使用固定乳腺癌组织切片检测内分泌治疗敏感性的定制检测的技术有效性。

Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue.

机构信息

Department of Translational Molecular Pathology, UT MD Anderson Cancer Center, Houston, TX.

Department of Medicine, Yale University School of Medicine, New Haven, CT.

出版信息

Clin Chem. 2020 Jul 1;66(7):934-945. doi: 10.1093/clinchem/hvaa105.

DOI:10.1093/clinchem/hvaa105

PMID:32613237

Abstract

BACKGROUND

We translated a multigene expression index to predict sensitivity to endocrine therapy for Stage II-III breast cancer (SET2,3) to hybridization-based expression assays of formalin-fixed paraffin-embedded (FFPE) tissue sections. Here we report the technical validity with FFPE samples, including preanalytical and analytical performance.

METHODS

We calibrated SET2,3 from microarrays (Affymetrix U133A) of frozen samples to hybridization-based assays of FFPE tissue, using bead-based QuantiGene Plex (QGP) and slide-based NanoString (NS). The following preanalytical and analytical conditions were tested in controlled studies: replicates within and between frozen and fixed samples, age of paraffin blocks, homogenization of fixed sections versus extracted RNA, core biopsy versus surgically resected tumor, technical replicates, precision over 20 weeks, limiting dilution, linear range, and analytical sensitivity. Lin's concordance correlation coefficient (CCC) was used to measure concordance between measurements.

RESULTS

SET2,3 index was calibrated to use with QGP (CCC 0.94) and NS (CCC 0.93) technical platforms, and was validated in two cohorts of older fixed samples using QGP (CCC 0.72, 0.85) and NS (CCC 0.78, 0.78). QGP assay was concordant using direct homogenization of fixed sections versus purified RNA (CCC 0.97) and between core and surgical sample types (CCC 0.90), with 100% accuracy in technical replicates, 1-9% coefficient of variation over 20 weekly tests, linear range 3.0-11.5 (log2 counts), and analytical sensitivity ≥2.0 (log2 counts).

CONCLUSIONS

Measurement of the novel SET2,3 assay was technically valid from fixed tumor sections of biopsy or resection samples using simple, inexpensive, hybridization methods, without the need for RNA purification.

摘要

背景

我们将一个多基因表达指数转化为预测 II-III 期乳腺癌（SET2,3）对内分泌治疗敏感性的方法，应用于福尔马林固定石蜡包埋（FFPE）组织切片的杂交表达分析。在此，我们报告了该方法在 FFPE 样本中的技术有效性，包括分析前和分析性能。

方法

我们使用基于珠子的 QuantiGene Plex（QGP）和基于玻片的 NanoString（NS）技术，将 SET2,3 从冷冻样本的微阵列（Affymetrix U133A）校准到 FFPE 组织的杂交分析。在对照研究中测试了以下分析前和分析条件：冷冻和固定样本内和样本间的重复、石蜡块的年龄、固定切片的均一化与提取 RNA 相比、核心活检与手术切除肿瘤、技术重复、20 周以上的精密度、稀释极限、线性范围和分析灵敏度。使用 Lin 的一致性相关系数（CCC）来衡量测量之间的一致性。

结果

SET2,3 指数已校准为与 QGP（CCC 0.94）和 NS（CCC 0.93）技术平台一起使用，并在使用 QGP（CCC 0.72，0.85）和 NS（CCC 0.78，0.78）的两个较旧固定样本队列中得到验证。QGP 分析使用固定切片的直接均一化与纯化 RNA（CCC 0.97）之间以及核心与手术样本类型之间（CCC 0.90）的一致性较好，技术重复的准确率为 100%，20 周以上的变异系数为 1-9%，线性范围为 3.0-11.5（log2 计数），分析灵敏度≥2.0（log2 计数）。