{ "source": { "repository": "https://github.com/iskandr/osteosarc", "input_id": "af299e74992360e7892c7effbe163bcec7d61d044981807b2dc100bca55d845d", "snapshot": { "id": "efb65d4b683bda162879c86c0ea889afcc64704b5228224c061109f306503b91", "name": "2026-09-28" }, "osteosarc_version": "0.15.0", "membership_policy": "union of index vaccine_count, source_variants flags, and vaccine-overlap membership", "provenance": { "aliases": { "tumor_scrnaseq_T1.bam": "kamil/tumor/output/T1/outs/per_sample_outs/T1/sample_alignments.bam", "tumor_scrnaseq_T2.bam": "kamil/tumor/output/T2/outs/per_sample_outs/T2/sample_alignments.bam", "tumor_scrnaseq_T3.bam": "kamil/tumor/output/T3/outs/per_sample_outs/T3/sample_alignments.bam", "tumor_scrnaseq_T3_CD45neg.bam": "kamil/tumor/output/T3_CD45neg/outs/per_sample_outs/T3_CD45neg/sample_alignments.bam" }, "aliases_basis": "Explicit T1/T2/T3/CD45neg CellRanger sample paths in bams.json", "allele_resolutions_sha256": "ade4b130e4031fa853c961798418df5c5ae0208e2ea4f2d2f981276a2fc4c18d", "corrections": "osteosarc curated snapshot; corrections retained per row/variant", "curation_sha256": "6eb51bb504bd5dfae0090bdbdddfa70346ab7cf27b637eae8a98c6a9044f373c", "sources": { "bam_metadata": { "retrieved_at": "2026-09-28T03:09:30.841374+00:00", "sha256": "1a1fd0d84a2027988aba0f996a5908329bbc33bc3671c96c4323f3e3c78c9c6a", "size": 23005, "url": "https://gitlab.com/slowkow/osteosarc.com/-/raw/main/scripts/data/bam-metadata-consolidated.tsv" }, "bams": { "retrieved_at": "2026-09-28T03:09:24.588217+00:00", "sha256": "7d90c733a3cb157ff70e9302a7f7ea302cc5cac0cfd244b6d65a24d7b245e2e7", "size": 45478, "url": "https://osteosarc.com/bams/bams.json" }, "source_variants": { "retrieved_at": "2026-09-28T03:09:30.195437+00:00", "sha256": "f90e2d8c896cb45a002610f233212ed1b28d0e56891365590947d31485947e16", "size": 6411344, "url": "https://gitlab.com/slowkow/osteosarc.com/-/raw/main/src/data/variants.json" }, "specimens": { "retrieved_at": "2026-09-28T03:09:33.919413+00:00", "sha256": "c42c48b41e4b29a7c7feaa60d9401e8ccfb1faf30ac24ec5011945b32016ff56", "size": 6990, "url": "https://gitlab.com/slowkow/osteosarc.com/-/raw/main/scripts/data/samples-consolidated.tsv" }, "vaccine_overlap": { "retrieved_at": "2026-09-28T03:09:29.118440+00:00", "sha256": "3572f7ded10bc10e4dae92805210e858a024449e037e7f47320a05c93991053f", "size": 33292, "url": "https://osteosarc.com/data/vaccine_overlap.json" }, "vaf_columns": { "retrieved_at": "2026-09-28T03:09:28.375868+00:00", "sha256": "935507a2cf33688243b92285e5107c6e814aee635c5ce5f8963f2b8f3ec0535f", "size": 1482, "url": "https://osteosarc.com/variants/variant_vafs_long.columns.tsv" }, "vafs": { "retrieved_at": "2026-09-28T03:09:27.703470+00:00", "sha256": "e5627735897ba62d19c207e40d7e8516c81bd0fc793a339c8aa5138ab63f3913", "size": 1631141, "url": "https://osteosarc.com/variants/variant_vafs_long.tsv" }, "variant_index": { "retrieved_at": "2026-09-28T03:09:26.857774+00:00", "sha256": "91036401893aa14ad69091825d3636ce0990bdd47cc5e2fca297ddfd7acddb48", "size": 545438, "url": "https://osteosarc.com/variants/" } } } }, "selection_policy": "Keep published_vaccine_peptides entries with a nonempty sequence and nonempty in_vaccines. Include a variant if it has at least one such entry. Preserve full peptides and mRNA minimal epitopes as recorded; do not include pVACtools predictions or peptides without vaccine membership. Membership does not establish expression or RNA recovery.", "peptide_scoring_policy": "reference_supported_terminal_tags_v2", "peptide_context_sha256": "4ae72fa99211384dc5fcb081ac8e07a99a7673ea62af93cae0369900e26be957", "n_catalogue_variants": 51, "n_variants": 36, "n_peptides": 78, "n_unique_sequences": 77, "variants": [ { "variant_id": "ZNF436-chr1-23362762", "gene": "ZNF436", "chrom": "chr1", "pos": 23362762, "ref": "G", "alt": "C", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ser207Cys", "consequence": "missense_variant", "vaccines": [ "CeGaT", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "ZNF436-chr1-23362762.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 15, "sequence": "RTHTGERPYDCNECGKSFGRSCHLIQHQTIH", "scoring_region": { "sequence": "RTHTGERPYDCNECGKSFGRSCHLIQHQTIH", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "ZNF436-chr1-23362762.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "KSFGRSCHL", "scoring_region": { "sequence": "KSFGRSCHL", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "ZNF436-chr1-23362762.peptide-3", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 1, "sequence": "GKSFGRSCHLIQHQTI", "scoring_region": { "sequence": "GKSFGRSCHLIQHQTI", "start": 0, "end": 16, "terminal_tags": [] } } ] }, { "variant_id": "VPS72-chr1-151185547", "gene": "VPS72", "chrom": "chr1", "pos": 151185547, "ref": "T", "alt": "C", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Lys115Arg", "consequence": "missense_variant", "vaccines": [ "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "VPS72-chr1-151185547.