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 周围T细胞淋巴瘤（PTCL）约占西方世界所有NHL的12-15％，并且是 与沮丧的预后有关。此外，诊断是具有挑战性的，因为30-50％的PTCL病例不能是 分配给特定实体，并被归类为PTCL，而不是指定的（PTCL-NOS）。我们已经定义了 可以区分五个常见PTCL实体的强大基因表达特征：血管免疫细胞T细胞 淋巴瘤（AITL），变性淋巴瘤激酶阳性对塑性大细胞淋巴瘤（ALK（+）ALCL），ALK- 阴性的大型大细胞淋巴瘤（ALK（ - ）ALCL），成人T细胞白血病/淋巴瘤（ATLL）和节点外 天然杀伤/T细胞淋巴瘤（ENKTCL）。 PTCL-NOS可以分为两个不同的生物学和预后 亚组（PTCL-TBX21和PTCL-GATA3子组）。我们翻译了基于RNA的诊断和预后 福尔马林固定石蜡嵌入（FFPE）组织的算法，用于广泛的临床使用，具有高灵敏度和 特异性。我们还使用相应的DNA和 证明可以使用相应的整个基因组分析（SWGA）验证这种病变 血浆无细胞DNA，因此液体活检可以帮助诊断和疾病监测。 由于生物测量处理及其质量在常规临床病理实验室的差异很大，所以 需要在可变情况下评估RNA或基于DNA的签名的可靠性。至关重要 在新诊断之前，确定测定方法的鲁棒性如何受到分析前变量的影响 工具可以应用于大型研究或常规临床实践。我们假设对 生物测量前的分析前变量将导致优化的生物特异性采购框架，导致 在组织和液体活检设置中提高了诊断准确性和可重复性，可以在 常规临床实践/试验的室内实验室设置。该建议旨在建立标准化的，基于证据的 生物特异性（RNA/DNA）处理，存储和运输的程序，以确保准确，可重复 测定性能。确定的条件和参数将在前瞻性样本上进行验证，最好是 临床试验设置，因此发现可以与临床数据相关。因此，提出了三个具体目标： 特定目的1：确定影响基于RNA测定的可靠性的分析前变量 FFPE组织 特定目的2：确定影响循环肿瘤DNA（CT-DNA）检测的分析前因子和 PTCL患者的定量 特定目标3：验证在改善PTCL诊断或 在临床实验室改善修订）实验室环境中的预后测定 这些研究将导致可靠的方案，以优化组织活检或等离子体中的保存生物分子 确保分子测定的准确性和可重复性，改善PTCL分类和预后。