一种基于液滴数字聚合酶链反应的辅助黑色素瘤诊断工具：利用164例黑素细胞肿瘤开发四基因检测板

A Droplet Digital Polymerase Chain Reaction-Based Tool to Aid in Melanoma Diagnosis: Development of a 4-Gene Panel Using 164 Melanocytic Neoplasms.

作者信息

McFadden Jason R, Salem Iman, Stevanovic Mirjana, Barney Rachael E, Chaudhari Advaita S, Chambers Meagan Ann, O'Hern Keegan, Cloutier Jeffrey M, Yan Shaofeng, Ramos-Rodriguez Alvaro J, Kerr Darcy Arendt, Momtahen Shabnam, LeBlanc Robert E, Tsongalis Gregory J, Hughes Edward G, Sriharan Aravindhan

机构信息

From the Department of Biological Sciences (McFadden, Chaudhari), and the Geisel School of Medicine (Stevanovic, Kerr, Tsongalis, Sriharan), Dartmouth College, Hanover, New Hampshire.

the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire.

出版信息

Arch Pathol Lab Med. 2025 May 1;149(5):410-421. doi: 10.5858/arpa.2024-0027-OA.

DOI:10.5858/arpa.2024-0027-OA

PMID:39084636

Abstract

CONTEXT.—: Detecting copy number variations (CNVs) at certain loci can aid in the diagnosis of histologically ambiguous melanocytic neoplasms. Droplet digital polymerase chain reaction (ddPCR) is a rapid, automated, and inexpensive method for CNV detection in other cancers, but not yet melanoma.

OBJECTIVE.—: To evaluate the performance of a 4-gene ddPCR panel that simultaneously tests for ras responsive binding element protein 1 (RREB1) gain; cyclin-dependent kinase inhibitor 2A (CDKN2A) loss; MYC proto-oncogene, bHLH transcription factor (MYC) gain; and MYB proto-oncogene, transcription factor (MYB) loss in melanocytic neoplasms.

DESIGN.—: One hundred sixty-four formalin-fixed, paraffin-embedded skin samples were used to develop the assay, of which 65 were used to evaluate its performance. Chromosomal microarray analysis (CMA) data were used as the gold standard.

RESULTS.—: ddPCR demonstrated high concordance with CMA in detecting RREB1 gain (sensitivity, 86.7%; specificity, 88.9%), CDKN2A loss (sensitivity, 80%; specificity, 100%), MYC gain (sensitivity, 70%; specificity, 100%), and MYB loss (sensitivity, 71.4%; specificity, 100%). When one CNV was required to designate the test as positive, the 4-gene ddPCR panel distinguished nevi from melanomas with a sensitivity of 78.4% and a specificity of 71.4%. For reference, CMA had a sensitivity of 86.2% and a specificity of 78.6%. Our data also revealed interesting relationships with histology, namely (1) a positive correlation between RREB1 ddPCR copy number and degree of tumor progression; (2) a statistically significant correlation between MYC gain and nodular growth; and (3) a statistically significant correlation between MYB loss and a sheetlike pattern of growth.

CONCLUSIONS.—: With further validation, ddPCR may aid both in our understanding of melanomagenesis and in the diagnosis of challenging melanocytic neoplasms.

摘要

背景

在某些基因座检测拷贝数变异（CNV）有助于诊断组织学上难以明确的黑素细胞肿瘤。液滴数字聚合酶链反应（ddPCR）是一种用于检测其他癌症中CNV的快速、自动化且廉价的方法，但尚未用于黑色素瘤检测。

目的

评估一个四基因ddPCR检测板在黑素细胞肿瘤中同时检测ras反应元件结合蛋白1（RREB1）扩增、细胞周期蛋白依赖性激酶抑制剂2A（CDKN2A）缺失、MYC原癌基因、bHLH转录因子（MYC）扩增以及MYB原癌基因、转录因子（MYB）缺失的性能。

设计

使用164份福尔马林固定、石蜡包埋的皮肤样本开发该检测方法，其中65份用于评估其性能。染色体微阵列分析（CMA）数据用作金标准。

结果

ddPCR在检测RREB1扩增（敏感性86.7%；特异性88.9%）、CDKN2A缺失（敏感性80%；特异性100%）、MYC扩增（敏感性70%；特异性100%）和MYB缺失（敏感性71.4%；特异性100%）方面与CMA具有高度一致性。当需要一个CNV将检测判定为阳性时，四基因ddPCR检测板区分痣和黑色素瘤的敏感性为78.4%，特异性为71.4%。作为参考，CMA的敏感性为86.2%，特异性为78.6%。我们的数据还揭示了与组织学的有趣关系，即（1）RREB1 ddPCR拷贝数与肿瘤进展程度呈正相关；（2）MYC扩增与结节状生长之间存在统计学显著相关性；（3）MYB缺失与片状生长模式之间存在统计学显著相关性。