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 20, "sequence": "KSLRPRKVNTPAGSSQKAREERALLPLELQD", "scoring_region": { "sequence": "KSLRPRKVNTPAGSSQKAREERALLPLELQD", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "VPS72-chr1-151185547.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "ERALLPLEL", "scoring_region": { "sequence": "ERALLPLEL", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "VPS72-chr1-151185547.peptide-3", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 8, "sequence": "GSSQKAREERALLPLELQDDGSDSRKS", "scoring_region": { "sequence": "GSSQKAREERALLPLELQDDGSDSRKS", "start": 0, "end": 27, "terminal_tags": [] } } ] }, { "variant_id": "PIP5K1A-chr1-151242178", "gene": "PIP5K1A", "chrom": "chr1", "pos": 151242178, "ref": "AG", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Gly474fs", "consequence": "frameshift_variant", "vaccines": [ "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "PIP5K1A-chr1-151242178.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 10, "sequence": "FRSGSSFSRRAAPVATPALLTSHRSLGNTRHK", "scoring_region": { "sequence": "FRSGSSFSRRAAPVATPALLTSHRSLGNTRHK", "start": 0, "end": 32, "terminal_tags": [] } }, { "peptide_id": "PIP5K1A-chr1-151242178.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "AAPVATPAL", "scoring_region": { "sequence": "AAPVATPAL", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "PIP5K1A-chr1-151242178.peptide-3", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 6, "sequence": "SSFSRRAAPVATPALLTSHR", "scoring_region": { "sequence": "SSFSRRAAPVATPALLTSHR", "start": 0, "end": 20, "terminal_tags": [] } } ] }, { "variant_id": "PRRC2C-chr1-171540477", "gene": "PRRC2C", "chrom": "chr1", "pos": 171540477, "ref": "G", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Arg1004Met", "consequence": "missense_variant", "vaccines": [ "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "PRRC2C-chr1-171540477.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 15, "sequence": "YKSKSETRWGPRPSSNRMEEVNDRPVRR", "scoring_region": { "sequence": "YKSKSETRWGPRPSSNRMEEVNDRPVRR", "start": 0, "end": 28, "terminal_tags": [] } }, { "peptide_id": "PRRC2C-chr1-171540477.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "NRMEEVNDR", "scoring_region": { "sequence": "NRMEEVNDR", "start": 0, "end": 9, "terminal_tags": [] } } ] }, { "variant_id": "CENPL-chr1-173811223", "gene": "CENPL", "chrom": "chr1", "pos": 173811223, "ref": "G", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Pro26His", "consequence": "missense_variant", "vaccines": [ "JLF V3" ], "published_vaccine_peptides": [ { "peptide_id": "CENPL-chr1-173811223.peptide-1", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "SSRPEDYFIGATHLQKRLESVRK", "scoring_region": { "sequence": "SSRPEDYFIGATHLQKRLESVRK", "start": 0, "end": 23, "terminal_tags": [] } } ] }, { "variant_id": "ASPM-chr1-197102716", "gene": "ASPM", "chrom": "chr1", "pos": 197102716, "ref": "C", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Gly2179Arg", "consequence": "missense_variant", "vaccines": [ "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "ASPM-chr1-197102716.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 18, "sequence": "REKYLTILKAVKVLQASFRRVRVRRTLRKMQ", "scoring_region": { "sequence": "REKYLTILKAVKVLQASFRRVRVRRTLRKMQ", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "ASPM-chr1-197102716.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "RRVRVRRTLR", "scoring_region": { "sequence": "RRVRVRRTLR", "start": 0, "end": 10, "terminal_tags": [] } } ] }, { "variant_id": "DYNC1H1-chr14-101980529", "gene": "DYNC1H1", "chrom": "chr14", "pos": 101980529, "ref": "G", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Val314Ile", "consequence": "missense_variant", "vaccines": [ "CeGaT", "JLF V2", "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "DYNC1H1-chr14-101980529.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 11, "sequence": "VLLTLDILKHGKRFHATISFDTDTGLKQAL", "scoring_region": { "sequence": "VLLTLDILKHGKRFHATISFDTDTGLKQAL", "start": 0, "end": 30, "terminal_tags": [] } }, { "peptide_id": "DYNC1H1-chr14-101980529.peptide-2", "experiments": [ { "additional_testing": "", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15)", "peptide_id": "P10-3.DYNC1H1", "pool": "S3", "result": "Negative", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "KRFHATISF", "scoring_region": { "sequence": "KRFHATISF", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "DYNC1H1-chr14-101980529.peptide-3", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.52.DYNC1H1", "pool": "L2", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038R.MT.52.DYNC1H1.2", "pool": "Pool 1", "result": "Positive (Weak)", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038R.MT.52.DYNC1H1.2", "pool": "", "result": "Positive (Weak)", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "Sent to MUSC for expansion", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.52.DYNC1H1.2", "pool": "NA", "result": "Positive (Strong)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V3", "JLF V2" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 1, "sequence": "GKRFHATISFDTDTGLKQALETKK", "scoring_region": { "sequence": "GKRFHATISFDTDTGLKQALET", "start": 0, "end": 22, "terminal_tags": [ { "terminus": "C", "start": 22, "end": 24, "sequence": "KK" } ] } }, { "peptide_id": "DYNC1H1-chr14-101980529.peptide-4", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 3, "sequence": "KHGKRFHATISFDTDTGL", "scoring_region": { "sequence": "KHGKRFHATISFDTDTGL", "start": 0, "end": 18, "terminal_tags": [] } } ] }, { "variant_id": "SPG11-chr15-44660435", "gene": "SPG11", "chrom": "chr15", "pos": 44660435, "ref": "T", "alt": "C", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ile147Val", "consequence": "missense_variant", "vaccines": [ "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "SPG11-chr15-44660435.