Advancing Clinical Genomic Analysis with a Skill-Centred Agent

Qiaoyu Zheng; Weike Zhao; Yanjie Fan; Ye Cao; Mengqi Jiang; Xiao Zhou; Xiaoman Zhang; Pengcheng Qiu; Yongguo Yu; Yanfeng Wang; Ya Zhang; Chaoyi Wu; Weidi Xie

arXiv · 2610.40556

Advancing Clinical Genomic Analysis with a Skill-Centred Agent

Qiaoyu Zheng·Weike Zhao·Yanjie Fan·Ye Cao·Mengqi Jiang·Xiao Zhou·Xiaoman Zhang·Pengcheng Qiu·Yongguo Yu·Yanfeng Wang·Ya Zhang·Chaoyi Wu·Weidi Xie

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Abstract

Clinical genomic analysis requires experts to integrate evolving guidelines, databases, and computational evidence. As sequencing has become increasingly accessible, this complex and labor-intensive process has become a major bottleneck to the timely use of genomic information in clinical decision-making. To fill this gap, we developed ClinGeX, a large-language-model agent that composes 105 curated executable skills through task-specific retrieval and dependency-aware orchestration. On 223 temporally held-out benchmark cases, ClinGeX achieved 71.7\% macro-averaged task-level concordance with expert reference classifications, compared with 45.7\% for the strongest comparator. In a three-condition, counterbalanced human-AI collaboration study, 45 clinical genomic professionals assessed 135 clinically derived cases under routine (no AI assistance), DeepSeek-assisted and ClinGeX-assisted conditions. ClinGeX assistance increased raw case-level concordance across criterion-level variant analysis, genomic interpretation in rare disease and molecular oncology decision-making (51.1\%, 57.8\%, 64.4\% versus 15.6\%, 31.1\%, 20.0\% in comparator conditions) and reduced reported interpretation time in all scenarios. During an exploratory one-month real-world non-interventional assessment, 11 experienced professionals submitted feedback on 96 self-selected analysis episodes and reported frequent conclusion adoption and time savings. These findings support executable domain skills as a promising approach to augment specialist genomic interpretation.

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Qiaoyu Zheng, Weike Zhao, Yanjie Fan, Ye Cao, Mengqi Jiang, Xiao Zhou, Xiaoman Zhang, Pengcheng Qiu, Yongguo Yu, Yanfeng Wang, Ya Zhang, Chaoyi Wu, Weidi Xie. 2026-10-29. Advancing Clinical Genomic Analysis with a Skill-Centred Agent. https://arxiv.org/abs/2610.40556

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