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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...used for mitochondrial recovery and species identification. Long-read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation...
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Method: A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
- Yi Qiao,
- Xiaomeng Huang,
- Philip J. Moos,
- Jonathan M. Ahmann,
- Anthony D. Pomicter,
- Michael W. Deininger,
- John C. Byrd,
- Jennifer A. Woyach,
- Deborah M. Stephens,
- and Gabor T. Marth
Genome Res. January 2024 34: 94-105; Published in Advance January 9, 2024, doi:10.1101/gr.278234.123
...A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data Yi Qiao1,6, Xiaomeng Huang1,6, Philip J. Moos2, Jonathan M. Ahmann3, Anthony D. Pomicter3, Michael W. Deininger3,4, John C. Byrd5, Jennifer A. Woyach5, Deborah M. Stephens3...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...et al. 2006). Extensive sequencing of MHC-I transcript and genomic DNA PCR amplicons suggests that this expansion of MHC-B genes is common in both rhesus and cynomolgus macaques (Otting et al. 2005; Doxiadis et al. 2013; Wiseman et al. 2013; Karl et al. 2017; Shortreed et al. 2020). These MHC...
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Method: Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks
- Jin Li,
- Yan Li,
- Wei Li,
- Huaibing Luo,
- Yanping Xi,
- Shihua Dong,
- Ming Gao,
- Peng Xu,
- Baolong Zhang,
- Ying Liang,
- Qingping Zou,
- Xin Hu,
- Lina Peng,
- Dan Zou,
- Ting Wang,
- Hongbo Yang,
- Cizhong Jiang,
- Shaoliang Peng,
- Feizhen Wu,
- and Wenqiang Yu
Genome Res. February 2019 29: 270-280; Published in Advance January 22, 2019, doi:10.1101/gr.240606.118
...methylation levels that were then confirmed by bisulfite TA clone sequencing (Fig. 1H). Moreover, we validated 13 additional regions using bisulfite pyrosequencing, the results of which continue to demonstrate the efficiency of GPS in detecting global DNA methylation (Supplemental Fig. S3C,D).We next compared...
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Research: The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A
- Xiaoyang Dou,
- Jerome D. Boyd-Kirkup,
- Joseph McDermott,
- Xiaoli Zhang,
- Fang Li,
- Bowen Rong,
- Rui Zhang,
- Bisi Miao,
- Peilin Chen,
- Hao Cheng,
- Jianhuang Xue,
- David Bennett,
- Jiemin Wong,
- Fei Lan,
- and Jing-Dong J. Han
Genome Res. October 2019 29: 1622-1634; Published in Advance September 19, 2019, doi:10.1101/gr.234021.117
...), but are of great potential importance because alterations to mtDNA expression or coding sequences are directly causative of premature aging (Trifunovic et al. 2004) and metabolic and neurodegenerative diseases (Schapira 2012).Discovery of mtDNA methylation was reported in the 1970s using radiolabeling (Nass 1973...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
....arnaud@uca.frAbstractIn cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution...
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LETTER: Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA
- Yulia Korshunova,
- Rebecca K. Maloney,
- Nathan Lakey,
- Robert W. Citek,
- Blaire Bacher,
- Arief Budiman,
- Jared M. Ordway,
- W. Richard McCombie,
- Jorge Leon,
- Jeffrey A. Jeddeloh,
- and John D. McPherson
Genome Res. January 2008 18: 19-29; Published in Advance November 21, 2007, doi:10.1101/gr.6883307
...al. 2006 ). The use of such technology, for sequencing bisulphite-mutagenized DNA, eliminates the cloning step and yet delivers a detailed picture of the cytosine-methylation landscape with more reduced labor and time than the conventional clone-based strategy. Since pyrosequencing technologies...
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LETTER: HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
- Gary P. Wang,
- Angela Ciuffi,
- Jeremy Leipzig,
- Charles C. Berry,
- and Frederic D. Bushman
Genome Res. August 2007 17: 1186-1194; Published in Advance June 1, 2007, doi:10.1101/gr.6286907
...). However, whether integration in host-cell chromosomal DNA takes place in nucleosome-wrapped DNA has not previously been studied. Here we present a study of integration site selection by HIV, taking advantage of massively parallel DNA sequencing based on pyrophosphate release (“pyrosequencing”) ( Margulies...
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Methods: Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
- Chunlin Wang,
- Yumi Mitsuya,
- Baback Gharizadeh,
- Mostafa Ronaghi,
- and Robert W. Shafer
Genome Res. August 2007 17: 1195-1201; Published in Advance June 28, 2007, doi:10.1101/gr.6468307
...20 sequencing platform allows massively parallel picoliter-scale amplification and pyrosequencing of individual DNA molecules ( Margulies et al. 2005 ). Simons and colleagues described two cases in which ultra-deep pyrosequencing detected minority variant drug-resistance mutations in a previously...
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Methods: Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)
- Zhenyi Liu,
- Anna C. Obenauf,
- Michael R. Speicher,
- and Raphael Kopan
Genome Res. November 2009 19: 2081-2089; Published in Advance October 1, 2009, doi:10.1101/gr.093856.109
...these quantitative problems into a determination of single nucleotide variation (SNV) frequencies by pyrosequencing. Pyrosequencing sequences single-strand DNA by coupling nucleotide incorporation onto a sequencing primer with the production of bioluminescence signals, producing readouts called ‘‘pyrograms...

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