Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain.
Exp Mol Pathol. 2018 Jun;104(3):161-169. doi: 10.1016/j.yexmp.2018.03.006. Epub 2018 Mar 31.
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.
病理档案与关联的临床数据是转化研究的宝贵资源，但大多数癌症样本都是经福尔马林固定、石蜡包埋（FFPE）的组织。因此，FFPE 组织是基因组分析研究的重要资源，但由于提取的核酸数量少且质量低，其利用率较低。我们使用从 FFPE 组织中提取的 DNA 通过浅层全基因组测序对 356 名乳腺癌患者的拷贝数图谱进行了分析。我们总共从 2 个试剂盒中生成了 491 个测序文库，获得了 98.4%的文库数据，其中 86.4%的文库质量良好。我们从低至 3.8ng 的输入 DNA 中生成了文库，并且发现文库的成功生成与输入 DNA 的量和质量、处理地点以及固定组织的年龄无关。由于拷贝数改变（CNA）在乳腺癌中起着重要作用，因此我们必须能够使用 FFPE 档案，本研究表明 sWGS 是进行此类分析的一种可靠方法。
