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(A) Discovery of novel TR alleles. High-quality genome assemblies from the HPRC were analyzed using gAIRR-annotate to identify both reference TR alleles from the IMGT database (blue) and candidate novel alleles (red). (B) Crosscheck between gAIRR-annotate and gAIRR-call results, and creation of a flanking sequence database. This panel illustrates the orthogonal validation process between two independent pipelines. On one side, gAIRR-annotate identifies TR alleles from genome assemblies. On the other, gAIRR-seq captures <t>genomic</t> <t>DNA</t> for targeted sequencing, and gAIRR-call infers alleles from NGS reads. The allele database used by both pipelines includes IMGT reference alleles (blue) and candidate novel alleles (red) discovered in panel (a). Annotated alleles and called alleles are crosschecked to identify validated novel alleles (brown), which are then included in the final allele database. Flanking sequences are extracted to construct a comprehensive flanking sequence database.
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(A) Discovery of novel TR alleles. High-quality genome assemblies from the HPRC were analyzed using gAIRR-annotate to identify both reference TR alleles from the IMGT database (blue) and candidate novel alleles (red). (B) Crosscheck between gAIRR-annotate and gAIRR-call results, and creation of a flanking sequence database. This panel illustrates the orthogonal validation process between two independent pipelines. On one side, gAIRR-annotate identifies TR alleles from genome assemblies. On the other, gAIRR-seq captures <t>genomic</t> <t>DNA</t> for targeted sequencing, and gAIRR-call infers alleles from NGS reads. The allele database used by both pipelines includes IMGT reference alleles (blue) and candidate novel alleles (red) discovered in panel (a). Annotated alleles and called alleles are crosschecked to identify validated novel alleles (brown), which are then included in the final allele database. Flanking sequences are extracted to construct a comprehensive flanking sequence database.
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(A) Discovery of novel TR alleles. High-quality genome assemblies from the HPRC were analyzed using gAIRR-annotate to identify both reference TR alleles from the IMGT database (blue) and candidate novel alleles (red). (B) Crosscheck between gAIRR-annotate and gAIRR-call results, and creation of a flanking sequence database. This panel illustrates the orthogonal validation process between two independent pipelines. On one side, gAIRR-annotate identifies TR alleles from genome assemblies. On the other, gAIRR-seq captures <t>genomic</t> <t>DNA</t> for targeted sequencing, and gAIRR-call infers alleles from NGS reads. The allele database used by both pipelines includes IMGT reference alleles (blue) and candidate novel alleles (red) discovered in panel (a). Annotated alleles and called alleles are crosschecked to identify validated novel alleles (brown), which are then included in the final allele database. Flanking sequences are extracted to construct a comprehensive flanking sequence database.
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(A) Discovery of novel TR alleles. High-quality genome assemblies from the HPRC were analyzed using gAIRR-annotate to identify both reference TR alleles from the IMGT database (blue) and candidate novel alleles (red). (B) Crosscheck between gAIRR-annotate and gAIRR-call results, and creation of a flanking sequence database. This panel illustrates the orthogonal validation process between two independent pipelines. On one side, gAIRR-annotate identifies TR alleles from genome assemblies. On the other, gAIRR-seq captures <t>genomic</t> <t>DNA</t> for targeted sequencing, and gAIRR-call infers alleles from NGS reads. The allele database used by both pipelines includes IMGT reference alleles (blue) and candidate novel alleles (red) discovered in panel (a). Annotated alleles and called alleles are crosschecked to identify validated novel alleles (brown), which are then included in the final allele database. Flanking sequences are extracted to construct a comprehensive flanking sequence database.
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(A) Discovery of novel TR alleles. High-quality genome assemblies from the HPRC were analyzed using gAIRR-annotate to identify both reference TR alleles from the IMGT database (blue) and candidate novel alleles (red). (B) Crosscheck between gAIRR-annotate and gAIRR-call results, and creation of a flanking sequence database. This panel illustrates the orthogonal validation process between two independent pipelines. On one side, gAIRR-annotate identifies TR alleles from genome assemblies. On the other, gAIRR-seq captures genomic DNA for targeted sequencing, and gAIRR-call infers alleles from NGS reads. The allele database used by both pipelines includes IMGT reference alleles (blue) and candidate novel alleles (red) discovered in panel (a). Annotated alleles and called alleles are crosschecked to identify validated novel alleles (brown), which are then included in the final allele database. Flanking sequences are extracted to construct a comprehensive flanking sequence database.

Journal: bioRxiv

Article Title: Unmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite

doi: 10.1101/2025.05.24.655452

Figure Lengend Snippet: (A) Discovery of novel TR alleles. High-quality genome assemblies from the HPRC were analyzed using gAIRR-annotate to identify both reference TR alleles from the IMGT database (blue) and candidate novel alleles (red). (B) Crosscheck between gAIRR-annotate and gAIRR-call results, and creation of a flanking sequence database. This panel illustrates the orthogonal validation process between two independent pipelines. On one side, gAIRR-annotate identifies TR alleles from genome assemblies. On the other, gAIRR-seq captures genomic DNA for targeted sequencing, and gAIRR-call infers alleles from NGS reads. The allele database used by both pipelines includes IMGT reference alleles (blue) and candidate novel alleles (red) discovered in panel (a). Annotated alleles and called alleles are crosschecked to identify validated novel alleles (brown), which are then included in the final allele database. Flanking sequences are extracted to construct a comprehensive flanking sequence database.

Article Snippet: Genomic DNA reference materials for these subjects were obtained from the Coriell Institute ( https://www.coriell.org ).

Techniques: Sequencing, Biomarker Discovery, Construct