Democratizing Clinical Tumor Whole Genome Sequencing: 18-hour End-to-end Analysis via Trillion-parameter Large Language Models Locally Deployed on Consumer-grade Hardware

Abstract:Whole genome sequencing (WGS) is essential for precision oncology, yet its clinical adoption remains limited by prohibitive computational costs and multi-day turnaround times. This work presents a fully localized low-resource framework enabling stable deployment of a trillion-parameter biomedical LLM on a single consumer-grade RTX 4060 laptop with 32GB system memory and 8GB VRAM, as well as on routine clinical workstations in general hospitals, completing the entire tumor-paired WGS workflow from raw FASTQ input to clinical-grade full-variation-spectrum report output. Under standard 30X depth configurations, our implementation finishes a single tumor-paired WGS analysis within 18 hours, achieving 99.62% F1 score for somatic variant detection with over 99.9% concordance to the industrial-standard A100 cluster pipeline, fully meeting clinical oncology accuracy requirements. Quantitative profiling shows adaptive heterogeneous memory scheduling accounts for 71% of total execution time, while model optimization introduces less than 9% of total detection error. This work is the first engineering implementation of trillion-parameter biomedical LLM-driven clinical-grade genomic analysis on consumer-grade hardware, breaking the industry paradigm that trillion-scale genomic LLMs require hundred-thousand-dollar GPU clusters and multi-day turnaround, establishing a low-resource pathway for global primary medical institutions to adopt whole-genome precision oncology at zero additional cost.

11 pages. Corresponding author: Yili Xu(22465225@qq.com)

Genomics (q-bio.GN); Machine Learning (cs.LG)

arXiv:2609.17620 [q-bio.GN]

(or arXiv:2609.17620v1 [q-bio.GN] for this version)

https://doi.org/10.48550/arXiv.2609.17620 Focus to learn more arXiv-issued DOI via DataCite

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