
@article{2376957,
author = {Smirnova, Anastasia O and Miroshnichenkova, Anna M and Olshanskaya, Yulia V and Maschan, Michael A and Lebedev, Yuri B and Chudakov, Dmitriy and Mamedov, Ilgar Z and Komkov, Alexander},
article_location = {CAMBRIDGE},
article_number = {Jan},
doi = {http://dx.doi.org/10.7554/eLife.69157},
keywords = {immune receptor repertoire; high-throughput sequencing; multiplex PCR; PCR bias correction; adaptive immunity; TCR},
language = {eng},
issn = {2050-084X},
journal = {elife},
title = {The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling},
url = {https://elifesciences.org/articles/69157},
volume = {12},
year = {2023}
}
TY - JOUR
ID - 2376957
AU - Smirnova, Anastasia O - Miroshnichenkova, Anna M - Olshanskaya, Yulia V - Maschan, Michael A - Lebedev, Yuri B - Chudakov, Dmitriy - Mamedov, Ilgar Z - Komkov, Alexander
PY - 2023
TI - The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling
JF - elife
VL - 12
IS - Jan
SP - 1-17
EP - 1-17
PB - ELIFE SCIENCES PUBLICATIONS LTD
SN - 2050084X
KW - immune receptor repertoire
KW - high-throughput sequencing
KW - multiplex PCR
KW - PCR bias correction
KW - adaptive immunity
KW - TCR
UR - https://elifesciences.org/articles/69157
N2 - High-throughput sequencing of adaptive immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful TCR/BCR repertoire reconstruction and analysis methods have been developed in the past decade. However, detecting and correcting the discrepancy between real and experimentally observed lymphocyte clone frequencies are still challenging. Here, we discovered a hallmark anomaly in the ratio between read count and clone count -based frequencies of non-functional clonotypes in multiplex PCR- based immune repertoires. Calculating this anomaly, we formulated a quantitative measure of V-and J -genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on the OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5' RACE (Rapid Amplification of cDNA Ends) -based and multiplex PCR- based approaches and compared with a biological spike -in -based method for PCR bias evaluation. The developed approach can increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.
ER -
SMIRNOVA, Anastasia O, Anna M MIROSHNICHENKOVA, Yulia V OLSHANSKAYA, Michael A MASCHAN, Yuri B LEBEDEV, Dmitriy CHUDAKOV, Ilgar Z MAMEDOV and Alexander KOMKOV. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. \textit{elife}. CAMBRIDGE: ELIFE SCIENCES PUBLICATIONS LTD, 2023, vol.~12, Jan, p.~1-17. ISSN~2050-084X. Available from: https://dx.doi.org/10.7554/eLife.69157.
|
