TY - JOUR

T1 - Reconstructing antibody repertoires from error-prone immunosequencing reads

AU - Shlemov, Alexander

AU - Safonova, Yana

AU - Pevzner, Pavel A.

AU - Банкевич, Сергей Викторович

AU - Бзикадзе, Андрей Важевич

PY - 2017/11/1

Y1 - 2017/11/1

N2 - Transforming error-prone immunosequencing datasets into Ab repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released in the last 3 y, it remains unclear how to benchmark them and how to assess the accuracy of the reconstructed repertoires. We describe an accurate IgReC algorithm for constructing Ab repertoires from high-throughput immunosequencing datasets and a new framework for assessing the quality of reconstructed repertoires. Surprisingly, Ab repertoires constructed by IgReC from barcoded immunosequencing datasets in the blind mode (without using information about unique molecular identifiers) improved upon the repertoires constructed by the state-of-the-art tools that use barcoding. This finding suggests that IgReC may alleviate the need to generate repertoires using the barcoding technology (the workhorse of current immunogenomics efforts) because our computational approach to error correction of immunosequencing data is nearly as powerful as the experimental approach based on barcoding.

AB - Transforming error-prone immunosequencing datasets into Ab repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released in the last 3 y, it remains unclear how to benchmark them and how to assess the accuracy of the reconstructed repertoires. We describe an accurate IgReC algorithm for constructing Ab repertoires from high-throughput immunosequencing datasets and a new framework for assessing the quality of reconstructed repertoires. Surprisingly, Ab repertoires constructed by IgReC from barcoded immunosequencing datasets in the blind mode (without using information about unique molecular identifiers) improved upon the repertoires constructed by the state-of-the-art tools that use barcoding. This finding suggests that IgReC may alleviate the need to generate repertoires using the barcoding technology (the workhorse of current immunogenomics efforts) because our computational approach to error correction of immunosequencing data is nearly as powerful as the experimental approach based on barcoding.

UR - http://www.scopus.com/inward/record.url?scp=85032021010&partnerID=8YFLogxK

U2 - 10.4049/jimmunol.1700485

DO - 10.4049/jimmunol.1700485

M3 - Article

C2 - 28978691

AN - SCOPUS:85032021010

VL - 199

SP - 3369

EP - 3380

JO - Journal of Immunology

JF - Journal of Immunology

SN - 0022-1767

IS - 9

ER -