scholarly journals Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis

2008 ◽  
Vol 36 (5) ◽  
pp. e34-e34 ◽  
Author(s):  
C. Rohde ◽  
Y. Zhang ◽  
T. P. Jurkowski ◽  
H. Stamerjohanns ◽  
R. Reinhardt ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Web Server ◽  
Sequencing Data ◽  
Methylation Analysis ◽  
Data Presentation ◽  
Bisulfite Sequencing Data ◽  
Dna Methylation Analysis

scholarly journals Bisulfite sequencing Data Presentation and Compilation (BDPC) web server – a useful tool for DNA methylation analysis

2008 ◽  
Vol 2008 (Spring) ◽  
Author(s):  
Christian Rohde ◽  
Yingying Zhang ◽  
Tomasz P. Jurkowski ◽  
Heinrich Stamerjohanns ◽  
Richard Reinhardt* ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Web Server ◽  
Sequencing Data ◽  
Methylation Analysis ◽  
Data Presentation ◽  
Bisulfite Sequencing Data ◽  
Dna Methylation Analysis

scholarly journals BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing

2018 ◽  
Author(s):  
Haoyu Cheng ◽  
Yun Xu
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Standard Technique ◽  
Whole Genome ◽  
Sequencing Data ◽  
Methylation Analysis ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Computational Bottleneck ◽  
Dna Methylation Analysis

AbstractAs a gold-standard technique for DNA methylation analysis, whole-genome bisulfite sequencing (WGBS) helps researchers to study the genome-wide DNA methylation at single-base resolution. However, aligning WGBS reads to the large reference genome is a major computational bottleneck in DNA methylation analysis projects. Although several WGBS aligners have been developed in recent years, it is difficult for them to efficiently process the ever-increasing bisulfite sequencing data. Here we propose BitMapperBS, an ultrafast and memory-efficient aligner that is designed for WGBS reads. To improve the performance of BitMapperBS, we propose various strategies specifically for the challenges that are unique to the WGBS aligners, which are ignored in most existing methods. Our experiments on real and simulated datasets show that BitMapperBS is one order of magnitude faster than the state-of-the-art WGBS aligners, while achieves similar or better sensitivity and precision. BitMapperBS is freely available at https://github.com/chhylp123/BitMapperBS.

scholarly journals New clustering module in BDPC bisulfite sequencing data presentation and compilation web application for DNA methylation analyses

BioTechniques ◽  
2009 ◽  
Vol 47 (3) ◽  
pp. 781-783 ◽  
Author(s):  
Christian Rohde ◽  
Yingying Zhang ◽  
Heinrich Stamerjohanns ◽  
Kurt Hecher ◽  
Richard Reinhardt ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Web Application ◽  
Bisulfite Sequencing ◽  
Sequencing Data ◽  
Data Presentation ◽  
Bisulfite Sequencing Data

scholarly journals Focal disruption of DNA methylation dynamics at enhancers in IDH-mutant AML cells

Leukemia ◽  
2021 ◽  
Author(s):  
Elisabeth R. Wilson ◽  
Nichole M. Helton ◽  
Sharon E. Heath ◽  
Robert S. Fulton ◽  
Jacqueline E. Payton ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Myeloid Leukemia ◽  
Bisulfite Sequencing ◽  
Sequencing Data ◽  
Genome Wide ◽  
Cd34 Cells ◽  
Recurrent Mutations ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data ◽  
Acute Myeloid

AbstractRecurrent mutations in IDH1 or IDH2 in acute myeloid leukemia (AML) are associated with increased DNA methylation, but the genome-wide patterns of this hypermethylation phenotype have not been comprehensively studied in AML samples. We analyzed whole-genome bisulfite sequencing data from 15 primary AML samples with IDH1 or IDH2 mutations, which identified ~4000 focal regions that were uniquely hypermethylated in IDHmut samples vs. normal CD34+ cells and other AMLs. These regions had modest hypermethylation in AMLs with biallelic TET2 mutations, and levels of 5-hydroxymethylation that were diminished in IDH and TET-mutant samples, indicating that this hypermethylation results from inhibition of TET-mediated demethylation. Focal hypermethylation in IDHmut AMLs occurred at regions with low methylation in CD34+ cells, implying that DNA methylation and demethylation are active at these loci. AML samples containing IDH and DNMT3AR882 mutations were significantly less hypermethylated, suggesting that IDHmut-associated hypermethylation is mediated by DNMT3A. IDHmut-specific hypermethylation was highly enriched for enhancers that form direct interactions with genes involved in normal hematopoiesis and AML, including MYC and ETV6. These results suggest that focal hypermethylation in IDH-mutant AML occurs by altering the balance between DNA methylation and demethylation, and that disruption of these pathways at enhancers may contribute to AML pathogenesis.

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