CelFiE-ISH：根据单分子 DNA 甲基化单倍型进行多细胞类型解旋的概率模型

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-06-10 DOI:10.1186/s13059-024-03275-x

Irene Unterman, Dana Avrahami, Efrat Katsman, Triche Tim Jr., Benjamin Glaser, Benjamin P. Berman

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引用次数: 0

摘要

解卷积方法可从混合样本（包括血液和组织）的大量测量中推断出定量的细胞类型估计值。DNA 甲基化测序能测量每个读数的多个 CpGs，但现有的解卷积方法很少能利用读数内信息。我们开发了 CelFiE-ISH，它扩展了现有方法（CelFiE），使用了读数内单体型信息。CelFiE-ISH 优于 CelFiE 和其他现有方法，准确率提高了 30%，对罕见细胞类型的检测也更加灵敏。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。虽然我们在这里使用的是黄金标准的短线程测序数据，但单体型感知方法将非常适合长线程测序。

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CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes

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.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.