Improved Graft Function following Desensitization of Anti-AT1R and Autoantibodies in a Heart Transplant Recipient Negative for Donor-Specific Antibodies with Antibody-Mediated Rejection: A Case Report.

HLA donor-specific antibodies (DSAs) pre and post transplant increase the risk of antibody-mediated rejection (AMR) and lead to poor graft survival. Increasing data exist to support the involvement of non-HLA antibodies in triggering an immunological response. The development of non-HLA antibodies specific for AT1R is associated with poor clinical outcomes in orthotopic heart transplant recipients. This case presents an investigation of non-HLA antibodies in a 56-year-old female heart transplant recipient diagnosed with AMR in the absence of DSAs.

Chimerism Testing by Next Generation Sequencing for Detection of Engraftment and Early Disease Relapse in Allogeneic Hematopoietic Cell Transplantation and an Overview of NGS Chimerism Studies.

Chimerism monitoring after allogenic Hematopoietic Cell Transplantation (allo-HCT) is critical to determine how well donor cells have engrafted and to detect relapse for early therapeutic intervention. The aim of this study was to establish and detect mixed chimerism and minimal residual disease using Next Generation Sequencing (NGS) testing for the evaluation of engraftment and the detection of early relapse after allo-HCT. Our secondary aim was to compare the data with the existing laboratory method based on Short Tandem Repeat (STR) analysis. One hundred and seventy-four DNA specimens from 46 individuals were assessed using a commercially available kit for NGS, AlloSeq HCT NGS (CareDx), and the STR-PCR assay. The sensitivity, precision, and quantitative accuracy of the assay were determined using artificially created chimeric constructs. The accuracy and linearity of the assays were evaluated in 46 post-transplant HCT samples consisting of 28 levels of mixed chimerism, which ranged from 0.3-99.7%. There was a 100% correlation between NGS and STR-PCR chimerism methods. In addition, 100% accuracy was attained for the two external proficiency testing surveys (ASHI EMO). The limit of detection or sensitivity of the NGS assay in artificially made chimerism mixtures was 0.3%. We conducted a review of all NGS chimerism studies published online, including ours, and concluded that NGS-based chimerism analysis using the AlloSeq HCT assay is a sensitive and accurate method for donor-recipient chimerism quantification and minimal residual disease relapse detection in patients after allo-HCT compared to STR-PCR assay.

Characterization of the novel HLA-B*57:169 allele by next generation sequencing.

HLA-B*57:169 differs from HLA-B*57:01:01:12 by one nucleotide substitution at position 2512, codon 320 located in exon 6.

Full genomic sequence of the HLA-DRB3*02:32 allele by Single Molecule Real-time Sequencing Technology.

Full-length sequence covers the 5'-untranslated region (UTR), all introns and exons and the 3' UTR.

Characterization of the novel HLA-C*05:01:72 allele by next generation sequencing.

Full-length sequence of HLA-C*05:01:72 covers the 5'-untranslated region (UTR), all introns and exons and the 3' UTR.

Characterization of the novel HLA-DPA1*02:03:05 allele by next generation sequencing.

HLA-DPA1*02:03:05 differs from HLA-DPA*02:03:04 by three nucleotide substitution located in exon 3.

Characterization of the novel HLA-DPA1*01:144 allele by next generation sequencing.

HLA-DPA1*01:144 differs from HLA-DPA*01:03:01:04 by one nucleotide substitution at position 44, codon-17 located in exon 1.

Full-length genomic sequence of HLA-DQA1*02:19 by next generation sequencing.

Full-length sequence of HLA-DQA1*02:19 covers the 5'-untranslated region (UTR), all introns and exons and the 3' UTR.

Characterization of the novel HLA-A*32:172 allele by next generation sequencing.

HLA-A*32:172 differs from HLA-A*32:01:01:01 by one nucleotide substitution at position 1013, codon 314 located in exon 6.

Characterization of the novel HLA-DPB1*04:02:01:40 allele by Oxford nanopore sequencing (ONT) technology.

Full-length sequence of HLA-DPB1*04:02:01:40 covers the 5'-untranslated region (UTR), all introns and exons and the 3' UTR.

Full genomic sequence of the HLA-DRB3*03:46 allele identified by third generation sequencing.

Full-length sequence of HLA-DRB3*03:46 covers the 5'-untranslated region (UTR), all introns and exons and the 3' UTR.

Full genomic sequence of the HLA-DPA1*01:115 allele identified by next generation sequencing.

Full-length sequence of HLA-DPA1*01:115 covers the 5'-untranslated region (UTR), all introns and exons and the 3'-UTR.

Full genomic sequence of the HLA-DRB3*02:22:01 allele by single molecule real-time sequencing technology.

Full-length sequence covers the 5'-untranslated region (UTR), all introns and exons, and the 3' UTR.

Full genomic sequence of the HLA-DPA1*02:46 allele identified by next generation sequencing.

Full-length sequence of HLA-DPA1*02:46 covers the 5'-untranslated region (UTR), all introns and exons and the 3' UTR.

Full genomic sequence of the HLA-C*15:02:03 allele identified by next generation sequencing.

Full-length sequence of HLA-C*15:02:03 covers all introns and exons and the 3' UTR.

Full genomic sequence of the HLA-C*07:308 allele identified by next generation sequencing.

Full-length sequence of HLA-C*07:308 covers the 5'-untranslated region (UTR), all introns and exons and the 3' UTR.

Full genomic sequence of the HLA-DQB1*04:51 allele identified by next-generation sequencing.

Full-length sequence of HLA-DQB1*04:51 covers the 5'-untranslated region (UTR), all introns and exons and the 3'-UTR.

A novel allele, HLA-DPA1*01:87Q identified by next generation sequencing.

A point mutation in Exon 1, 1-3 (ATG>ACG) causes a non-synonymous change to the start codon, which may affect expression.

Characterization of the novel HLA-DPA1*02:72 allele by next generation sequencing.

HLA-DPA1*02:72 differs from HLA-DPA1*02:02:02:01 by one nucleotide substitution at position 4273, codon 86 located in exon 3.

Relevant SARS-CoV-2 Genome Variation through Six Months of Worldwide Monitoring.

Real-time genome monitoring of the SARS-CoV-2 pandemic outbreak is of utmost importance for designing diagnostic tools, guiding antiviral treatment and vaccination strategies. In this study, we present an accurate method for temporal and geographical comparison of mutational events based on GISAID database genome sequencing. Among 42523 SARS-CoV-2 genomes analyzed, we found 23202 variants compared to the reference genome. The Ti/Tv (transition/transversion) ratio was used to filter out possible false-positive errors. Transition mutations generally occurred more frequently than transversions. Our clustering analysis revealed remarkable hotspot mutation patterns for SARS-CoV-2. Mutations were clustered based on how their frequencies changed over time according to each geographical location. We observed some clusters showing a clear variation in mutation frequency and continuously evolving in the world. However, many mutations appeared in specific periods without a clear pattern over time. Various important nonsynonymous mutations were observed, mainly in Oceania and Asia. More than half of these mutations were observed only once. Four hotspot mutations were found in all geographical locations at least once: T265I (NSP2), P314L (NSP12), D614G (S), and Q57H (ORF3a). The current analysis of SARS-CoV-2 genomes provides valuable information on the geographical and temporal mutational evolution of SARS-CoV-2.