PMC:7307149 / 15479-16539 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T99","span":{"begin":61,"end":64},"obj":"Body_part"},{"id":"T100","span":{"begin":345,"end":348},"obj":"Body_part"},{"id":"T101","span":{"begin":384,"end":387},"obj":"Body_part"},{"id":"T102","span":{"begin":448,"end":451},"obj":"Body_part"},{"id":"T103","span":{"begin":461,"end":464},"obj":"Body_part"},{"id":"T104","span":{"begin":478,"end":481},"obj":"Body_part"},{"id":"T105","span":{"begin":503,"end":506},"obj":"Body_part"},{"id":"T106","span":{"begin":516,"end":519},"obj":"Body_part"},{"id":"T107","span":{"begin":533,"end":536},"obj":"Body_part"},{"id":"T108","span":{"begin":875,"end":878},"obj":"Body_part"}],"attributes":[{"id":"A99","pred":"fma_id","subj":"T99","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A100","pred":"fma_id","subj":"T100","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A101","pred":"fma_id","subj":"T101","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A102","pred":"fma_id","subj":"T102","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A103","pred":"fma_id","subj":"T103","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A104","pred":"fma_id","subj":"T104","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A105","pred":"fma_id","subj":"T105","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A106","pred":"fma_id","subj":"T106","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A107","pred":"fma_id","subj":"T107","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A108","pred":"fma_id","subj":"T108","obj":"http://purl.org/sig/ont/fma/fma84795"}],"text":"Finally, we acknowledge that nearly all individuals have two HLA-A/B/C haplotypes constituting as few as three but as many as six distinct alleles, potentially buffering against the lack of presentation from a single poorly presenting allele. We sought to determine whether allele-specific variability in SARS-CoV-2 presentation extends to full HLA haplotypes and to whole individual HLA genotypes. For six representative alleles with the highest (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) and lowest (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) predicted capacity for SARS-CoV-2 epitope presentation, these differences remain significant at the haplotype level, albeit with wide variability in presentation among different haplotypes (Fig. 6). Haplotype-level data for all 145 alleles are included in Fig. S5 and Data File S2. We then identified 3,382 individuals with full HLA genotype data and noted wide variability in their capacity to present peptides from the SARS-CoV-2 proteome, albeit with a small minority of individuals at either extreme (Fig. S6)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T69","span":{"begin":305,"end":313},"obj":"Disease"},{"id":"T70","span":{"begin":569,"end":577},"obj":"Disease"},{"id":"T71","span":{"begin":967,"end":975},"obj":"Disease"}],"attributes":[{"id":"A69","pred":"mondo_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A70","pred":"mondo_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A71","pred":"mondo_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Finally, we acknowledge that nearly all individuals have two HLA-A/B/C haplotypes constituting as few as three but as many as six distinct alleles, potentially buffering against the lack of presentation from a single poorly presenting allele. We sought to determine whether allele-specific variability in SARS-CoV-2 presentation extends to full HLA haplotypes and to whole individual HLA genotypes. For six representative alleles with the highest (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) and lowest (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) predicted capacity for SARS-CoV-2 epitope presentation, these differences remain significant at the haplotype level, albeit with wide variability in presentation among different haplotypes (Fig. 6). Haplotype-level data for all 145 alleles are included in Fig. S5 and Data File S2. We then identified 3,382 individuals with full HLA genotype data and noted wide variability in their capacity to present peptides from the SARS-CoV-2 proteome, albeit with a small minority of individuals at either extreme (Fig. S6)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T161","span":{"begin":65,"end":66},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T162","span":{"begin":67,"end":68},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T163","span":{"begin":208,"end":209},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T164","span":{"begin":452,"end":453},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T165","span":{"begin":465,"end":466},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T166","span":{"begin":507,"end":508},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T167","span":{"begin":520,"end":521},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T168","span":{"begin":807,"end":809},"obj":"http://purl.obolibrary.org/obo/CLO_0008933"},{"id":"T169","span":{"begin":824,"end":826},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T170","span":{"begin":824,"end":826},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"},{"id":"T171","span":{"begin":949,"end":957},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T172","span":{"begin":1000,"end":1001},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T173","span":{"begin":1042,"end":1049},"obj":"http://www.ebi.ac.uk/efo/EFO_0000876"}],"text":"Finally, we acknowledge that nearly all individuals have two HLA-A/B/C haplotypes constituting as few as three but as many as six distinct alleles, potentially buffering against the lack of presentation from a single poorly presenting allele. We sought to determine whether allele-specific variability in SARS-CoV-2 presentation extends to full HLA haplotypes and to whole individual HLA genotypes. For six representative alleles with the highest (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) and lowest (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) predicted capacity for SARS-CoV-2 