The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor–normal genomic DNA (gDNA) samples derived from a breast cancer cell line—which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations—and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking ‘tumor-only’ or ‘matched tumor–normal’ analyses.

缺乏用于生成标准化 DNA 数据集以建立测序管道或对不同算法的性能进行基准测试的样本限制了癌症基因组学的实施和采用。在这里，我们描述了从来自乳腺癌细胞系的成对肿瘤-正常基因组 DNA (gDNA) 样本获得的参考调用集——该细胞系具有高度异质性，具有非整倍体基因组，并且富含体细胞改变——以及匹配的类淋巴母细胞系。我们通过使用不同测序平台的全外显子组测序 (WES) 和具有 >2,000 倍覆盖率的靶向测序，以高置信度跨越 82% 的基因组区域，部分验证了这些调用集中的体细胞突变和种系变异。尽管 gDNA 参考样本不能代表临床样本中的原发性癌细胞，