A Statistical Method for Observing Personal Diploid Methylomes and Transcriptomes with Single-Molecule Real-Time Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Source
2.2. Assignment of Reads to Each Haplotype for AK1 and HG002
2.3. Generating the Diploid Methylomes
2.4. Calculating the Distribution of Phased Heterozygous Variants with Respect to CpG Islands or Exons
2.5. Allele-Specific Expression Analysis of AK1
2.6. Identifying CpG Islands with Allele-Specific Methylation
3. Results
3.1. A Statistical Model for Accurate Read Assignment
3.2. Generating Diploid Methylomes and Transcriptomes for the AK1 and HG002 Datasets
3.3. Distribution of Phased Heterozygous Variants in Two Personal Genomes
3.4. Allele-Specific Methylation of CpG Islands and Allele-Specific Expresion
3.5. Statistics of Allele-Specific Methylation CpG Islands
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ASM | Allele-specific methylation |
ASE | Allele-specific expresssion |
SNP | Single nucleotide polymorphism |
SNV | Single nucleotide variant |
PHV | Phased heterozygous variant |
IPD | Inter-pulse duration |
CGI | CpG island |
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Suzuki, Y.; Wang, Y.; Au, K.F.; Morishita, S. A Statistical Method for Observing Personal Diploid Methylomes and Transcriptomes with Single-Molecule Real-Time Sequencing. Genes 2018, 9, 460. https://doi.org/10.3390/genes9090460
Suzuki Y, Wang Y, Au KF, Morishita S. A Statistical Method for Observing Personal Diploid Methylomes and Transcriptomes with Single-Molecule Real-Time Sequencing. Genes. 2018; 9(9):460. https://doi.org/10.3390/genes9090460
Chicago/Turabian StyleSuzuki, Yuta, Yunhao Wang, Kin Fai Au, and Shinichi Morishita. 2018. "A Statistical Method for Observing Personal Diploid Methylomes and Transcriptomes with Single-Molecule Real-Time Sequencing" Genes 9, no. 9: 460. https://doi.org/10.3390/genes9090460
APA StyleSuzuki, Y., Wang, Y., Au, K. F., & Morishita, S. (2018). A Statistical Method for Observing Personal Diploid Methylomes and Transcriptomes with Single-Molecule Real-Time Sequencing. Genes, 9(9), 460. https://doi.org/10.3390/genes9090460