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 13, "sequence": "ATILYSCSREALQKLIDDQDVSISLLSLRIL", "scoring_region": { "sequence": "ATILYSCSREALQKLIDDQDVSISLLSLRIL", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "SPG11-chr15-44660435.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "KLIDDQDVSI", "scoring_region": { "sequence": "KLIDDQDVSI", "start": 0, "end": 10, "terminal_tags": [] } } ] }, { "variant_id": "MYO9A-chr15-71994488", "gene": "MYO9A", "chrom": "chr15", "pos": 71994488, "ref": "T", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Asp523Val", "consequence": "missense_variant", "vaccines": [ "JLF V2" ], "published_vaccine_peptides": [ { "peptide_id": "MYO9A-chr15-71994488.peptide-1", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.53.MYO9A", "pool": "L3", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038R.MT.53.MYO9A.1", "pool": "Pool 1", "result": "Positive (Weak)", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038R.MT.53.MYO9A.1", "pool": "", "result": "Negative", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.53.MYO9A.1", "pool": "NA", "result": "Positive (Strong)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "KKFDWIVFRINHALLNSKVLEHNTK", "scoring_region": { "sequence": "FDWIVFRINHALLNSKVLEHNTK", "start": 2, "end": 25, "terminal_tags": [ { "terminus": "N", "start": 0, "end": 2, "sequence": "KK" } ] } } ] }, { "variant_id": "NR2F2-chr15-96332299", "gene": "NR2F2", "chrom": "chr15", "pos": 96332299, "ref": "G", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Gly65Val", "consequence": "missense_variant", "vaccines": [ "CeGaT", "JLF V2" ], "published_vaccine_peptides": [ { "peptide_id": "NR2F2-chr15-96332299.peptide-1", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.58.NR2F2", "pool": "L3", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.58.NR2F2.2", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "AQTAAGGQGGPGVPGSDKQQQQQHIE", "scoring_region": { "sequence": "AQTAAGGQGGPGVPGSDKQQQQQHIE", "start": 0, "end": 26, "terminal_tags": [] } }, { "peptide_id": "NR2F2-chr15-96332299.peptide-2", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "AGGQGGPGVPGSDKQQQ", "scoring_region": { "sequence": "AGGQGGPGVPGSDKQQQ", "start": 0, "end": 17, "terminal_tags": [] } } ] }, { "variant_id": "KIF1C-chr17-5007293", "gene": "KIF1C", "chrom": "chr17", "pos": 5007293, "ref": "G", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Glu456Lys", "consequence": "missense_variant", "vaccines": [ "JLF V1", "JLF V2" ], "published_vaccine_peptides": [ { "peptide_id": "KIF1C-chr17-5007293.peptide-1", "experiments": [ { "additional_testing": "", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.60.KIF1C", "pool": "L1", "result": "Negative", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038R.MT.60.KIF1C.2", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.60.KIF1C.2", "pool": "NA", "result": "Positive (Weak)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2", "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "TEKIIAELNKTWEEKLRKTEA", "scoring_region": { "sequence": "TEKIIAELNKTWEEKLRKTEA", "start": 0, "end": 21, "terminal_tags": [] } } ] }, { "variant_id": "NME1-chr17-51154443", "gene": "NME1", "chrom": "chr17", "pos": 51154443, "ref": "G", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Gly24Arg", "consequence": "intron_variant", "vaccines": [ "CeGaT" ], "published_vaccine_peptides": [ { "peptide_id": "NME1-chr17-51154443.peptide-1", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "PPISSCDTRTMAN", "scoring_region": { "sequence": "PPISSCDTRTMAN", "start": 0, "end": 13, "terminal_tags": [] } } ] }, { "variant_id": "MYO15B-chr17-75589953", "gene": "MYO15B", "chrom": "chr17", "pos": 75589953, "ref": "GC", "alt": "G", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "fs", "consequence": "frameshift_variant", "vaccines": [ "JLF V1", "JLF V2" ], "published_vaccine_peptides": [ { "peptide_id": "MYO15B-chr17-75589953.peptide-1", "experiments": [ { "additional_testing": "", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038.MT.67.MYO15B", "pool": "L1", "result": "Negative", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038R.MT.67.MYO15B.1", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.67.MYO15B.1", "pool": "NA", "result": "Positive (Weak)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2", "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "AGRRAQAPTRVLGLAPP", "scoring_region": { "sequence": "AGRRAQAPTRVLGLAPP", "start": 0, "end": 17, "terminal_tags": [] } } ] }, { "variant_id": "EPG5-chr18-45925851", "gene": "EPG5", "chrom": "chr18", "pos": 45925851, "ref": "C", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ala869Thr", "consequence": "missense_variant", "vaccines": [ "CeGaT", "JLF V1", "JLF V2" ], "published_vaccine_peptides": [ { "peptide_id": "EPG5-chr18-45925851.peptide-1", "experiments": [ { "additional_testing": "", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.76.EPG5", "pool": "L1", "result": "Negative", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038R.MT.76.EPG5.2", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.76.EPG5.2", "pool": "NA", "result": "Positive (Weak)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "KELPLYLWQPSTSEIAVIRDWKK", "scoring_region": { "sequence": "KELPLYLWQPSTSEIAVIRDW", "start": 0, "end": 21, "terminal_tags": [ { "terminus": "C", "start": 21, "end": 23, "sequence": "KK" } ] } }, { "peptide_id": "EPG5-chr18-45925851.peptide-2", "experiments": [], "in_vaccines": [ "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "KELPLYLWQPSTSEIAVIRD", "scoring_region": { "sequence": "KELPLYLWQPSTSEIAVIRD", "start": 0, "end": 20, "terminal_tags": [] } }, { "peptide_id": "EPG5-chr18-45925851.peptide-3", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "KKSVIRTLSTIDDVEDRENEKGR", "scoring_region": { "sequence": "KKSVIRTLSTIDDVEDRENEKGR", "start": 0, "end": 23, "terminal_tags": [] } } ] }, { "variant_id": "SLC25A12-chr2-171813470", "gene": "SLC25A12", "chrom": "chr2", "pos": 171813470, "ref": "A", "alt": "G", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ile347Thr", "consequence": "missense_variant", "vaccines": [ "CeGaT", "JLF V1", "JLF V2", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "SLC25A12-chr2-171813470.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 14, "sequence": "AYRFTLGSVAGAVGATAVYPTDLVKTRMQNQ", "scoring_region": { "sequence": "AYRFTLGSVAGAVGATAVYPTDLVKTRMQNQ", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "SLC25A12-chr2-171813470.peptide-2", "experiments": [ { "additional_testing": "", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15)", "peptide_id": "P6-2.SLC25A12", "pool": "S2", "result": "Negative", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "ATAVYPTDL", "scoring_region": { "sequence": "ATAVYPTDL", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "SLC25A12-chr2-171813470.peptide-3", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038.MT.8.SLC25A12", "pool": "L2", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038R.MT.8.SLC25A12.3", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038R.MT.8.SLC25A12.3", "pool": "Pool 1", "result": "Positive (Weak)", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038R.MT.8.SLC25A12.3", "pool": "", "result": "Negative", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.8.SLC25A12.3", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2", "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 8, "sequence": "GSVAGAVGATAVYPTDLVKTRMQNQR", "scoring_region": { "sequence": "GSVAGAVGATAVYPTDLVKTRMQNQR", "start": 0, "end": 26, "terminal_tags": [] } }, { "peptide_id": "SLC25A12-chr2-171813470.peptide-4", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 2, "sequence": "VGATAVYPTDLVKTRMQ", "scoring_region": { "sequence": "VGATAVYPTDLVKTRMQ", "start": 0, "end": 17, "terminal_tags": [] } } ] }, { "variant_id": "MAP2-chr2-209694768", "gene": "MAP2", "chrom": "chr2", "pos": 209694768, "ref": "CCTGGGCTACTGTGTGTTCAATAAGTACACAGT", "alt": "CAGGG", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Leu867fs", "consequence": "frameshift_variant", "vaccines": [ "JLF V1", "JLF V2", "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "MAP2-chr2-209694768.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 22, "sequence": "DSQLEDRAHCHHLFKTVRIYQGRVVPFTKALMIKFEEIWPQTFH", "scoring_region": { "sequence": "DSQLEDRAHCHHLFKTVRIYQGRVVPFTKALMIKFEEIWPQTFH", "start": 0, "end": 44, "terminal_tags": [] } }, { "peptide_id": "MAP2-chr2-209694768.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "RVVPFTKAL", "scoring_region": { "sequence": "RVVPFTKAL", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "MAP2-chr2-209694768.peptide-3", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 8, "sequence": "KTVRIYQGRVVPFTKALMIKFEE", "scoring_region": { "sequence": "KTVRIYQGRVVPFTKALMIKFEE", "start": 0, "end": 23, "terminal_tags": [] } }, { "peptide_id": "MAP2-chr2-209694768.peptide-4", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038.MT.14.MAP2", "pool": "L2", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038.MT.14.MAP2.2", "pool": "NA", "result": "Positive (Strong)", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038.MT.14.MAP2.2", "pool": "Pool 1", "result": "Positive (Weak)", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038.MT.14.MAP2.2", "pool": "", "result": "Positive (Weak)", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038.MT.14.MAP2.2", "pool": "NA", "result": "Positive (Strong**)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2", "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 8, "sequence": "KTVRIYQGRVVPFTKALMIKFEEI", "scoring_region": { "sequence": "KTVRIYQGRVVPFTKALMIKFEEI", "start": 0, "end": 24, "terminal_tags": [] } } ] }, { "variant_id": "BTD-chr3-15645183", "gene": "BTD", "chrom": "chr3", "pos": 15645183, "ref": "T", "alt": "G", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Phe445Val", "consequence": "missense_variant", "vaccines": [ "JLF V1", "JLF V2", "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "BTD-chr3-15645183.