Provenance: covid19-1.ireceptor.org

  • 2021-09-13: Study added
  • 2021-07-21: Study added
  • 2021-05-18: Study added
  • 2021-05-18: Study update, data added
    • Data from Schultheiß et al. (2020) "Next Generation Sequencing of T and B cell receptor repertoires from COVID-19 patients showed signatures associated with severity of disease" has been updated. This study was first available on 2020-07-02 as Study ID IR-Binder-000001. It has been updated as follows
      • IR-Binder-000001 annotations now include the full input sequence to facilitate data re-use. Sequences were exported with -targetSequences in MiXCR v 3.0.8. The original dataset from 2020-07-02 did not include input sequences. The original data associated with IR-Binder-000001 has been extended to include the full sequence which was left out of the original data load (using MiXCR with -targetSequences).
      • Consistent with the “living repository ” approach described by Schultheiß et al. –, a repository that is continuously fed with new annotated sequence data – a new data cohort has been added (Study ID IR-Binder-000002). It comprises 24 TRB repertoires from 14 subjects.
    • Special Notes: When the authors re-annotated IR-Binder-000001 to obtain full sequences, the annotations of some IGH samples changed in terms of both number of sequences and gene calls; these differences were approved by authors. Data accessed through the iReceptor Gateway prior to 2021-05-18 would have retrieved the original annotations, data accessed after 2021-05-18 will retrieve the new annotations. The table below documents affected samples (total # of sequences and % of annotations with different gene calls (V, D, and/or J), relative to the original file). The % difference ranges from 12-58% (average = 18%). For sample Pt-3-1 (58% difference), the majority of difference (87%) was due to IGHV1-69*13 calls being changed to IGHV1-69*01. All other samples appeared less dominated by IGHV1-69 in terms of both gene calls and gene calls changed. These differences likely arose from the challenge of computationally assigning highly variable sequence regions (having undergone somatic hypermutation) to highly similar IGHV1-69 reference alleles (only 2 SNPs differentiate *01, *12, and *13).