epitope presentation, these differences remain significant at the haplotype level, albeit with wide variability in presentation among different haplotypes (Fig. 6). Haplotype-level data for all 145 alleles are included in Fig. S5 and Data File S2. We then identified 3,382 individuals with full HLA genotype data and noted wide variability in their capacity to present peptides from the SARS-CoV-2 proteome, albeit with a small minority of individuals at either extreme (Fig. S6)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T92","span":{"begin":580,"end":587},"obj":"Chemical"},{"id":"T93","span":{"begin":807,"end":809},"obj":"Chemical"},{"id":"T94","span":{"begin":824,"end":826},"obj":"Chemical"},{"id":"T95","span":{"begin":949,"end":957},"obj":"Chemical"}],"attributes":[{"id":"A92","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A93","pred":"chebi_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/CHEBI_29386"},{"id":"A94","pred":"chebi_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A95","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"}],"text":"Finally, we acknowledge that nearly all individuals have two HLA-A/B/C haplotypes constituting as few as three but as many as six distinct alleles, potentially buffering against the lack of presentation from a single poorly presenting allele. We sought to determine whether allele-specific variability in SARS-CoV-2 presentation extends to full HLA haplotypes and to whole individual HLA genotypes. For six representative alleles with the highest (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) and lowest (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) predicted capacity for SARS-CoV-2 epitope presentation, these differences remain significant at the haplotype level, albeit with wide variability in presentation among different haplotypes (Fig. 6). Haplotype-level data for all 145 alleles are included in Fig. S5 and Data File S2. We then identified 3,382 individuals with full HLA genotype data and noted wide variability in their capacity to present peptides from the SARS-CoV-2 proteome, albeit with a small minority of individuals at either extreme (Fig. S6)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"298","span":{"begin":61,"end":68},"obj":"Gene"},{"id":"299","span":{"begin":448,"end":453},"obj":"Gene"},{"id":"300","span":{"begin":461,"end":466},"obj":"Gene"},{"id":"301","span":{"begin":478,"end":483},"obj":"Gene"},{"id":"302","span":{"begin":503,"end":508},"obj":"Gene"},{"id":"303","span":{"begin":516,"end":521},"obj":"Gene"},{"id":"304","span":{"begin":533,"end":538},"obj":"Gene"},{"id":"305","span":{"begin":305,"end":315},"obj":"Species"},{"id":"306","span":{"begin":569,"end":579},"obj":"Species"},{"id":"307","span":{"begin":967,"end":977},"obj":"Species"}],"attributes":[{"id":"A298","pred":"tao:has_database_id","subj":"298","obj":"Gene:3105"},{"id":"A299","pred":"tao:has_database_id","subj":"299","obj":"Gene:3105"},{"id":"A300","pred":"tao:has_database_id","subj":"300","obj":"Gene:3106"},{"id":"A301","pred":"tao:has_database_id","subj":"301","obj":"Gene:3107"},{"id":"A302","pred":"tao:has_database_id","subj":"302","obj":"Gene:3105"},{"id":"A303","pred":"tao:has_database_id","subj":"303","obj":"Gene:3106"},{"id":"A304","pred":"tao:has_database_id","subj":"304","obj":"Gene:3107"},{"id":"A305","pred":"tao:has_database_id","subj":"305","obj":"Tax:2697049"},{"id":"A306","pred":"tao:has_database_id","subj":"306","obj":"Tax:2697049"},{"id":"A307","pred":"tao:has_database_id","subj":"307","obj":"Tax:2697049"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Finally, we acknowledge that nearly all individuals have two HLA-A/B/C haplotypes constituting as few as three but as many as six distinct alleles, potentially buffering against the lack of presentation from a single poorly presenting allele. We sought to determine whether allele-specific variability in SARS-CoV-2 presentation extends to full HLA haplotypes and to whole individual HLA genotypes. For six representative alleles with the highest (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) and lowest (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) predicted capacity for SARS-CoV-2 epitope presentation, these differences remain significant at the haplotype level, albeit with wide variability in presentation among different haplotypes (Fig. 6). Haplotype-level data for all 145 alleles are included in Fig. S5 and Data File S2. We then identified 3,382 individuals with full HLA genotype data and noted wide variability in their capacity to present peptides from the SARS-CoV-2 proteome, albeit with a small minority of individuals at either extreme (Fig. S6)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T86","span":{"begin":243,"end":398},"obj":"Sentence"},{"id":"T87","span":{"begin":399,"end":744},"obj":"Sentence"},{"id":"T88","span":{"begin":745,"end":827},"obj":"Sentence"},{"id":"T89","span":{"begin":828,"end":1060},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Finally, we acknowledge that nearly all individuals have two HLA-A/B/C haplotypes constituting as few as three but as many as six distinct alleles, potentially buffering against the lack of presentation from a single poorly presenting allele. We sought to determine whether allele-specific variability in SARS-CoV-2 presentation extends to full HLA haplotypes and to whole individual HLA genotypes. For six representative alleles with the highest (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) and lowest (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) predicted capacity for SARS-CoV-2 epitope presentation, these differences remain significant at the haplotype level, albeit with wide variability in presentation among different haplotypes (Fig. 6). Haplotype-level data for all 145 alleles are included in Fig. S5 and Data File S2. We then identified 3,382 individuals with full HLA genotype data and noted wide variability in their capacity to present peptides from the SARS-CoV-2 proteome, albeit with a small minority of individuals at either extreme (Fig. S6)."}