Allele-specific methylation (ASM) is an epigenetic modification whereby one parental allele becomes methylated and the other unmethylated at a specific locus. ASM is most often driven by the presence of nearby heterozygous variants that influence methylation, but also occurs somatically in the context of genomic imprinting. In this study, we investigate ASM using publicly available single-cell reduced representation bisulfite sequencing (scRRBS) data on 608 B cells sampled from six healthy B cell samples and 1,230 cells from 11 chronic lymphocytic leukemia (CLL) samples. We developed a likelihood-based criterion to test whether a CpG exhibited ASM, based on the distributions of methylated and unmethylated reads both within and across cells. Applying our likelihood ratio test, 65,998 CpG sites exhibited ASM in healthy B cell samples according to a Bonferroni criterion (p < 8.4 × 10), and 32,862 CpG sites exhibited ASM in CLL samples (p < 8.5 × 10). We also called ASM at the sample level. To evaluate the accuracy of our method, we called heterozygous variants from the scRRBS data, which enabled variant-based calls of ASM within each cell. Comparing sample-level ASM calls to the variant-based measures of ASM, we observed a positive predictive value of 76%–100% across samples. We observed high concordance of ASM across samples and an overrepresentation of ASM in previously reported imprinted genes and genes with imprinting binding motifs. Our study demonstrates that single-cell bisulfite sequencing is a potentially powerful tool to investigate ASM, especially as studies expand to increase the number of samples and cells sequenced.

中文翻译：

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研究单细胞 DNA 甲基化数据检测等位基因特异性甲基化和印记的潜力


等位基因特异性甲基化 (ASM) 是一种表观遗传修饰，其中一个亲本等位基因在特定位点甲基化，而另一个未甲基化。 ASM 通常是由影响甲基化的附近杂合变异的存在驱动的，但也会在基因组印记的背景下发生在体细胞上。在这项研究中，我们使用公开的单细胞还原代表性亚硫酸氢盐测序 (scRRBS) 数据对从 6 个健康 B 细胞样本中采样的 608 个 B 细胞和从 11 个慢性淋巴细胞白血病 (CLL) 样本中采样的 1,230 个细胞进行了 ASM 研究。我们开发了一种基于可能性的标准，根据细胞内和细胞间甲基化和非甲基化读数的分布来测试 CpG 是否表现出 ASM。应用我们的似然比检验，根据 Bonferroni 标准，65,998 个 CpG 位点在健康 B 细胞样本中表现出 ASM (p < 8.4 × 10)，32,862 个 CpG 位点在 CLL 样本中表现出 ASM (p < 8.5 × 10)。我们还在样本级别称为 ASM。为了评估我们方法的准确性，我们从 scRRBS 数据中调用杂合变体，这使得每个细胞内能够基于变体调用 ASM。将样本级 ASM 调用与基于变体的 ASM 测量进行比较，我们观察到样本的阳性预测值为 76%–100%。我们观察到样品间 ASM 的高度一致性，以及先前报道的印记基因和具有印记结合基序的基因中 ASM 的过度表达。我们的研究表明，单细胞亚硫酸氢盐测序是研究 ASM 的潜在强大工具，特别是随着研究的扩展以增加测序样本和细胞的数量。