We performed shallow single-cell sequencing of genomic DNA across 1475 cells from a cell-line, COLO829, to resolve overall complexity and clonality. This melanoma tumor-line has been previously characterized by multiple technologies and is a benchmark for evaluating somatic alterations. In some of these studies, COLO829 has shown conflicting and/or indeterminate copy number and, thus, single-cell sequencing provides a tool for gaining insight. Following shallow single-cell sequencing, we first identified at least four major sub-clones by discriminant analysis of principal components of single-cell copy number data. Based on clustering, break-point and loss of heterozygosity analysis of aggregated data from sub-clones, we identified distinct hallmark events that were validated within bulk sequencing and spectral karyotyping. In summary, COLO829 exhibits a classical Dutrillaux’s monosomic/trisomic pattern of karyotype evolution with endoreduplication, where consistent sub-clones emerge from the loss/gain of abnormal chromosomes. Overall, our results demonstrate how shallow copy number profiling can uncover hidden biological insights.

我们对来自COLO829细胞系的1475个细胞进行了基因组DNA的浅层单细胞测序，以解决总体复杂性和克隆性问题。该黑素瘤肿瘤细胞系先前已通过多种技术表征，并且是评估体细胞变化的基准。在其中一些研究中，COLO829已显示出冲突的和/或不确定的拷贝数，因此，单细胞测序提供了获得洞察力的工具。浅层单细胞测序后，我们通过判别分析单细胞拷贝数数据的主要成分，首先鉴定出至少四个主要的亚克隆。基于聚类分析，断点分析和杂合子丢失，分析了来自亚克隆的汇总数据，我们确定了独特的标志性事件，这些事件在批量测序和光谱核型分析中得到了验证。综上所述，COLO829表现出经典的Dutrillaux核型复制的单体/三体模式和核内复制，其中一致的亚克隆来自异常染色体的丢失/获得。总体而言，我们的结果表明，浅拷贝数分析可以揭示隐藏的生物学见解。