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Research: Genome-scale analysis of aberrant DNA methylation in colorectal cancer
- Toshinori Hinoue,
- Daniel J. Weisenberger,
- Christopher P.E. Lange,
- Hui Shen,
- Hyang-Min Byun,
- David Van Den Berg,
- Simeen Malik,
- Fei Pan,
- Houtan Noushmehr,
- Cornelis M. van Dijk,
- Rob A.E.M. Tollenaar,
- and Peter W. Laird
Genome Res. February 2012 22: 271-282; Published in Advance June 9, 2011, doi:10.1101/gr.117523.110
...and deletions of subchromosomal genomic regions, and loss of heterozygosity (LOH) (Pino and Chung 2010).Two major types of epigenetic modifications closely linked to CRC are DNA methylation and covalent histone modifications (Jones and Baylin 2007). Aberrant DNA methylation of CpG islands has been reported...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
..., as well as a current drug target against Huntington's disease. The D haplotype at this locus harbors a cluster of variants near the 5′ end of Msh3, including multiple missense variants near the DNA mismatch recognition domain. In contrast, the B haplotype contains a unique retrotransposon insertion...
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Research: The role of DNA methylation in directing the functional organization of the cancer epigenome
- Fides D. Lay,
- Yaping Liu,
- Theresa K. Kelly,
- Heather Witt,
- Peggy J. Farnham,
- Peter A. Jones,
- and Benjamin P. Berman
Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
...-deficient derivative. The NOMe-seq accessibility assay unexpectedly revealed symmetrical and transcription-independent nucleosomal phasing across active, poised, and inactive genomic elements. DNA methylation abolished this phasing primarily at enhancers and CpG island (CGI) promoters, with little effect on insulators...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...long-read DNA libraries, which is a limitation as most archival tumor samples are formalin-fixed paraffin-embedded (FFPE). To distinguish between germline and somatic variants, tumor samples are often complemented by matching normal samples (The ICGA/TCGA Pan-Cancer Analysis of Whole Genomes Consortium...
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Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
- Fiorella C. Grandi,
- James M. Rosser,
- Simon J. Newkirk,
- Jun Yin,
- Xiaoling Jiang,
- Zhuo Xing,
- Leanne Whitmore,
- Sanum Bashir,
- Zoltán Ivics,
- Zsuzsanna Izsvák,
- Ping Ye,
- Y. Eugene Yu,
- and Wenfeng An
Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
...genes have a lower frequency of L1s and SINEs near their transcription start sites, suggesting retrotransposons may modulate predisposition to DNA methylation in cancer (Estécio et al. 2010). In the male germline, proper remethylation of retrotransposons after -wide demethylation is crucial...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...These authors contributed equally to this review. Corresponding author: christopher.pearson@sickkids.caAbstractExpansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans...
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Research: Extensive somatic L1 retrotransposition in colorectal tumors
- Szilvia Solyom,
- Adam D. Ewing,
- Eric P. Rahrmann,
- Tara Doucet,
- Heather H. Nelson,
- Michael B. Burns,
- Reuben S. Harris,
- David F. Sigmon,
- Alex Casella,
- Bracha Erlanger,
- Sarah Wheelan,
- Kyle R. Upton,
- Ruchi Shukla,
- Geoffrey J. Faulkner,
- David A. Largaespada,
- and Haig H. Kazazian, Jr.
Genome Res. December 2012 22: 2328-2338; Published in Advance September 11, 2012, doi:10.1101/gr.145235.112
...family members (Bogerd et al. 2006; Chen et al. 2006; Muckenfuss et al. 2006; Stenglein and Harris 2006) or DNA repair enzymes (Gasior et al. 2006; Suzuki et al. 2009; Coufal et al. 2011). Here we applied two high-throughput L1-targeted resequencing methods to discover retrotransposon activity...
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Research: Age-related epigenetic drift in the pathogenesis of MDS and AML
- Shinji Maegawa,
- Sheryl M. Gough,
- Naoko Watanabe-Okochi,
- Yue Lu,
- Nianxiang Zhang,
- Ryan J. Castoro,
- Marcos R.H. Estecio,
- Jaroslav Jelinek,
- Shoudan Liang,
- Toshio Kitamura,
- Peter D. Aplan,
- and Jean-Pierre J. Issa
Genome Res. April 2014 24: 580-591; Published in Advance January 10, 2014, doi:10.1101/gr.157529.113
...-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res 17: 1529–1536. Estecio MR, Gallegos J, Vallot C, Castoro RJ, Chung W, Maegawa S, Oki Y, Kondo Y, Jelinek J, Shen L, et al. 2010. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer...

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