Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Genomics. 2013 Oct;102(4):270-7. doi: 10.1016/j.ygeno.2013.05.005. Epub 2013 Jun 3.
Two common sources of DNA for whole exome sequencing (WES) are whole blood (WB) and immortalized lymphoblastoid cell line (LCL). However, it is possible that LCLs have a substantially higher rate of mutation than WB, causing concern for their use in sequencing studies. We compared results from paired WB and LCL DNA samples for 16 subjects, using LCLs of low passage number (<5). Using a standard analysis pipeline we detected a large number of discordant genotype calls (approximately 50 per subject) that we segregated into categories of "confidence" based on read-level quality metrics. From these categories and validation by Sanger sequencing, we estimate that the vast majority of the candidate differences were false positives and that our categories were effective in predicting valid sequence differences, including LCLs with putative mosaicism for the non-reference allele (3-4 per exome). These results validate the use of DNA from LCLs of low passage number for exome sequencing.
两种常见的用于全外显子组测序（WES）的 DNA 来源是全血（WB）和永生化淋巴母细胞系（LCL）。然而，LCL 可能比 WB 具有更高的突变率，这引起了人们对其在测序研究中应用的担忧。我们比较了 16 个个体配对的 WB 和 LCL DNA 样本，使用传代数低（<5）的 LCL。使用标准的分析流程，我们检测到大量不一致的基因型调用（每个个体约 50 个），我们根据读取级别的质量指标将它们分为“置信度”类别。从这些类别和 Sanger 测序的验证中，我们估计绝大多数候选差异是假阳性，并且我们的类别有效地预测了有效的序列差异，包括具有非参考等位基因潜在镶嵌性的 LCL（每个外显子 3-4 个）。这些结果验证了使用低传代数的 LCL 进行外显子组测序的用途。
