Department of Computer Science, Rice University, Houston, TX, USA.
Oxford Nanopore Technologies Inc, New York, NY, USA.
Nat Commun. 2024 Jun 22;15(1):5327. doi: 10.1038/s41467-024-49588-0.
The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease. However, phasing is limited by read length and stretches of homozygosity along the genome. To overcome this limitation, we designed MethPhaser, a method that utilizes methylation signals from Oxford Nanopore Technologies to extend Single Nucleotide Variation (SNV)-based phasing. We demonstrate that haplotype-specific methylations extensively exist in Human genomes and the advent of long-read technologies enabled direct report of methylation signals. For ONT R9 and R10 cell line data, we increase the phase length N50 by 78%-151% at a phasing accuracy of 83.4-98.7% To assess the impact of tissue purity and random methylation signals due to inactivation, we also applied MethPhaser on blood samples from 4 patients, still showing improvements over SNV-only phasing. MethPhaser further improves phasing across HLA and multiple other medically relevant genes, improving our understanding of how mutations interact across multiple phenotypes. The concept of MethPhaser can also be extended to non-human diploid genomes. MethPhaser is available at https://github.com/treangenlab/methphaser .
跨单倍型分配变异，即相位，对于预测突变的后果、相互作用和遗传至关重要，是提高我们对表型和疾病理解的关键步骤。然而，相位受到读长和基因组中同态区域的限制。为了克服这一限制，我们设计了 MethPhaser，这是一种利用 Oxford Nanopore Technologies 的甲基化信号来扩展基于单核苷酸变异 (SNV) 的相位的方法。我们证明了单倍型特异性甲基化在人类基因组中广泛存在，长读长技术的出现使我们能够直接报告甲基化信号。对于 ONT R9 和 R10 细胞系数据，我们将相位长度 N50 提高了 78%-151%，相位准确率为 83.4-98.7%。为了评估组织纯度和由于失活而产生的随机甲基化信号的影响，我们还将 MethPhaser 应用于 4 名患者的血液样本，结果仍然显示出比仅基于 SNV 的相位更好的效果。MethPhaser 进一步改善了 HLA 和多个其他医学相关基因的相位，提高了我们对突变如何在多个表型中相互作用的理解。MethPhaser 的概念也可以扩展到非人类二倍体基因组。MethPhaser 可在 https://github.com/treangenlab/methphaser 获得。
