Liquid Biopsy for Rapid Detection and Real Time Monitoring of FGFR-altered Cancers

液体活检用于快速检测和真实的实时监测FGFR改变的癌症 由成纤维细胞生长因子受体（FGFR）改变驱动的晚期癌症患者，包括基因 融合和单核苷酸变体（SNV）受益于几种新的FGFR激酶抑制剂。 Erdafitinib和pemigatinib最近被FDA批准用于膀胱癌和胆管癌， 其他FGFR抑制剂已获得快速通道指定，并正在探索在肿瘤 不可知论篮子试验。患者的总生存期和无进展生存期有所改善， 总体反应率较高。不幸的是，几乎所有的患者最终都会对这些抑制剂产生耐药性， 通常通过获得继发性FGFR突变。FGFR抑制剂的形成受到以下因素的阻碍： 缺乏准确和全面的方法来1）快速检测FGFR改变以鉴定患者 对于临床试验，2）监测治疗反应，3）表征新出现的耐药性。的 开发新的检测策略，如非侵入性液体活检，可以满足这些未满足的需求， 诊断、预后和治疗选择。液体活组织检查评估血液样本，其中无细胞DNA 对肿瘤脱落的CfDNA（cfDNA）进行测序以检测基因组改变。现有技术规格 商业cfDNA测试显示，这些测定法未被验证用于FGFR融合，并且具有不充分的 FGFR融合的灵敏度约为30%。此外，商业测试规模太大，重复成本太高 经常用于治疗和疾病监测。因此，我们建议开发和验证一个以FGFR为中心， 用于实时检测的准确且具有成本效益的cfDNA测序分析（FGFR-Dx），以支持快速检测， 反应监测和早期检测耐药性。我们在俄亥俄州州立大学的团队有六个活跃的FGFR 抑制剂临床试验，FGFR真阳性的大型队列，以及临床实验室改进修正案 符合CLIA标准的癌症基因组学实验室，在临床级肿瘤测序方面拥有丰富的经验 以及用于检测和解释基因融合体和单核苷酸变体的生物信息学分析。 此外，我们将cfDNA的开发与快速研究尸检研究相结合，这将使第一个 通过评估观察到的异质性的准确程度，系统评价cfDNA的检测限 来自多个位点的肿瘤样品中的DNA序列以cfDNA表示。我们提出以下目标， PAR-18-317标准：1）分析验证靶向液体活检测定（FGFR-Dx）以检测融合 和FGFR 1 -3中的单核苷酸变异（SNV）; 2）建立FGFR-Dx检测FGFR的临床有效性 融合和SNV。总之，将聚焦FGFR的液体活检的发展与快速研究结合起来， 尸检可以广泛地影响该领域对cfDNA方法在患有癌症的患者中的理解和应用。 FGFR改变和其他癌症。

Liquid Biopsy for Rapid Detection and Real Time Monitoring of FGFR-altered Cancers Patients with advanced cancers driven by fibroblast growth factor receptor (FGFR) alterations, including gene fusions and single nucleotide variants (SNVs), are benefiting from several new FGFR kinase inhibitors. Erdafitinib and pemigatinib were recently FDA approved for bladder cancer and cholangiocarcinoma, respectively, and other FGFR inhibitors have received fast-track designation and are being explored in tumor agnostic basket trials. Patients are experiencing improved overall survival and progression free survival, with high overall response rates. Unfortunately, virtually all patients eventually develop resistance to these inhibitors, oftentimes through acquisition of secondary FGFR mutations. FGFR inhibitor development is hindered by the lack of accurate and comprehensive methods to 1) rapidly detect FGFR alterations in order to qualify patients for clinical trials, 2) monitor therapeutic response, and 3) characterize emerging drug resistance. The development of novel testing strategies, such as non-invasive liquid biopsies, can fulfill these unmet needs for diagnosis, prognosis, and therapy selection. Liquid biopsies evaluate a blood sample, from which cell-free DNA (cfDNA) shed by the tumor is sequenced to detect genomic alterations. The technical specifications for existing commercial cfDNA tests show that these assays are not validated for FGFR fusions and have insufficient sensitivities of ~30% for FGFR fusions. Additionally, commercial tests are too large and costly to repeat frequently for therapy and disease monitoring. Thus, we propose to develop and validate an FGFR-focused, accurate, and cost-effective cfDNA sequencing assay (FGFR-Dx) for real-time testing to support rapid detection, response monitoring, and early detection of resistance. Our team at Ohio State University has six active FGFR inhibitor clinical trials, a large cohort of FGFR true positives, and a Clinical Laboratory Improvement Amendments (CLIA)-compliant Cancer Genomics Lab with extensive experience performing clinical-grade tumor sequencing and bioinformatics analysis for detection and interpretation of gene fusions and single nucleotide variants. Further, we have paired this cfDNA development with a rapid research autopsy study that will enable the first systematic evaluation of detection limits for cfDNA by assessing how accurately the heterogeneity observed across tumor samples from multiple sites is represented in cfDNA. We propose the following Aims to address the criteria for PAR-18-317: 1) Analytically validate a targeted liquid biopsy assay (FGFR-Dx) to detect fusions and single nucleotide variants (SNVs) in FGFR1-3; 2) Establish the clinical validity of FGFR-Dx to detect FGFR fusions and SNVs. In summary, coupling the development of an FGFR-focused liquid biopsy with rapid research autopsy can broadly impact the field’s understanding and application of cfDNA approaches in patients with FGFR-altered and other cancers.