PDF(Pubmed)
Abstract：
Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and tissue. DNA methylation sequencing measures multiple CpGs per read, but few existing deconvolution methods leverage this within-read information. We develop CelFiE-ISH, which extends an existing method (CelFiE) to use within-read haplotype information. CelFiE-ISH outperforms CelFiE and other existing methods, achieving 30% better accuracy and more sensitive detection of rare cell types. We also demonstrate the importance of marker selection and of tailoring markers for haplotype-aware methods. While here we use gold-standard short-read sequencing data, haplotype-aware methods will be well-suited for long-read sequencing.
摘要：
去卷积方法从包括血液和组织的混合样品的批量测量推断定量细胞类型估计。DNA甲基化测序测量每个读数多个CpG，但很少有现有的反卷积方法利用这种读内信息。我们开发CelFiE-ISH,它扩展了现有方法(CelFiE)以使用读内单倍型信息。CelFiE-ISH优于CelFiE和其他现有方法，达到30％更好的准确性和更灵敏的检测稀有细胞类型。我们还证明了标记选择和定制标记对于单倍型感知方法的重要性。在这里，我们使用黄金标准的短读取测序数据，单倍型感知方法将非常适合于长读数测序。