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 16, "sequence": "YLLYERPTLSKELYALGVVDGLHTVHGTYYI", "scoring_region": { "sequence": "YLLYERPTLSKELYALGVVDGLHTVHGTYYI", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "BTD-chr3-15645183.peptide-2", "experiments": [ { "additional_testing": "", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15)", "peptide_id": "P4-2.BTD", "pool": "S1", "result": "Negative", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "GVVDGLHTV", "scoring_region": { "sequence": "GVVDGLHTV", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "BTD-chr3-15645183.peptide-3", "experiments": [ { "additional_testing": "", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038.MT.19.BTD", "pool": "L1", "result": "Negative", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038R.MT.19.BTD.1", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.19.BTD.1", "pool": "NA", "result": "Positive (Strong)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V3", "JLF V2", "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 11, "sequence": "RPTLSKELYALGVVDGLHTVHGT", "scoring_region": { "sequence": "RPTLSKELYALGVVDGLHTVHGT", "start": 0, "end": 23, "terminal_tags": [] } } ] }, { "variant_id": "PTH1R-chr3-46898732", "gene": "PTH1R", "chrom": "chr3", "pos": 46898732, "ref": "A", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ile237Phe", "consequence": "missense_variant", "vaccines": [ "JLF V3" ], "published_vaccine_peptides": [ { "peptide_id": "PTH1R-chr3-46898732.peptide-1", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "SFMLRAVSFFVKDAVLYSGAKKK", "scoring_region": { "sequence": "SFMLRAVSFFVKDAVLYSGA", "start": 0, "end": 20, "terminal_tags": [ { "terminus": "C", "start": 20, "end": 23, "sequence": "KKK" } ] } } ] }, { "variant_id": "ABI3BP-chr3-100850671", "gene": "ABI3BP", "chrom": "chr3", "pos": 100850671, "ref": "C", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Arg472Met", "consequence": "missense_variant", "vaccines": [ "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "ABI3BP-chr3-100850671.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 17, "sequence": "TATSDRILDSIPPKTSRTLEQPMATLAPSET", "scoring_region": { "sequence": "TATSDRILDSIPPKTSRTLEQPMATLAPSET", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "ABI3BP-chr3-100850671.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "TLEQPMATL", "scoring_region": { "sequence": "TLEQPMATL", "start": 0, "end": 9, "terminal_tags": [] } } ] }, { "variant_id": "ANKRD17-chr4-73097139", "gene": "ANKRD17", "chrom": "chr4", "pos": 73097139, "ref": "C", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Gly1719Arg", "consequence": "missense_variant", "vaccines": [ "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "ANKRD17-chr4-73097139.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 17, "sequence": "PNGKLTVASPKRGQKREERWKEVVRRSKKV", "scoring_region": { "sequence": "PNGKLTVASPKRGQKREERWKEVVRRSKKV", "start": 0, "end": 30, "terminal_tags": [] } }, { "peptide_id": "ANKRD17-chr4-73097139.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "ERWKEVVRR", "scoring_region": { "sequence": "ERWKEVVRR", "start": 0, "end": 9, "terminal_tags": [] } } ] }, { "variant_id": "KDM3B-chr5-138391529", "gene": "KDM3B", "chrom": "chr5", "pos": 138391529, "ref": "C", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Pro633Ser", "consequence": "missense_variant", "vaccines": [ "CeGaT", "JLF V1", "JLF V2" ], "published_vaccine_peptides": [ { "peptide_id": "KDM3B-chr5-138391529.peptide-1", "experiments": [ { "additional_testing": "", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.29.KDM3B", "pool": "L1", "result": "Negative", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038R.MT.29.KDM3B.1", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.29.KDM3B.1", "pool": "NA", "result": "Positive (Strong)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2", "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "HENLFLQPPKLSREESSNPFLAFVEK", "scoring_region": { "sequence": "HENLFLQPPKLSREESSNPFLAFVEK", "start": 0, "end": 26, "terminal_tags": [] } }, { "peptide_id": "KDM3B-chr5-138391529.peptide-2", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "PPKLSREESSNPFLAFV", "scoring_region": { "sequence": "PPKLSREESSNPFLAFV", "start": 0, "end": 17, "terminal_tags": [] } } ] }, { "variant_id": "WWC1-chr5-168399513", "gene": "WWC1", "chrom": "chr5", "pos": 168399513, "ref": "T", "alt": "G", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Val179Gly", "consequence": "missense_variant", "vaccines": [ "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "WWC1-chr5-168399513.