Table_1_High-Throughput MICA/B Genotyping of Over Two Million Samples: Workflow and Allele Frequencies.XLSX

MICA and MICB are ligands of the NKG2D receptor and thereby influence NK and T cell activity. MICA/B gene polymorphisms, expression levels and the amount of soluble MICA/B in the serum have been linked to autoimmune diseases, infections, and cancer. In hematopoietic stem cell transplantation, MICA matching between donor and patient has been correlated with reduced acute and chronic graft-vs.-host disease and improved survival. Hence, we developed an extremely cost-efficient high-throughput workflow for genotyping MICA/B for newly registered potential stem cell donors. Since mid-2017, we have genotyped over two million samples using NGS amplicon sequencing for MICA/B exons 2–5. In donors of German origin, MICA*008 is the most common MICA allele with a frequency of 42.3%. It is followed by MICA*002 (11.7%) and MICA*009 (8.8%). The three most common MICB alleles are MICB*005 (43.9%), MICB*004 (21.7%), and MICB*002 (18.9%). In general, MICB is less diverse than MICA and only 6 alleles, instead of 15, account for a cumulative allele frequency of 99.5%. In 0.5% of the samples we observed at least one allele of MICA or MICB which has so far not been reported to the IPD/IMGT-HLA database. By providing MICA/B typed voluntary donors, clinicians become empowered to include MICA/B into their donor selection process to further improve unrelated hematopoietic stem cell transplantation.</p

An unusually high substitution rate in transplant-associated BK polyomavirus <i>in vivo</i> is further concentrated in HLA-C-bound viral peptides - Fig 4

Fraction of amino acid substitutions within and outside of predicted epitopes presented by HLA-A, -B and -C molecules across individuals. The detected amino acid substitutions of a viral population were mapped onto reference proteins and the fraction of mutated amino acids within and outside of predicted epitopes of each viral protein and hosts HLA allele were calculated for each viral population found in patient and donor respectively. The fraction of substituted amino acids within HLA-A and -B presented epitopes (yellow) is significantly lower compared with the fraction outside (blue), while the fraction of amino acid substitutions in HLA-C binding epitopes is significantly higher compared with the fraction outside.</p

Maximum likelihood phylogenetic trees of BK polyomavirus.

Three major groups are found: genotype I in blue, a single group including genotypes II/III in red, and genotype IV in green. (A) Unrooted ML phylogenetic tree with 309 complete genome published sequences retrieved from NCBI. (B) Unrooted ML phylogenetic tree with 309 VP1 gene sequences retrieved from NCBI. (C) Unrooted ML phylogenetic tree with 225 complete genome consensus sequences obtained in this study by next-generation sequencing and one reference strain of each genotype and subtype. Reference strains are marked with dots (Ia, Ib1, Ib2, Ic, II, III, IVa1, IVa2, IVb1, IVb2, IVc1, IVc2).</p

Distribution of the normalized dN-dS per codon among proteins.

The six proteins are represented (Agnoprotein, VP1 to VP3, large T antigen “LTA” and small t antigen “stA”). Non-significant values are shown in blue, and significant values in red (positive values for positive selection and negative values for purifying selection, two-tailed binomial distribution). P-values correspond to the Nei-Gojobori test of neutrality for each gene.</p

Genomic evolutionary rates for the major Baltimore groups and BKV.

Substitution rates are given as substitutions per nucleotide site per year (s/s/y). For the major groups (dsDNA: double-stranded DNA viruses—BKV [5, 7, 28] (time span of sequences (TSS) of 29 years (y), 25 y, and 32 y, respectively), JC polyomavirus [27, 31] (TSS 33 y and 13 y, respectively), herpes simplex virus 1 [32, 33] (TSS not available and 21 y, respectively), human papillomavirus 18 [34] (TSS not available), monkeypox virus [35] (TSS 7 y), variola virus [5] (TSS 31 y), varicella zoster virus [5] (TSS 37 y); ssDNA: single-stranded DNA viruses—African cassava mosaic virus [25] (TSS 5 y), banana bunchy top virus [36] (TSS 2 months), human bocavirus [37] (TSS 1 y), human parvovirus B19 [38, 39] (TSS 14 y and 28 y, respectively), porcine circovirus 2 [40] (TSS 27 y), tomato yellow leaf curl virus [41] (TSS 29 y); RT: retroviruses—avian hepatitis B virus [42] (TSS 22 y), human hepatitis B virus [42–44] (TSS 22 y, 25 y and 35 y, respectively); human immunodeficiency virus 1 [45] (TSS 2 y), primate T-cell lymphotropic virus [45] (TSS 2 y); dsRNA: double-stranded RNA viruses—bluetongue virus [46] (TSS 48 y), human rotavirus [47] (TSS 16 y), homalodisca vitripennis virus [48] (TSS 2 y); ss(-)RNA: single-stranded RNA viruses with negative polarity–Ebola virus [49] (TSS 4 months), fever, thrombocytopenia and leukocytopenia syndrome virus [50] (TSS 4 y), influenza A virus [51, 52] (TSS 28 y and 1 y, respectively), hepatitis delta virus [53] (TSS 3 y), human respiratory syncytial virus [54] (TSS 10 y), rabies virus [55] (TSS 30 y), rift valley fever virus [56] (TSS 10 y); and ss(+)RNA: single-stranded RNA viruses with positive polarity—avian coronavirus [57] (TSS 41 y), barley yellow dwarf virus [58] (TSS 2 y), dengue virus [59](TSS 29 y), foot-and-mouth disease virus [60] (TSS 75 y), hepatitis A virus [61] (TSS 13 y), hepatitis C virus [62] (TSS 20 y), Japanese encephalitis virus [63] (TSS 60 y), Middle East respiratory syndrome coronavirus [64](TSS 4 months), porcine reproductive and respiratory syndrome virus [65] (TSS 3 y), rubella virus [66] (TSS not available), severe acute respiratory syndrome coronavirus [67] (TSS 4 months), St. Louis encephalitis virus [68] (TSS 46 y), Venezuelan equine encephalitis virus [69] (TSS 54 y)). Each point represents the value of a previously published genomic evolutionary rate (note that for some references, more than one substitution rate is represented in the caption). Red circles represent short time span estimates ( 5 years). Medians with interquartile ranges are indicated. In the case of the inter- and intra-host genomic evolutionary rates of BKV, the values are represented as a range of values obtained in this study.</p

Supplementary Data from Matrix-Targeting Immunotherapy Controls Tumor Growth and Spread by Switching Macrophage Phenotype

Supplementary figures and table</p