Hi-C sequencing is a DNA-based next-generation sequencing method that preserves the 3D genome conformation and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate Hi-C as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens. Archived viable and non-viable frozen leukemic cells and formalin-fixed paraffin-embedded (FFPE) tumor specimens were analyzed. Pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to Hi-C to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases without known genomic rearrangements based on prior clinical diagnostic testing was evaluated to determine whether Hi-C could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, we observed 100% concordance between Hi-C and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study provides an institutional proof of principle evaluation of Hi-C sequencing to medical diagnostic testing as it identified several clinically relevant rearrangements, including those that were missed by current clinical testing workflows.
Hi-C测序是一种基于DNA的新一代测序技术，能够保留基因组的三维构象，在转化医学研究中已展现出检测基因组重排的应用潜力。为评估Hi-C作为临床诊断平台的可行性，本研究采用原代儿童白血病及肉瘤标本，通过对比常规实验室检测方法进行技术一致性验证。研究对存档的活性/非活性冷冻白血病细胞及福尔马林固定石蜡包埋（FFPE）肿瘤样本进行分析。首先选取已知基因组重排的儿童急性髓系白血病（AML）和肺泡状横纹肌肉瘤（A-RMS）样本进行Hi-C检测以验证技术一致性；随后对一组经前期临床诊断未发现已知基因组重排的AML和急性淋巴细胞白血病（ALL）病例进行探索性队列研究，以验证Hi-C检测重排的能力。在标准测序深度（每样本5000万原始读长对，约相当于5倍原始基因组覆盖度）条件下，Hi-C检测结果与临床细胞遗传学及分子检测结果的一致性达到100%。在探索性队列中，45%（5/11）的白血病病例检测出具有临床意义的基因融合。本研究通过机构层面的原理验证评估表明，Hi-C测序技术能够识别包括当前临床检测流程遗漏在内的多种临床相关重排，为将该技术应用于医学诊断提供了实证依据。
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