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 17, "sequence": "AEIATAKSRVNKLKREMGHLQHELQFKERGF", "scoring_region": { "sequence": "AEIATAKSRVNKLKREMGHLQHELQFKERGF", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "WWC1-chr5-168399513.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "GHLQHELQF", "scoring_region": { "sequence": "GHLQHELQF", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "WWC1-chr5-168399513.peptide-3", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 7, "sequence": "NKLKREMGHLQHELQFKERG", "scoring_region": { "sequence": "NKLKREMGHLQHELQFKERG", "start": 0, "end": 20, "terminal_tags": [] } } ] }, { "variant_id": "H1_2-chr6-26055824", "gene": "H1-2", "chrom": "chr6", "pos": 26055824, "ref": "ACCTTGGGCTTAGCGG", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ala197_Lys201del", "consequence": "inframe_deletion", "vaccines": [ "CeGaT" ], "published_vaccine_peptides": [ { "peptide_id": "H1_2-chr6-26055824.peptide-1", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "AAKAVKPKVVKPKKAA", "scoring_region": { "sequence": "AAKAVKPKVVKPKKAA", "start": 0, "end": 16, "terminal_tags": [] } } ] }, { "variant_id": "CUL9-chr6-43186384", "gene": "CUL9", "chrom": "chr6", "pos": 43186384, "ref": "G", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Asp403Tyr", "consequence": "missense_variant", "vaccines": [ "JLF V2" ], "published_vaccine_peptides": [ { "peptide_id": "CUL9-chr6-43186384.peptide-1", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.33.CUL9", "pool": "L3", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.33.CUL9.1", "pool": "NA", "result": "Positive (Weak)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "RMLDYYEEISAGDEGEFRQSKKK", "scoring_region": { "sequence": "RMLDYYEEISAGDEGEFRQS", "start": 0, "end": 20, "terminal_tags": [ { "terminus": "C", "start": 20, "end": 23, "sequence": "KKK" } ] } } ] }, { "variant_id": "ADGRF5-chr6-46856758", "gene": "ADGRF5", "chrom": "chr6", "pos": 46856758, "ref": "T", "alt": "C", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Asn1279Ser", "consequence": "missense_variant", "vaccines": [ "JLF V2" ], "published_vaccine_peptides": [ { "peptide_id": "ADGRF5-chr6-46856758.peptide-1", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.34.ADGRF5", "pool": "L3", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.34.ADGRF5.1", "pool": "NA", "result": "Positive (Weak)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "VQEALLSKFSLSRWSSQHSKST", "scoring_region": { "sequence": "VQEALLSKFSLSRWSSQHSKST", "start": 0, "end": 22, "terminal_tags": [] } } ] }, { "variant_id": "CD109-chr6-73818405", "gene": "CD109", "chrom": "chr6", "pos": 73818405, "ref": "G", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Arg1310Met", "consequence": "missense_variant", "vaccines": [ "JLF V3" ], "published_vaccine_peptides": [ { "peptide_id": "CD109-chr6-73818405.peptide-1", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "SFSGPGMSGMALMEVNLLSGKKK", "scoring_region": { "sequence": "SFSGPGMSGMALMEVNLLSG", "start": 0, "end": 20, "terminal_tags": [ { "terminus": "C", "start": 20, "end": 23, "sequence": "KKK" } ] } } ] }, { "variant_id": "CDC40-chr6-110228838", "gene": "CDC40", "chrom": "chr6", "pos": 110228838, "ref": "G", "alt": "C", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Trp475Ser", "consequence": "missense_variant", "vaccines": [ "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "CDC40-chr6-110228838.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 10, "sequence": "EPSMHSMPAVTLSPNGKSLACQSMDNQILIF", "scoring_region": { "sequence": "EPSMHSMPAVTLSPNGKSLACQSMDNQILIF", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "CDC40-chr6-110228838.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "TLSPNGKSL", "scoring_region": { "sequence": "TLSPNGKSL", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "CDC40-chr6-110228838.peptide-3", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 6, "sequence": "HSMPAVTLSPNGKSLACQSMDNQKK", "scoring_region": { "sequence": "HSMPAVTLSPNGKSLACQSMDNQ", "start": 0, "end": 23, "terminal_tags": [ { "terminus": "C", "start": 23, "end": 25, "sequence": "KK" } ] } } ] }, { "variant_id": "TECPR1-chr7-98241127", "gene": "TECPR1", "chrom": "chr7", "pos": 98241127, "ref": "TG", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Thr259fs", "consequence": "frameshift_variant", "vaccines": [ "CeGaT", "JLF V1", "JLF V2", "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "TECPR1-chr7-98241127.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 75, "sequence": "VQISCGPHDLLWAHSGRDRPWSGKESTGAIPKEVPGPSWSLLDLKTGSCTSRWESAWSGLSPRTGRCGSEEASTLTIPAAPVGLRWLVR", "scoring_region": { "sequence": "VQISCGPHDLLWAHSGRDRPWSGKESTGAIPKEVPGPSWSLLDLKTGSCTSRWESAWSGLSPRTGRCGSEEASTLTIPAAPVGLRWLVR", "start": 0, "end": 89, "terminal_tags": [] } }, { "peptide_id": "TECPR1-chr7-98241127.