Pre-analytical variables of bioanalytes affecting the accuracy of PTCL diagnostic and prognostic genetic signatures

生物分析物的分析前变量影响 PTCL 诊断和预后遗传特征的准确性

• 批准号: 10684317
• 负责人: Wing C. Chan
• 金额: $ 35.99万
• 依托单位: UNIVERSITY OF NEBRASKA MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-20 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10684317
• 关键词: Adult T-Cell Leukemia/Lymphoma; Affect; Biological; Biological Assay; Biopsy; Blood; Categories; Classification; Clinical; Clinical Data; Clinical Laboratory Improvement Amendments; Clinical Pathology; Clinical Trials; Complex; DNA; DNA Maintenance; DNA Sequence Alteration; Detection; Diagnosis; Diagnostic; Disease; Disease Progression; Ensure; Evaluation; Extranodal; Formalin; Freezing; Future; GATA3 gene; Gene Expression; Gene Expression Profile; Genes; Genetic; Genotype; Goals; Immunoblastic Lymphadenopathy; Immunophenotyping; International; Ki-1 Large-Cell Lymphoma; Laboratories; Lesion; Logistics; Measures; Messenger RNA; Methods; Molecular; Monitor; Morphology; Mutation; Non-Hodgkin' s Lymphoma; Outcome; Paraffin Embedding; Patients; Performance; Peripheral; Plasma; Plasma Cells; Procedures; Process; Prognosis; Protocols documentation; RNA; Reproducibility; Sampling; Sensitivity and Specificity; Somatic Mutation; Specific qualifier value; Specimen; Standardization; Subgroup; T-Cell Lymphoma; Techniques; Tissue Banks; Tissue Embedding; Tissues; Translating; Transportation; Western World; accurate diagnosis; anaplastic lymphoma kinase; cell free DNA; clinical application; clinical center; clinical practice; diagnostic accuracy; diagnostic algorithm; diagnostic assay; diagnostic signature; diagnostic tool; diagnostic value; disease diagnosis; evidence base; genetic signature; genome analysis; improved; liquid biopsy; nano-string; new technology; novel diagnostics; predicting response; preservation; prognostic; prognostic algorithm; prognostic assays; prognostication; prospective; sample fixation; tissue processing; treatment response; tumor; tumor DNA; whole genome

Abstract Peripheral T-cell lymphomas (PTCL) represent approximately 12-15% of all NHL in the western world and are associated with dismal prognosis. Furthermore, the diagnosis is challenging as 30-50% of PTCL cases cannot be assigned to a specific entity and are categorized as PTCL-not otherwise specified (PTCL-NOS). We have defined robust gene expression signatures that can differentiate the five common PTCLs entities: angioimmunoblastic T-cell lymphoma (AITL), anaplastic lymphoma kinase positive anaplastic large-cell lymphoma (ALK (+) ALCL), ALK- negative anaplastic large-cell lymphoma (ALK (-) ALCL), adult T-cell leukemia/lymphoma (ATLL), and extra-nodal natural killer/T-cell lymphoma (ENKTCL). PTCL-NOS can be divided into two distinct biological and prognostic subgroups (PTCL-TBX21 and PTCL-GATA3 subgroups). We translated the RNA based diagnostic and prognostic algorithms for formalin fixed paraffin embedded (FFPE) tissues for widespread clinical usage with high sensitivity and specificity. We also identified distinguishing genetic lesions in PTCL subtypes using corresponding DNA , and demonstrated that such lesion can be validated using shallow whole genome analysis (sWGA) in corresponding plasma cell-free DNA, thus liquid biopsy can aid in diagnosis and disease monitoring. Since the biospecimen processing, and hence quality, varies significantly in routine clinical pathology laboratories, the reliability of RNA or DNA based signatures need to be evaluated under variable circumstances. It is essential to determine how the robustness of the assay may be affected by pre-analytical variables before the novel diagnostic tools can be applied to large studies or routine clinical practice. We hypothesize that a comprehensive evaluation of pre-analytical variables of biospecimen will lead to optimized bio-specimen procurement framework leading to improved diagnostic accuracy and reproducibility in tissue and liquid biopsy setting and can be standardized in an inter-CLIA lab setting for routine clinical practice/trials. This proposal aims to establish standardized, evidence-based procedures on bio-specimen (RNA/DNA) processing, storage and transportation to ensure accurate, reproducible assay performance. The identified conditions and parameters will be validated on prospective samples, preferably in a clinical trial setting, so findings can be correlated with clinical data. Thus, three specific aims are proposed: Specific Aim 1: To determine pre-analytical variables that affects the reliability of RNA-based assays in FFPE tissue Specific Aim 2: To identify pre-analytical factors affecting circulating tumor DNA (ct-DNA) detection and quantification in patients with PTCL Specific Aim 3: To validate harmonization of the pre-analytical variables in improving PTCL diagnostic or prognostic assay in an inter-CLIA (Clinical Laboratory Improvement Amendments) lab setting The studies will lead to robust protocols that optimize the preservation biomolecules in tissue biopsies or plasma to ensure accuracy and reproducibility of molecular assays, improving PTCL classification and prognostication.

