It became apparent several years ago that RNAseq and exome files prepared from tissue could be mined for adaptive immune receptor (IR) recombinations, which has given extra value to datasets originally intended for gene expression or mutation studies. For example, recovery of IR recombination reads from tumour specimen genomics files can correlate with survival rates. In particular, many benchmarking processes have been applied to the two sets of the IR recombination reads obtained from the cancer genome atlas files, but these two sets have never been directly compared. Here we show that both sets largely agree regarding several parameters. For example, recovery of TRB recombination reads from both WXS and RNAseq files representing metastatic melanoma was associated with a better outcome (p < .0004 in both cases); and T-cell receptor recombination read recovery, for both genomics file types, associated very strongly with T-cell gene expression markers. However, the use of CDR3 chemical features for survival distinctions was not consistent. This topic, and the surprising result that both datasets indicated that primary melanoma with recovery of IR recombination reads, in stark contrast to metastatic melanoma, represents a worse outcome, are discussed.

中文翻译：

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来自肿瘤外显子组或 RNAseq 文件的免疫受体重组数据库的比较：验证原发性和转移性黑色素瘤之间的免疫学区别

几年前很明显，从组织中制备的 RNAseq 和外显子组文件可以用于适应性免疫受体 (IR) 重组，这为最初用于基因表达或突变研究的数据集提供了额外的价值。例如，从肿瘤样本基因组文件中恢复 IR 重组读数可以与存活率相关。特别是，许多基准测试过程已应用于从癌症基因组图谱文件中获得的两组 IR 重组读数，但从未直接比较这两组。在这里，我们表明两组在几个参数方面基本一致。例如，从代表转移性黑色素瘤的 WXS 和 RNAseq 文件中恢复 TRB 重组读数与更好的结果相关（p < .0004 在两种情况下）；对于这两种基因组文件类型，T 细胞受体重组读取恢复与 T 细胞基因表达标记密切相关。然而，使用 CDR3 化学特征来区分生存并不一致。讨论了这个主题，以及两个数据集都表明原发性黑色素瘤与 IR 重组读数恢复的令人惊讶的结果，与转移性黑色素瘤形成鲜明对比，代表了更糟糕的结果。