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "TIPAAPVGL", "scoring_region": { "sequence": "TIPAAPVGL", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "TECPR1-chr7-98241127.peptide-3", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038.MT.38.TECPR1.1", "pool": "L2", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038R.MT.38.TECPR1.1", "pool": "NA", "result": "Positive (Weak)", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.38.TECPR1.1", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V3", "JLF V2", "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 8, "sequence": "GSEEASTLTIPAAPVGLRWLVR", "scoring_region": { "sequence": "GSEEASTLTIPAAPVGLRWLVR", "start": 0, "end": 22, "terminal_tags": [] } }, { "peptide_id": "TECPR1-chr7-98241127.peptide-4", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038.MT.38.TECPR1.2", "pool": "L2", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2023-09-22", "experiment": "UNC Immune Monitoring (Spring, 2024)", "outcomes": "Observed reactivity to MAP2 / TECPR1; no sequencing performed", "pbmcs_label": "(2023/09/22, 2023/11/28)", "peptide_id": "JLF-100-038.MT.38.TECPR1.2", "pool": "NA", "result": "Negative", "summary": "Whole PBMCs stimulated with 9 pooled CSBio long peptides. ELISPOT performed with individual peptide stimulation." }, { "additional_testing": "", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038.MT.38.TECPR1.2", "pool": "NA", "result": "Positive (Weak)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V2", "JLF V1" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "TSRWESAWSGLSPRTGR", "scoring_region": { "sequence": "TSRWESAWSGLSPRTGR", "start": 0, "end": 17, "terminal_tags": [] } }, { "peptide_id": "TECPR1-chr7-98241127.peptide-5", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "LWAHSGRDRPWSGKES", "scoring_region": { "sequence": "LWAHSGRDRPWSGKES", "start": 0, "end": 16, "terminal_tags": [] } } ] }, { "variant_id": "EXOC4-chr7-133274996", "gene": "EXOC4", "chrom": "chr7", "pos": 133274996, "ref": "G", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ser34Ile", "consequence": "missense_variant", "vaccines": [ "CeGaT", "JLF V2", "JLF V3" ], "published_vaccine_peptides": [ { "peptide_id": "EXOC4-chr7-133274996.peptide-1", "experiments": [ { "additional_testing": "Sent to Celldom", "date": "2023-09-22", "experiment": "PFO Lab 14-day stim, PFO-S18 (Spring, 2025)", "outcomes": "Identification of 2x TECPR1 SCT-binding TCR-Ts via Celldom", "pbmcs_label": "Sample #1: pre-vaccine PBMCs (2023/09/22) Sample #2: apheresis (2024/05/15) Sample #3: combined PBMCs (2024/07/16, 2024/08/03) Sample #4: PBMCs (2024/08/20) Sample #5: combined PBMCs (2024/10/10, 2024/11/21, 2024/12/13)", "peptide_id": "JLF-100-038R.MT.39.EXOC4", "pool": "L3", "result": "Positive", "summary": "Various peptide pools; CD8 T cells co-cultured with irradiated EBV-LCLs. ELISPOT and 10x single cell TCR sequencing" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038R.MT.39.EXOC4.1", "pool": "Pool 1", "result": "Positive (Weak)", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "", "date": "2024-05-15", "experiment": "PFO Lab ex vivo ELISPOT, PFO-S45 (Fall, 2025)", "outcomes": "ex vivo responses observed in pooled and invididual peptides (MAP2, DYNC1H1); classII blockade supports CD8 resposes", "pbmcs_label": "Apheresis (2024/05/15)", "peptide_id": "JLF-100-038R.MT.39.EXOC4.1", "pool": "", "result": "Positive (Weak)", "summary": "ex vivo ELISPOT optimizing detection of CD8 T cell responses" }, { "additional_testing": "Sent to MUSC for expansion", "date": "2024-05-15", "experiment": "UNC Immune Monitoring (Summer, 2024)", "outcomes": "26 TCRs extracted; 4 reactive to CSBio peptides (1x DYNC1H1, 3x EXOC4) via Class-II stimulation", "pbmcs_label": "Apheresis (2024/05/15), Whole PBMCs", "peptide_id": "JLF-100-038R.MT.39.EXOC4.1", "pool": "NA", "result": "Positive (Strong)", "summary": "Whole PBMCs individually stimulated with 15 CSBio long peptides. ELISPOT and 10x single cell TCR sequencing" } ], "in_vaccines": [ "JLF V3", "JLF V2" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "KKSVIRTLSTIDDVEDRENEKGR", "scoring_region": { "sequence": "SVIRTLSTIDDVEDRENEKGR", "start": 2, "end": 23, "terminal_tags": [ { "terminus": "N", "start": 0, "end": 2, "sequence": "KK" } ] } }, { "peptide_id": "EXOC4-chr7-133274996.peptide-2", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "SVIRTLSTIDDVEDREN", "scoring_region": { "sequence": "SVIRTLSTIDDVEDREN", "start": 0, "end": 17, "terminal_tags": [] } } ] }, { "variant_id": "BMP1-chr8-22192067", "gene": "BMP1", "chrom": "chr8", "pos": 22192067, "ref": "T", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ser366Thr", "consequence": "missense_variant", "vaccines": [ "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "BMP1-chr8-22192067.