抽象的 外周 T 细胞淋巴瘤 (PTCL) 约占西方世界所有 NHL 的 12-15%， 与不良预后相关。此外，诊断具有挑战性，因为 30-50% 的 PTCL 病例无法被诊断出来。 分配给特定实体并归类为 PTCL-未另行指定 (PTCL-NOS)。我们已经定义了 强大的基因表达特征，可以区分五种常见的 PTCL 实体：血管免疫母细胞 T 细胞 淋巴瘤 (AITL)、间变性淋巴瘤激酶阳性间变性大细胞淋巴瘤 (ALK (+) ALCL)、ALK- 阴性间变性大细胞淋巴瘤 (ALK (-) ALCL)、成人 T 细胞白血病/淋巴瘤 (ATLL) 和结外 自然杀伤/T 细胞淋巴瘤 (ENKTCL)。 PTCL-NOS可分为两种不同的生物学和预后类型 亚组（PTCL-TBX21 和 PTCL-GATA3 亚组）。我们翻译了基于 RNA 的诊断和预后 福尔马林固定石蜡包埋 (FFPE) 组织的算法，广泛应用于临床，具有高灵敏度和 特异性。我们还使用相应的 DNA 鉴定了 PTCL 亚型中的独特遗传病变，并且 证明这种病变可以使用相应的浅层全基因组分析（SWGA）进行验证 血浆游离DNA，因此液体活检可以帮助诊断和疾病监测。 由于常规临床病理实验室的生物样本处理以及质量差异很大， 基于 RNA 或 DNA 的签名的可靠性需要在不同的情况下进行评估。至关重要的是 在新的诊断之前确定分析前的变量如何影响测定的稳健性 工具可应用于大型研究或常规临床实践。我们假设综合评价 生物样本的预分析变量将导致优化的生物样本采购框架 提高了组织和液体活检环境中的诊断准确性和可重复性，并且可以在 用于常规临床实践/试验的 CLIA 实验室间设置。该提案旨在建立标准化、基于证据的 生物样本 (RNA/DNA) 处理、储存和运输程序，以确保准确、可重复 测定性能。确定的条件和参数将在预期样品上进行验证，最好是在 临床试验设置，因此研究结果可以与临床数据相关联。因此，提出了三个具体目标： 具体目标 1：确定影响基于 RNA 的检测可靠性的分析前变量 FFPE 纸巾 具体目标 2：确定影响循环肿瘤 DNA (ct-DNA) 检测和检测的分析前因素 PTCL 患者的量化 具体目标 3：验证分析前变量在改善 PTCL 诊断或 在 CLIA（临床实验室改进修正案）实验室环境中进行预后测定 这些研究将产生稳健的方案，优化组织活检或血浆中的保存生物分子，以 确保分子检测的准确性和可重复性，改善 PTCL 分类和预后。