Assessment of antibody library diversity through next generation sequencing and technical error compensation

PloS One
Marco FantiniAntonino Cattaneo

Abstract

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit th...Continue Reading

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Citations

Feb 24, 2018·Frontiers in Immunology·Romain RouetDaniel Christ
Nov 2, 2019·Molecular Biology and Evolution·Marco FantiniAnnalisa Pastore
Mar 24, 2018·Frontiers in Immunology·Sara D'AngeloAndrew R M Bradbury
May 20, 2020·Bioinformatics and Biology Insights·Andréa Queiroz MaranhãoMarcelo Macedo Brigido
Mar 30, 2021·Ageing Research Reviews·Rohan GuptaPravir Kumar

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Methods Mentioned

BETA
Illumina sequencing
PCR
Assay
single domain sequencing
nucleic acid handling

Software Mentioned

DEAL ( Diversity Estimator of Antibody Library )
fastq
DEAL
Excel VBA script
VH
R scripts
Visual Studio
Windows
Phi

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