Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals

Gong, Wentao; Pan, Xiangchun; Xu, Dantong; Ji, Guanyu; Wang, Yifei; Tian, Yuhan; Cai, Jiali; Li, Jiaqi; Zhang, Zhe; Yuan, Xiaolong

doi:10.1016/j.csbj.2022.08.051

Cited by 8 publications

(8 citation statements)

References 60 publications

(84 reference statements)

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“…Apart from the data qualification, the mapping ratio was the second challenge mainly affected by computational methods and would impact the final methylation calls [ 27 ]. Herein, we then focused on comparing the mapping ratio and subsequently methylation conversion from the perspective of the platforms as well as data processing pipelines.…”

Section: Resultsmentioning

confidence: 99%

“…Coupled with a proliferation of bisulfite-seq mapping tools [ 22 ], benchmarking studies have been implemented using real data downloaded and generated from platforms [ 23 , 24 ]. According to those studies, in those dazzling tools, BSMAP [ 24 – 27 ], Bismark [ 22 , 24 , 27 ], BatMeth2 [ 28 ], and BS Seeker2 [ 27 ] outperform substantially all of the other pipelines based on different aligning algorithms, and corresponding information was listed in Table 1 For the mapping algorithm, Bowtie2 is much better for PE150 [ 29 , 30 ], and Bowtie is much better for a shorter read [ 31 ]. Thus, in terms of our PE150 reads, we choose Bowtie2 as Bismark’s and BS Seeker2’s aligners (Table 1 ).…”

Section: Introductionmentioning

confidence: 99%

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Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform

et al. 2023

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Background Whole genome bisulfite sequencing (WGBS), possesses the aptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine (5-mC) on a genome-wide scale. It is a powerful technique for epigenome in various cell types, and tissues. As a recently established next-generation sequencing (NGS) platform, GenoLab M is a promising alternative platform. However, its comprehensive evaluation for WGBS has not been reported. We sequenced two bisulfite-converted mammal DNA in this research using our GenoLab M and NovaSeq 6000, respectively. Then, we systematically compared those data via four widely used WGBS tools (BSMAP, Bismark, BatMeth2, BS-Seeker2) and a new bisulfite-seq tool (BSBolt). We interrogated their computational time, genome depth and coverage, and evaluated their percentage of methylated Cs. Result Here, benchmarking a combination of pre- and post-processing methods, we found that trimming improved the performance of mapping efficiency in eight datasets. The data from two platforms uncovered ~ 80% of CpG sites genome-wide in the human cell line. Those data sequenced by GenoLab M achieved a far lower proportion of duplicates (~ 5.5%). Among pipelines, BSMAP provided an intriguing representation of 5-mC distribution at CpG sites with 5-mC levels > ~ 78% in datasets from human cell lines, especially in the GenoLab M. BSMAP performed more advantages in running time, uniquely mapped reads percentages, genomic coverage, and quantitative accuracy. Finally, compared with the previous methylation pattern of human cell line and mouse tissue, we confirmed that the data from GenoLab M performed similar consistency and accuracy in methylation levels of CpG sites with that from NovaSeq 6000. Conclusion Together we confirmed that GenoLab M was a qualified NGS platform for WGBS with high performance. Our results showed that BSMAP was the suitable pipeline that allowed for WGBS studies on the GenoLab M platform.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform

et al. 2023

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“…The sequencing of these libraries was performed on an Illumina Nova-Seq 6000 (Illumina, San Diego, CA, USA) using the PE150 model. The sequencing reads were filtered to exclude the low-quality reads (Phred score < 5), and then were aligned to the human reference genome (hg19) using BSMAP (Version 2.74) [ 18 ]. We identified the differentially methylated CpGs (DMCs) using metilene (Version 0.2-6) [ 19 ], selected the CpGs that were covered by more than 10× sequence reads, and reached the thresholds of differential methylation β ≥ 15% between the patients and controls for gene annotation.…”

Section: Methodsmentioning

confidence: 99%

cfDNA Methylation Profiles and T-Cell Differentiation in Women with Endometrial Polyps

Niu

et al. 2022

Cells

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DNA methylation is a part of the regulatory mechanisms of gene expression, including chromatin remodeling and the activity of microRNAs, which are involved in the regulation of T-cell differentiation and function. However, the role of cfDNA methylation in T-cell differentiation is entirely unknown. In patients with endometrial polyps (EPs), we have found an imbalance of T-cell differentiation and an aberrant cfDNA methylation profile, respectively. In this study, we investigated the relationship between cfDNA methylation profiles and T-cell differentiation in 14 people with EPs and 27 healthy controls. We found that several differentially methylated genes (DMGs) were associated with T-cell differentiation in people with EPs (ITGA2-Naïve CD4, r = −0.560, p = 0.037; CST9-EMRA CD4, r = −0.626, p = 0.017; and ZIM2-CM CD8, r = 0.576, p = 0.031), but not in healthy controls (all p > 0.05). When we combined the patients’ characteristics, we found a significant association between ITGA2 methylation and polyp diameter (r = 0.562, p = 0.036), but this effect was lost when adjusting the level of Naïve CD4 T-cells (r = 0.038, p = 0.903). Moreover, the circulating sex hormone levels were associated with T-cell differentiation (estradiol-Naïve CD4, r = −0.589, p = 0.027), and the cfDNA methylation profile (testosterone-ZIM2, r = −0.656, p = 0.011). In conclusion, this study has established a link between cfDNA methylation profiles and T-cell differentiation among people with EPs, which may contribute to the etiology of EPs. Further functional studies are warranted.

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“…Figure 3 summarizes the pipelines and components for evaluating WGBS datasets. In a recent benchmark study with 14 alignment algorithms for WGBS in mammals, Gong et al (2022) documented that Bwa-meth, BSBolt, BSMAP, Bismark-bwt2-e2e and Walt exhibited higher uniquely mapped reads, mapped precision, recall, and F1 score than others. However, performance statistics for mammalian genomes may not be directly applicable to crop genomes, which are typically more complex.…”

Section: Whole Genome Bisulfite Sequencingmentioning

confidence: 99%

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Agius

Kapazoglou²,

Avramidou³

et al. 2023

Front. Plant Sci.

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Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.

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Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals

Cited by 8 publications

References 60 publications

Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform

Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform

cfDNA Methylation Profiles and T-Cell Differentiation in Women with Endometrial Polyps

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

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