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<p>HLA typing from sequencing data is crucial for studying immune gene families, but high allele similarity challenges existing tools. We present ImmuSeeker, comprehensive software for extracting HLA genotypes, expression, and diversity at gene, one-field, and two-field allele levels, with improved Bayesian zygosity inference and graphical phylogenetic visualization. ImmuSeeker was benchmarked against nine established tools using gold-standard HLA datasets, repeated RNA sequencing (RNA-seq) and Isoform Sequencing (Iso-Seq) data, and a longitudinal patient cohort, demonstrating superior accuracy, consistency, and analytical utility. ImmuSeeker provides a scalable, robust framework for comprehensive HLA typing and immune system analyses.</p>

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ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年3月26日

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  • Limin Jiang,
  • Ivy Hurwitz,
  • Lukasz S. Wylezinski,
  • Michael K. Racke,
  • Fengyao Yan,
  • Fei Ye,
  • Quanhu Sheng,
  • Shuguang Leng,
  • Cecilia P. Chung,
  • C. Michael Stein,
  • Chung-I Li,
  • Naresh Kumar,
  • Michele Ceccarelli,
  • Steven F. Baker,
  • Douglas J. Perkins,
  • Charles F. Spurlock III,
  • Leng Han,
  • Yan Guo

摘要

HLA typing from sequencing data is crucial for studying immune gene families, but high allele similarity challenges existing tools. We present ImmuSeeker, comprehensive software for extracting HLA genotypes, expression, and diversity at gene, one-field, and two-field allele levels, with improved Bayesian zygosity inference and graphical phylogenetic visualization. ImmuSeeker was benchmarked against nine established tools using gold-standard HLA datasets, repeated RNA sequencing (RNA-seq) and Isoform Sequencing (Iso-Seq) data, and a longitudinal patient cohort, demonstrating superior accuracy, consistency, and analytical utility. ImmuSeeker provides a scalable, robust framework for comprehensive HLA typing and immune system analyses.