The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F23%3A00133611" target="_blank" >RIV/00216224:14740/23:00133611 - isvavai.cz</a>
Result on the web
<a href="https://elifesciences.org/articles/69157" target="_blank" >https://elifesciences.org/articles/69157</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.7554/eLife.69157" target="_blank" >10.7554/eLife.69157</a>
Alternative languages
Result language
angličtina
Original language name
The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
30102 - Immunology
Result continuities
Project
—
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
elife
ISSN
2050-084X
e-ISSN
2050-084X
Volume of the periodical
12
Issue of the periodical within the volume
Jan
Country of publishing house
GB - UNITED KINGDOM
Number of pages
17
Pages from-to
1-17
UT code for WoS article
000931254200001
EID of the result in the Scopus database
2-s2.0-85147154705