Allelic copy number.

(A) Summary of CNVs from DFT1 biopsies and cell lines whose footprint encompassed genotyped MIP alleles (S2 and S3 Tables), as presented in S10 Fig. MIP genotypes and CNVs are only listed in table if the CNV depth in a single direction (gain, loss) was ≥2 and if the MIP ALT allele was either present in the tumour(s) carrying the CNV (gains) or inferred to be present in an ancestor tumour (losses). Details of the sample (clade group, purity), CNV (CNV ID, coordiantes, type (gain, loss), copy number state) and MIP (MIP ID, coordinate, REF and ALT alleles, VAF within the indicated sample) are provided. The best fit genotype (in increments of 0.5) and allele implicated in the CNV are shown. CNVs 3R1 and 9, the parental CNVs of the recurrent chromosome 4 back mutations observed in cell lines, are shown three times each in order to illustrate informative genotyped loci that were captured in different samples. (B) Genotypes at four informative loci in 16 DFT1s (15 cell lines, 1 biopsy) within the chromosome 4 region repeatedly lost in cell lines (CNV IDs 3R1 and 9). The cell lines have CN2, whereas the biopsy, similar to the DFT1 MRCA, has CN3 at these loci. The 3 chromosomal copies (designated chromosomes A, A1, and B, where A and A1 are somatic duplicates) present in the DFT1 MRCA are shown, and the chromosome inferred to have been lost by each cell line is indicated. The clade group to which each cell line belongs is shown. Samples 87T2 and 90T are a single cell line collected at different passages sequenced independently with identical results. “N,” genotype undetermined. (XLSX)

(A) 本部分汇总了DFT1活检样本与细胞系的拷贝数变异（CNV，copy number variation），其变异区域涵盖已完成基因分型的MIP等位基因（详见附表S2、S3），如图S10所示。仅当CNV单方向变异（扩增、缺失）的深度≥2，且MIP的ALT等位基因存在于携带该CNV的肿瘤（对应扩增事件）或被推断存在于祖先肿瘤（对应缺失事件）中时，才会在表格中列出MIP基因型与CNV。本部分提供了样本（进化支群、纯度）、CNV（CNV编号、坐标、变异类型（扩增、缺失）、拷贝数状态）以及MIP（MIP编号、坐标、REF与ALT等位基因、指定样本内的变异等位基因频率（VAF，variant allele frequency））的详细信息。同时展示了以0.5为步长的最佳拟合基因型，以及与该CNV相关的等位基因。细胞系中观察到的复发性4号染色体回复突变的亲本CNV——3R1与9号CNV，各展示三次，以说明在不同样本中捕获到的具有信息价值的基因分型位点。
(B) 本部分展示了16份DFT1样本（15株细胞系、1份活检样本）中4号染色体区域内4个信息位点的基因型，该区域在细胞系中反复发生缺失（CNV编号3R1与9）。细胞系在该类位点的拷贝数为2（CN2），而该活检样本与DFT1最近共同祖先（MRCA，most recent common ancestor）一致，拷贝数为3（CN3）。本部分展示了DFT1 MRCA中存在的3条染色体（命名为A、A1与B，其中A与A1为体细胞复制产生的同源染色体），并标注了每株细胞系推断发生缺失的染色体。同时展示了每株细胞系所属的进化支群。样本87T2与90T为同一株细胞系在不同传代次数下的独立测序样本，测序结果一致。"N"代表基因型未确定。(XLSX)