Van der Linden Malaïka, Raman Lennart, Vander Trappen Ansel, Dheedene Annelies, De Smet Matthias, Sante Tom, Creytens David, Lievens Yolande, Menten Björn, Van Dorpe Jo, Van Roy Nadine
From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy).
Arch Pathol Lab Med. 2019 Dec 17. doi: 10.5858/arpa.2019-0010-OA.
CONTEXT.—: In routine clinical practice, tumor tissue is stored in formalin-fixed, paraffin-embedded blocks. However, the use of formalin-fixed, paraffin-embedded tissue for genome analysis is challenged by poorer DNA quality and quantity. Although several studies have reported genome-wide massive parallel sequencing applied on formalin-fixed, paraffin-embedded samples for mutation analysis, copy number analysis is not yet commonly performed.
OBJECTIVE.—: To evaluate the use of formalin-fixed, paraffin-embedded tissue for copy number alteration detection using shallow whole-genome sequencing, more generally referred to as copy number variation sequencing.
DESIGN.—: We selected samples from 21 patients, covering a range of different tumor entities. The performance of copy number detection was compared across 3 setups: array comparative genomic hybridization in combination with fresh material; copy number variation sequencing on fresh material; and copy number variation sequencing on formalin-fixed, paraffin-embedded material.
RESULTS.—: Very similar copy number profiles between paired samples were obtained. Although formalin-fixed, paraffin-embedded profiles often displayed more noise, detected copy numbers seemed equally reliable if the tumor fraction was at least 20%.
CONCLUSIONS.—: Copy number variation sequencing of formalin-fixed, paraffin-embedded material represents a trustworthy method. It is very likely that copy number variation sequencing of routinely obtained biopsy material will become important for individual patient care and research. Moreover, the basic technology needed for copy number variation sequencing is present in most molecular diagnostics laboratories.
在常规临床实践中，肿瘤组织被储存在福尔马林固定、石蜡包埋的组织块中。然而，使用福尔马林固定、石蜡包埋的组织进行基因组分析受到DNA质量和数量较差的挑战。尽管有几项研究报告了在福尔马林固定、石蜡包埋的样本上应用全基因组大规模平行测序进行突变分析，但拷贝数分析尚未普遍开展。
使用浅全基因组测序（更普遍称为拷贝数变异测序）评估福尔马林固定、石蜡包埋的组织在检测拷贝数改变方面的应用。
我们从21例患者中选取样本，涵盖一系列不同的肿瘤实体。在三种设置下比较拷贝数检测的性能：与新鲜材料联合使用的阵列比较基因组杂交；新鲜材料上的拷贝数变异测序；福尔马林固定、石蜡包埋材料上的拷贝数变异测序。
配对样本之间获得了非常相似的拷贝数谱。尽管福尔马林固定、石蜡包埋的谱通常显示出更多噪声，但如果肿瘤比例至少为20%，检测到的拷贝数似乎同样可靠。
福尔马林固定、石蜡包埋材料的拷贝数变异测序是一种可靠的方法。常规获取的活检材料的拷贝数变异测序很可能对个体患者的护理和研究变得重要。此外，大多数分子诊断实验室都具备拷贝数变异测序所需的基本技术。
