PO.BCS01.14 · 生物信息与计算

通过知识图谱筛选创新型与增量型肺癌试验以实现需求对齐的设计

A knowledge graph screen of innovative versus incremental lung cancer trials for need-aligned designs

海报缩略图:通过知识图谱筛选创新型与增量型肺癌试验以实现需求对齐的设计
编号 6865 展板 9 时间 4/22 09:00–12:00 区域 Section 3 主讲 Mahitha Simhambhatla, No Degree
分会场 Network Biology and Precision Medicine
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作者与单位 Authors & Affiliations

Mahitha Simhambhatla1, Maya Ylagan1, Praneeth Sajja1, Daruka Mahadevan2, Erik S. Ferlanti1, James Carson1, Boone Goodgame3, Ehsan Irajizad4, Samir M. Hanash4, Jeanne Kowalski1

1The University of Texas at Austin, Austin, TX,2UT Health Science Center at San Antonio, San Antonio, TX,3The university of Texas at Austin, Austin, TX,4UT MD Anderson Cancer Center, Houston, TX

摘要 Abstract

中文摘要
背景。ClinicalTrials.gov列出了超过500,000项研究,这引出了一个问题:"新"试验究竟有多少是真正新颖的,又有多少只是增量式的设计变体。肺癌仍是全球癌症相关死亡的主要原因,这凸显了创新型试验相对于增量型试验的必要性。既往工作已使用临床试验知识图谱(KG)来支持设计推荐。在此,我们应用一个以小细胞肺癌(SCLC)患者为锚点的KG,将肺癌靶向治疗试验分类为"新颖新增"与"聚合相似",并识别需要新的、需求对齐的试验设计的空白领域。 方法。我们从ClinicalTrials.gov整理了286项成人肺癌靶向治疗试验,这些试验是作为一个SCLC病例的匹配项检索到的。我们通过将每项试验与关键实体(如肿瘤类型、基因组改变、靶点/通路、药物类别)关联,构建了试验间的KG,并学习基于图的嵌入以获得试验水平的表示。使用余弦相似度量化嵌入之间的试验相似性;使用社区检测定义试验聚类。含≥5项试验且聚类内中位相似度≥0.80的聚类被标记为"聚合相似"。将新颖性评分(1减去与任何其他试验的最大相似度)与介数中心性相结合以标记"新颖新增"。将一组预定义的SCLC分子报告匹配试验进行交叉引用,以表征其在识别出的聚类中的分布。 结果。总体而言,我们定义了4个试验聚类(中位规模67),其中三个符合我们的聚合相似标准,占大型社区中设计高度相似试验的74%(n=212)。在全部286项试验中,中位成对相似度(0.74)和最近邻相似度(0.98)与现有的、由生物标志物和治疗线定义的模板的密集复制相一致。基于综合新颖性(中位=0.070)和介数中心性(中位0.004)阈值,仅有38项试验(13%)被分类为新颖新增,且在两项指标上的中位得分均显著(p < 0.01)高于非新颖试验。新颖新增试验富集于单个聚合相似聚类(24/74项试验)中,该聚类包含了大多数病例分子报告匹配试验(65/68)。其余试验聚类的新颖新增比例为1-10%,表明病例水平的匹配发生在密集的靶向治疗社区内,而KG分析可以揭示结构上独特的新颖新增试验。 结论。对肺癌试验的KG分析为在组合层面操作化"新颖新增"与"聚合相似"提供了一种有原则的方法。这一以患者为锚点的框架可支持申办方、研究者和监管机构优先考虑创新型试验,减少已然拥挤的肺癌试验格局中的冗余,并最终使试验开发与未满足的患者需求相一致。
查看英文原文 English abstract
Background. ClinicalTrials.gov lists >500,000 studies, raising the question of how often “new” trials are truly novel versus incremental design variants. Lung cancer remains a leading cause of cancer-related death worldwide, underscoring the need for innovative over incremental trials. Prior work has used clinical trial knowledge graphs (KGs) to support design recommendations. Here, we apply a small cell lung cancer (SCLC) patient-anchored KG to classify lung cancer targeted therapy trials as “novel additions” versus “aggregate similarity” and to identify gaps where new, need-aligned trial designs are warranted. Methods. We curated 286 adult lung cancer targeted therapy trials from ClinicalTrials.gov that were retrieved as matches to a SCLC case. We built a trial-to-trial KG by linking each trial to key entities (e.g., tumor type, genomic alterations, targets/pathways, drug classes) and learned graph-based embeddings to obtain trial-level representations. Cosine similarity was used to quantify trial similarity between embeddings; community detection was used to define trial clusters. Clusters with ≥5 trials and median within-cluster similarity ≥0.80 were labeled “aggregate similar.” A novelty score (1 − maximum similarity to any other trial) and betweenness centrality were combined to label “novel additions”. A predefined set of SCLC molecular report-matched trials was cross-referenced to characterize their distribution across identified clusters. Results. Altogether, we defined 4 trial clusters (median size 67), three of which met our criteria for aggregate similarity, comprising 74% (n=212) of large community trials of highly similar designs. Across all 286 trials, median pairwise (0.74) and nearest-neighbor similarity (0.98) were consistent with dense replication of existing biomarker- and line-of-therapy-defined templates. Only 38 trials (13%) were classified as novel additions based on combined novelty (median=0.070) and betweenness centrality (median 0.004) thresholds, and showed significantly (p < 0.01) higher median scores in both as compared to non-novel trials. Novel additions were enriched in a single aggregate similarity cluster (24/74 trials) that contained most case molecular report-matched trials (65/68). The remaining trial clusters had 1-10% novel additions, indicating that case-level matching occurs within dense targeted therapy communities, whereas a KG analysis can surface structurally distinctive, novel addition trials. Conclusions. KG analysis of lung cancer trials provides a principled way to operationalize “novel addition” versus “aggregate similarity” at the portfolio level. This patient-anchored framework can support sponsors, investigators, and regulators in prioritizing innovative trials, reducing redundancy in an already crowded lung cancer trial landscape, and ultimately aligning trial development with unmet patient needs.
利益披露 Disclosure
M. Simhambhatla, None.. M. Ylagan, None.. P. Sajja, None.. E. S. Ferlanti, None.. J. Carson, None.. B. Goodgame, None.. E. Irajizad, None.. J. Kowalski, None.

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