Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
Genome Biol. 2024 Jun 10;25(1):151. doi: 10.1186/s13059-024-03275-x.
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.
去卷积方法从包括血液和组织在内的混合样本的批量测量中推断出定量的细胞类型估计。DNA 甲基化测序每条读取测量多个 CpG，但很少有现有的去卷积方法利用这种读取内信息。我们开发了 CelFiE-ISH，它扩展了现有的方法（CelFiE）来使用读取内单倍型信息。CelFiE-ISH 优于 CelFiE 和其他现有的方法，实现了 30%更好的准确性和更敏感的稀有细胞类型检测。我们还证明了标记选择和为单倍型感知方法定制标记的重要性。虽然这里我们使用了黄金标准的短读测序数据，但单倍型感知方法将非常适合长读测序。
Zotero 插件
