De Mattos-Arruda L, Weigelt B, Cortes J, Won H H, Ng C K Y, Nuciforo P, Bidard F-C, Aura C, Saura C, Peg V, Piscuoglio S, Oliveira M, Smolders Y, Patel P, Norton L, Tabernero J, Berger M F, Seoane J, Reis-Filho J S
Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona; Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA.
Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA.
Ann Oncol. 2014 Sep;25(9):1729-1735. doi: 10.1093/annonc/mdu239. Epub 2014 Jul 9.
Plasma-derived cell-free tumor DNA (ctDNA) constitutes a potential surrogate for tumor DNA obtained from tissue biopsies. We posit that massively parallel sequencing (MPS) analysis of ctDNA may help define the repertoire of mutations in breast cancer and monitor tumor somatic alterations during the course of targeted therapy.
A 66-year-old patient presented with synchronous estrogen receptor-positive/HER2-negative, highly proliferative, grade 2, mixed invasive ductal-lobular carcinoma with bone and liver metastases at diagnosis. DNA extracted from archival tumor material, plasma and peripheral blood leukocytes was subjected to targeted MPS using a platform comprising 300 cancer genes known to harbor actionable mutations. Multiple plasma samples were collected during the fourth line of treatment with an AKT inhibitor.
Average read depths of 287x were obtained from the archival primary tumor, 139x from the liver metastasis and between 200x and 900x from ctDNA samples. Sixteen somatic non-synonymous mutations were detected in the liver metastasis, of which 9 (CDKN2A, AKT1, TP53, JAK3, TSC1, NF1, CDH1, MML3 and CTNNB1) were also detected in >5% of the alleles found in the primary tumor sample. Not all mutations identified in the metastasis were reliably identified in the primary tumor (e.g. FLT4). Analysis of ctDNA, nevertheless, captured all mutations present in the primary tumor and/or liver metastasis. In the longitudinal monitoring of the patient, the mutant allele fractions identified in ctDNA samples varied over time and mirrored the pharmacodynamic response to the targeted therapy as assessed by positron emission tomography-computed tomography.
This proof-of-principle study is one of the first to demonstrate that high-depth targeted MPS of plasma-derived ctDNA constitutes a potential tool for de novo mutation identification and monitoring of somatic genetic alterations during the course of targeted therapy, and may be employed to overcome the challenges posed by intra-tumor genetic heterogeneity.
www.clinicaltrials.gov, NCT01090960.
血浆来源的游离肿瘤DNA（ctDNA）可作为从组织活检获取的肿瘤DNA的潜在替代物。我们推测，对ctDNA进行大规模平行测序（MPS）分析可能有助于明确乳腺癌的突变谱，并在靶向治疗过程中监测肿瘤体细胞改变。
一名66岁患者在诊断时患有同步性雌激素受体阳性/人表皮生长因子受体2阴性、高增殖性、2级、混合性浸润性导管-小叶癌，并伴有骨和肝转移。使用包含300个已知携带可操作突变的癌症基因的平台，对从存档肿瘤材料、血浆和外周血白细胞中提取的DNA进行靶向MPS分析。在使用AKT抑制剂进行第四线治疗期间收集了多个血浆样本。
存档原发性肿瘤的平均测序深度为287x，肝转移灶为139x，ctDNA样本为200x至900x。在肝转移灶中检测到16个体细胞非同义突变，其中9个（CDKN2A、AKT1、TP53、JAK3、TSC1、NF1、CDH1、MML3和CTNNB1）在原发性肿瘤样本中超过5%的等位基因中也被检测到。并非转移灶中鉴定出的所有突变都能在原发性肿瘤中可靠鉴定（例如FLT4）。然而，对ctDNA的分析捕获了原发性肿瘤和/或肝转移灶中存在的所有突变。在对该患者的纵向监测中，ctDNA样本中鉴定出的突变等位基因分数随时间变化，并反映了通过正电子发射断层扫描-计算机断层扫描评估的对靶向治疗的药效学反应。
这项原理验证研究是首批证明对血浆来源的ctDNA进行高深度靶向MPS可作为从头突变鉴定和在靶向治疗过程中监测体细胞遗传改变的潜在工具，并可用于克服肿瘤内遗传异质性带来的挑战的研究之一。
