Clonal Evolution in Multiple Myeloma

摘要 此应用程序的一个主要目标是进行所需的翻译工作，以预示介绍 下一代测序临床诊断多发性骨髓瘤（MM）。为了实现这一目标，我们 设计并试验了一种创新的MM特异性77基因组（M3 P）。该小组需要最少的DNA 数量，在显著深度处产生序列，同时跟踪拷贝数， 常见扩增和缺失的存在。利用这种新的资源， 广泛的临床注释，组织库和患者群体在马约，我们将首次 能够解决的患病率，预后的影响，并对治疗反应的每一个， 以相对较低的成本在大系列患者的MM细胞中鉴定出常见突变。 在目标1中，我们将询问77个最常见的突变或耐药相关基因中的每一个， 单独地或当通过来自726个新的肿瘤DNA中的通路或非监督簇组装时， 诊断患者这项工作将确定该群体中突变的谱和频率; 将个体突变的存在与基线临床和实验室特征、应答 以及它们对复发和生存的贡献。 在目标2中，我们将在治疗前、治疗期间和治疗后跟踪疾病的克隆演变，包括在 最小的存活疾病和早期的“前体”细胞隔室。具体而言，我们将进行一项 在所有马约研究中心进行的前瞻性2期临床试验，招募了124名复发患者，分配至 泊马度胺和地塞米松单独治疗或相同药物与卡非佐米联合治疗。 将使用M3 P测序来表征存活细胞的突变谱和克隆多样性。 不同骨髓区室和外周血中的肿瘤克隆;治疗前，第2周期结束时，以及 六个月大的时候。 最后，在目标3中，我们将生成一般关于突变谱的无偏序列数据， CRBN/IZKF 1/IKZF 3/IRF 4、IRE 1/XBP 1或NR 3C 1突变的频率，特别是有助于药物 高耐药患者的耐药性。为了覆盖已知的，但也寻求新的突变，我们将使用 全外显子组和RNA测序首次检测了真正的药物难治性肿瘤的分子特征， 60例MM患者，在MM死亡后6个月内或入组时采集骨髓样本 任何I期试验（包括此SPORE应用程序中的试验）。

ABSTRACT A major goal of this application is to conduct the translational work required to foreshadow the introduction of a next generation sequencing clinical diagnostic in Multiple Myeloma (MM). Underpinning this goal, we designed and piloted an innovative, MM specific, 77-gene panel (M3P). The panel requires minimal DNA quantities, generating sequence at significant depth while simultaneously tracking copy number and presence of common amplifications and deletions. Using this novel resource and capitalizing on the extensive clinically annotated, tissue banks and patient populations at Mayo, we will, for the first time be able to address the prevalence, prognostic implications, and effect on therapeutic responses of each of the common mutations identified in MM cells in large series of patients at relatively low cost. In Aim 1 we will interrogate each of the 77 most commonly mutated, or drug resistance related genes, individually or when assembled by pathways or non-supervised clusters in tumor DNA from 726 newly diagnosed patients. This work will define the spectrum and frequency of mutations in this population; correlate the presence of individual mutations to baseline clinical and laboratory characteristics, response to therapy, and their contribution to relapse and survival. In Aim 2 we will track clonal evolution of disease before, during and after therapy including in states of minimal surviving disease and in earlier “precursor” cell compartments. Specifically, we will conduct a prospective, phase 2 clinical trial across all Mayo sites enrolling 124 relapsing patients assigned to treatment with pomalidomide and dexamethasone alone or the same drugs in combination with carfilzomib. M3P sequencing will be used to characterize the mutational profile and clonal diversity of the surviving tumor clone in different marrow compartments and in peripheral blood; pre therapy, at end of cycle 2, and at 6 months. Finally, in Aim 3 we will generate unbiased sequence data on the mutational profile in general, and the frequency of CRBN/IZKF1/IKZF3/IRF4, IRE1/XBP1s or NR3C1 mutations in particular, contributing to drug resistance in highly drug resistant patients. To cover known, but also seek new mutations, we will use whole exome and RNA sequencing to examine for the first time the molecular profile of truly drug refractory MM in 60 patients with a marrow sample taken within 6 months of death from MM or at time of enrollment on any Phase I trial (including trials in this SPORE application).