EPICC: Evolutionary Predictions in Colorectal Cancer WGS-3

Primary tumour tissue and matched normal samples were prospectively collected from patients undergoing curatively-intentioned surgery at University College London Hospital (UCLH). All patients gave informed consent for collection of their materials to the UCLH Cancer Biobank (REC approval 15/YH/0311). Four regions of each primary cancer were sampled by punch biopsy or scalpel dissection, at 12, 3, 6 and 9 o’clock positions around the tumour periphery. Tissue pieces were manually dissociated under the microscope using two 16 G needles, where individual glands were pulled away from the tissue mass.Sequencing and mutation callingDNA fractions were extracted using the Zymo QuickDNA Microprep plus kit according to the manufacturer’s instructions. Only samples with a total DNA yield higher than 10 ng were taken forward for WGS library preparation. Libraries were prepared using the NEBnext Ultra II FS kit according to manufacturer’s instructions. Samples with sufficient library DNA yield and characteristic fragment size distribution (~200-500 bp) were further subjected to deep (~35x coverage) WGS. Sequence libraries were multiplexed and sequenced on an Illumina Novaseq.

本数据集从伦敦大学学院医院（University College London Hospital，简称UCLH）进行根治性手术的患者中前瞻性地收集了原发肿瘤组织及其匹配的正常样本。所有患者均已就其材料收集事宜向UCLH癌症生物库（REC批准号：15/YH/0311）提供了知情同意。每个原发癌症样本的四个区域通过打孔活检或手术刀切割获取，分别位于肿瘤边缘的12点、3点、6点和9点钟位置。在显微镜下，利用两个16号针头手动将组织切片分离，将单个腺体从组织块中分离出来。按照制造商的说明，使用Zymo QuickDNA Microprep plus试剂盒提取DNA片段。仅总DNA产量超过10纳克的样本用于全基因组测序（WGS）文库的制备。文库的制备遵循NEBnext Ultra II FS试剂盒的制造商指导。具有足够文库DNA产量和特征性片段大小分布（约200-500碱基对）的样本进一步进行深度全基因组测序（约35倍覆盖）。序列文库进行多重化，并在Illumina Novaseq平台上进行测序。