DNA fingerprinting of glioma cell lines and considerations on similarity measurements
DNA fingerprinting of glioma cell lines and considerations on similarity measurements
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DOI：
10.1093/neuonc/nos072
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发表时间：
2012-06-01
期刊：
影响因子：
15.9
通讯作者：
Hegi, Monika E.
中科院分区：
文献类型：
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作者：
Bady, Pierre;Diserens, Annie-Claire;Hegi, Monika E.
胶质瘤细胞系是基础和转化神经肿瘤学研究的重要工具。记录其遗传身份已成为科学期刊和资助申请的一项要求，以排除导致结果误解的交叉污染和错误识别。在这里，我们报告了 39 个广泛使用的神经胶质瘤细胞系的标准 16 标记短串联重复 (SIR) DNA 指纹作为参考。对指纹本身以及与包含 2278 个细胞系的 9 个标记 STR 的大型 DSMZ 数据库进行比较，发现了 3 个错误识别的细胞系，并证实了先前已知的交叉污染。此外，2 个神经胶质瘤细胞系的同一性得分为 0.8，建议将其作为检测交叉污染的临界值。其他特征，包括一个品系中缺乏 B-raf 突变以及另一个品系中与原始肿瘤组织的相似性得分为 1，排除了交叉污染。随后的模拟程序表明，当使用仅包含 9 个 SIR 标记的 DNA 指纹时，常用的相似性评分 0.8 不够严格，不足以明确区分起源。 DNA 指纹因癌细胞系中频繁的遗传改变而变得混乱，特别是杂合性的丧失，这降低了 SIR 标记的信息量，从而降低了整体区分能力。相似性得分取决于测量的标记数量；因此，可能需要更多的标记或额外的细胞系特征，例如有关特定突变的信息，以澄清起源。
Glioma cell lines are an important tool for research in basic and translational neuro-oncology. Documentation of their genetic identity has become a requirement for scientific journals and grant applications to exclude cross-contamination and misidentification that lead to misinterpretation of results. Here, we report the standard 16 marker short tandem repeat (SIR) DNA fingerprints for a panel of 39 widely used glioma cell lines as reference. Comparison of the fingerprints among themselves and with the large DSMZ database comprising 9 marker STRs for 2278 cell lines uncovered 3 misidentified cell lines and confirmed previously known cross-contaminations. Furthermore, 2 glioma cell lines exhibited identity scores of 0.8, which is proposed as the cutoff for detecting cross-contamination. Additional characteristics, comprising lack of a B-raf mutation in one line and a similarity score of 1 with the original tumor tissue in the other, excluded a cross-contamination. Subsequent simulation procedures suggested that, when using DNA fingerprints comprising only 9 SIR markers, the commonly used similarity score of 0.8 is not sufficiently stringent to unambiguously differentiate the origin. DNA fingerprints are confounded by frequent genetic alterations in cancer cell lines, particularly loss of heterozygosity, that reduce the informativeness of SIR markers and, thereby, the overall power for distinction. The similarity score depends on the number of markers measured; thus, more markers or additional cell line characteristics, such as information on specific mutations, may be necessary to clarify the origin.