Motivation: The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic hypermutation necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature. Results: We developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains and extract somatic mutations on the VDJ region. VDJPuzzle successfully reconstructed BCRs from 100% (n=117) human and 96.5% (n=200) murine B cells. The reconstructed BCRs were successfully validated with single-cell Sanger sequencing. Availability and implementation: VDJPuzzle is available at https://bitbucket.org/kirbyvisp/vdjpuzzle2. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic hypermutation necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature. Results: We developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains and extract somatic mutations on the VDJ region. VDJPuzzle successfully reconstructed BCRs from 100% (n=117) human and 96.5% (n=200) murine B cells. The reconstructed BCRs were successfully validated with single-cell Sanger sequencing. Availability and implementation: VDJPuzzle is available at https://bitbucket.org/kirbyvisp/vdjpuzzle2. Supplementary information: Supplementary data are available at Bioinformatics online.
Authors: Tommaso Andreani; Linda M Slot; Samuel Gabillard; Carsten Strübing; Claus Reimertz; Veeranagouda Yaligara; Aleida M Bakker; Reza Olfati-Saber; René E M Toes; Hans U Scherer; Franck Augé; Deimantė Šimaitė Journal: NAR Genom Bioinform Date: 2022-07-13
Authors: Nadiah S Alzahrani; Ghedeir M Alshammari; Afaf El-Ansary; Abu ElGasim A Yagoub; Musarat Amina; Ali Saleh; Mohammed Abdo Yahya Journal: Nutrients Date: 2022-04-25 Impact factor: 6.706
Authors: Sarah Pyfrom; Bam Paneru; James J Knox; Michael P Cancro; Sylvia Posso; Jane H Buckner; Montserrat C Anguera Journal: Proc Natl Acad Sci U S A Date: 2021-06-15 Impact factor: 11.205
Authors: Emily F Davis-Marcisak; Atul Deshpande; Genevieve L Stein-O'Brien; Won J Ho; Daniel Laheru; Elizabeth M Jaffee; Elana J Fertig; Luciane T Kagohara Journal: Cancer Cell Date: 2021-07-29 Impact factor: 38.585
Authors: Shunsuke Teraguchi; Dianita S Saputri; Mara Anais Llamas-Covarrubias; Ana Davila; Diego Diez; Sedat Aybars Nazlica; John Rozewicki; Hendra S Ismanto; Jan Wilamowski; Jiaqi Xie; Zichang Xu; Martin de Jesus Loza-Lopez; Floris J van Eerden; Songling Li; Daron M Standley Journal: Comput Struct Biotechnol J Date: 2020-07-17 Impact factor: 7.271