Accurate profiling of full-length Fv in highly homologous antibody libraries using UMI tagged short reads.

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  • Additional Information
    • Source:
      Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
    • Publication Information:
      Publication: 1992- : Oxford : Oxford University Press
      Original Publication: London, Information Retrieval ltd.
    • Subject Terms:
      Gene Library* ; Single-Chain Antibodies*/genetics; Immunoglobulin Heavy Chains/genetics ; High-Throughput Nucleotide Sequencing ; Machine Learning
    • Abstract:
      Deep parallel sequencing (NGS) is a viable tool for monitoring scFv and Fab library dynamics in many antibody engineering high-throughput screening efforts. Although very useful, the commonly used Illumina NGS platform cannot handle the entire sequence of scFv or Fab in a single read, usually focusing on specific CDRs or resorting to sequencing VH and VL variable domains separately, thus limiting its utility in comprehensive monitoring of selection dynamics. Here we present a simple and robust method for deep sequencing repertoires of full length scFv, Fab and Fv antibody sequences. This process utilizes standard molecular procedures and unique molecular identifiers (UMI) to pair separately sequenced VH and VL. We show that UMI assisted VH-VL matching allows for a comprehensive and highly accurate mapping of full length Fv clonal dynamics in large highly homologous antibody libraries, as well as identification of rare variants. In addition to its utility in synthetic antibody discovery processes, our method can be instrumental in generating large datasets for machine learning (ML) applications, which in the field of antibody engineering has been hampered by conspicuous paucity of large scale full length Fv data.
      (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
    • Comments:
      Erratum in: Nucleic Acids Res. 2023 May 17;:. (PMID: 37194706)
    • References:
      Front Immunol. 2018 Dec 21;9:3004. (PMID: 30622532)
      Nat Methods. 2016 Jul;13(7):581-3. (PMID: 27214047)
      Genome Res. 2011 Mar;21(3):494-504. (PMID: 21212162)
      Microbiome. 2014 Feb 24;2(1):6. (PMID: 24558975)
      Curr Opin Struct Biol. 2015 Aug;33:146-60. (PMID: 26451649)
      MAbs. 2018 Nov-Dec;10(8):1281-1290. (PMID: 30252602)
      Nat Commun. 2020 Jan 15;11(1):297. (PMID: 31941882)
      Oncoimmunology. 2019 Nov 4;9(1):1681869. (PMID: 32002288)
      NAR Genom Bioinform. 2020 May 25;2(2):lqaa037. (PMID: 33575591)
      PLoS Comput Biol. 2017 May 5;13(5):e1005480. (PMID: 28475621)
      MAbs. 2019 Apr;11(3):532-545. (PMID: 30735467)
      Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89. (PMID: 26542840)
      FEBS J. 2014 Jan;281(1):306-19. (PMID: 24279419)
      Nat Genet. 2018 Jun;50(6):874-882. (PMID: 29785012)
      Nat Biomed Eng. 2021 Jun;5(6):600-612. (PMID: 33859386)
      Cell Rep. 2018 Nov 20;25(8):2121-2131.e5. (PMID: 30463010)
      Methods Mol Biol. 2018;1785:89-118. (PMID: 29714014)
      MAbs. 2019 Apr;11(3):516-531. (PMID: 30663541)
      Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13456-61. (PMID: 21825149)
      Front Immunol. 2018 Mar 08;9:395. (PMID: 29568296)
      Sci Transl Med. 2016 Nov 30;8(367):367ra166. (PMID: 27903862)
      Front Immunol. 2020 Jun 30;11:1344. (PMID: 32714328)
      Sci Rep. 2021 Mar 12;11(1):5852. (PMID: 33712669)
      Trends Pharmacol Sci. 2022 Feb;43(2):123-135. (PMID: 34895944)
      Nucleic Acids Res. 2019 May 21;47(9):e50. (PMID: 30854567)
      Exp Mol Med. 2017 Mar 24;49(3):e308. (PMID: 28336957)
      Nucleic Acids Res. 2006 Jan 1;34(Database issue):D781-4. (PMID: 16381979)
      Nucleic Acids Res. 2010 Nov;38(21):e193. (PMID: 20846958)
      Front Immunol. 2018 Feb 02;9:118. (PMID: 29472918)
      Nat Methods. 2013 Oct;10(10):996-8. (PMID: 23955772)
      Protein Sci. 2022 Jan;31(1):141-146. (PMID: 34655133)
      Nat Med. 2015 Jan;21(1):86-91. (PMID: 25501908)
      Nat Biotechnol. 2018 Feb;36(2):152-155. (PMID: 29309060)
      Nucleic Acids Res. 2004 Dec 02;32(21):e169. (PMID: 15576676)
      Nucleic Acids Res. 2012 Jul;40(Web Server issue):W521-4. (PMID: 22675071)
      Nucleic Acids Res. 2011 Jul;39(12):e81. (PMID: 21490082)
      BMC Bioinformatics. 2011 Jan 28;12:38. (PMID: 21276213)
      Nat Biotechnol. 2019 Oct;37(10):1155-1162. (PMID: 31406327)
      Biomol Detect Quantif. 2014 Dec 04;2:11-29. (PMID: 27896140)
      Genome Med. 2018 Apr 27;10(1):34. (PMID: 29703216)
      J Biol Chem. 2015 Sep 4;290(36):21773-86. (PMID: 26088137)
      Annu Rev Immunol. 1994;12:433-55. (PMID: 8011287)
      Cell. 2020 Sep 3;182(5):1295-1310.e20. (PMID: 32841599)
      Nucleic Acids Res. 2015 Dec 2;43(21):e143. (PMID: 26187991)
      Nat Biotechnol. 1997 Jun;15(6):553-7. (PMID: 9181578)
      Nat Biotechnol. 2013 Feb;31(2):166-9. (PMID: 23334449)
      Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18523-8. (PMID: 23064642)
      PeerJ. 2016 Sep 20;4:e2492. (PMID: 27688981)
      Nat Biotechnol. 1997 Jan;15(1):29-34. (PMID: 9035102)
      Protein Eng Des Sel. 2013 Oct;26(10):599-609. (PMID: 23754530)
      Front Pharmacol. 2019 Jul 30;10:847. (PMID: 31417405)
      Methods Mol Biol. 2018;1706:223-232. (PMID: 29423801)
      Nat Methods. 2021 Feb;18(2):165-169. (PMID: 33432244)
      Nat Methods. 2014 Jun;11(6):653-5. (PMID: 24793455)
    • Accession Number:
      0 (Immunoglobulin Heavy Chains)
      0 (Single-Chain Antibodies)
    • Publication Date:
      Date Created: 20230404 Date Completed: 20230628 Latest Revision: 20231116
    • Publication Date:
      20231215
    • Accession Number:
      PMC10287906
    • Accession Number:
      10.1093/nar/gkad235
    • Accession Number:
      37014016