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 17, "sequence": "YSAHMHCVWRISVTPGEKIILNFTTLDLYRSRL", "scoring_region": { "sequence": "YSAHMHCVWRISVTPGEKIILNFTTLDLYRSRL", "start": 0, "end": 33, "terminal_tags": [] } }, { "peptide_id": "BMP1-chr8-22192067.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "KIILNFTTL", "scoring_region": { "sequence": "KIILNFTTL", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "BMP1-chr8-22192067.peptide-3", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 8, "sequence": "RISVTPGEKIILNFTTLDLYRSR", "scoring_region": { "sequence": "RISVTPGEKIILNFTTLDLYRSR", "start": 0, "end": 23, "terminal_tags": [] } } ] }, { "variant_id": "VPS13B-chr8-99861923", "gene": "VPS13B", "chrom": "chr8", "pos": 99861923, "ref": "C", "alt": "T", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ser3756Phe", "consequence": "missense_variant", "vaccines": [ "CeGaT", "JLF V3" ], "published_vaccine_peptides": [ { "peptide_id": "VPS13B-chr8-99861923.peptide-1", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "RQLPESLGEGLRQGLFRLGIS", "scoring_region": { "sequence": "RQLPESLGEGLRQGLFRLGIS", "start": 0, "end": 21, "terminal_tags": [] } }, { "peptide_id": "VPS13B-chr8-99861923.peptide-2", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "GEGLRQGLFRLGISLLGAIA", "scoring_region": { "sequence": "GEGLRQGLFRLGISLLGAIA", "start": 0, "end": 20, "terminal_tags": [] } } ] }, { "variant_id": "GLIS3-chr9-3856149", "gene": "GLIS3", "chrom": "chr9", "pos": 3856149, "ref": "CTGATGTGG", "alt": "C", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ser775fs", "consequence": "frameshift_variant", "vaccines": [ "JLF V3" ], "published_vaccine_peptides": [ { "peptide_id": "GLIS3-chr9-3856149.peptide-1", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "QPPESSSSFFNTAKNTASLYPAAIRFTPEVLSARNKLFFSTKWYPCPWILWAAAEVLSPTLPRFPENCAACQLLQCGAFV", "scoring_region": { "sequence": "QPPESSSSFFNTAKNTASLYPAAIRFTPEVLSARNKLFFSTKWYPCPWILWAAAEVLSPTLPRFPENCAACQLLQCGAFV", "start": 0, "end": 80, "terminal_tags": [] } } ] }, { "variant_id": "SMC5-chr9-70298024", "gene": "SMC5", "chrom": "chr9", "pos": 70298024, "ref": "G", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Arg371Lys", "consequence": "missense_variant", "vaccines": [ "JLF V3", "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "SMC5-chr9-70298024.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 16, "sequence": "EELQQALIVKQNEELDRQKRIGNTRKMIEDL", "scoring_region": { "sequence": "EELQQALIVKQNEELDRQKRIGNTRKMIEDL", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "SMC5-chr9-70298024.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "RQKRIGNTR", "scoring_region": { "sequence": "RQKRIGNTR", "start": 0, "end": 9, "terminal_tags": [] } }, { "peptide_id": "SMC5-chr9-70298024.peptide-3", "experiments": [], "in_vaccines": [ "JLF V3" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 1, "sequence": "DRQKRIGNTRKMIEDLQNELK", "scoring_region": { "sequence": "DRQKRIGNTRKMIEDLQNELK", "start": 0, "end": 21, "terminal_tags": [] } } ] }, { "variant_id": "EXD3-chr9-137373504", "gene": "EXD3", "chrom": "chr9", "pos": 137373504, "ref": "C", "alt": "G", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Glu72Asp", "consequence": "missense_variant", "vaccines": [ "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "EXD3-chr9-137373504.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 12, "sequence": "LAGLLDMLESCRGQRGDGPSLAAWISHQLQ", "scoring_region": { "sequence": "LAGLLDMLESCRGQRGDGPSLAAWISHQLQ", "start": 0, "end": 30, "terminal_tags": [] } }, { "peptide_id": "EXD3-chr9-137373504.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "GQRGDGPSL", "scoring_region": { "sequence": "GQRGDGPSL", "start": 0, "end": 9, "terminal_tags": [] } } ] }, { "variant_id": "MT_ND5-chrM-12994", "gene": "MT-ND5", "chrom": "chrM", "pos": 12994, "ref": "G", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Ala220Thr", "consequence": "missense_variant", "vaccines": [ "CeGaT" ], "published_vaccine_peptides": [ { "peptide_id": "MT_ND5-chrM-12994.peptide-1", "experiments": [], "in_vaccines": [ "CeGaT" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": null, "sequence": "PLLGLLLATAGKSAQLG", "scoring_region": { "sequence": "PLLGLLLATAGKSAQLG", "start": 0, "end": 17, "terminal_tags": [] } } ] }, { "variant_id": "PPP1R3F-chrX-49270761", "gene": "PPP1R3F", "chrom": "chrX", "pos": 49270761, "ref": "G", "alt": "A", "assembly": "GRCh38", "allele_status": "ready", "protein_change": "p.Gly298Arg", "consequence": "missense_variant", "vaccines": [ "mRNA" ], "published_vaccine_peptides": [ { "peptide_id": "PPP1R3F-chrX-49270761.peptide-1", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": false, "minimal_epitope_offset": 18, "sequence": "RNYTVLLRIAPAPTPTDAERLPQQQQLPQLE", "scoring_region": { "sequence": "RNYTVLLRIAPAPTPTDAERLPQQQQLPQLE", "start": 0, "end": 31, "terminal_tags": [] } }, { "peptide_id": "PPP1R3F-chrX-49270761.peptide-2", "experiments": [], "in_vaccines": [ "mRNA" ], "is_mrna_minimal_epitope": true, "minimal_epitope_offset": null, "sequence": "ERLPQQQQL", "scoring_region": { "sequence": "ERLPQQQQL", "start": 0, "end": 9, "terminal_tags": [] } } ] } ] }