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Method: Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples
- Hua Zhang,
- Vamsi Krishna Polavarapu,
- Pengwei Xing,
- Miao Zhao,
- Lucy Mathot,
- Linxuan Zhao,
- Gabriela Rosen,
- Fredrik J. Swartling,
- Tobias Sjöblom,
- and Xingqi Chen
Genome Res. January 2022 32: 150-161; Published in Advance July 14, 2021, doi:10.1101/gr.275269.121
...by sequencing (ATAC-seq) (Buenrostro et al. 2013) and DNase I hypersensitivity sequencing (DNase-seq) (Jin et al. 2015), allow profiling of chromatin accessibility in cells and frozen tissues. Archived formalin-fixed paraffin-embedded (FFPE) tissues are the global standard format for preservation...
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Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
..., small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using cap analysis gene expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...(Fig. 2E; Supplemental Fig. S2C–L). In EAC samples, somatic SNVs were determined by sequencing formalin-fixed paraffin-embedded (FFPE) tumor biopsies, which is known to cause false positive somatic SNV calls (Do and Dobrovic 2015; Robbe et al. 2018). This implies that the majority of the false positive...
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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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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...of microRNA expression analyses is reflected by the existence of thousands of sRNA-seq studies in which matched total RNA-seq data are often unavailable. The lack of paired sequencing experiments limits the analysis of microRNA–gene regulatory networks. Here, we explore whether protein-coding gene...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...Dayea Park and Can Cenik Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA Corresponding author: ccenik@austin.utexas.eduAbstractLong-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights...
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Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
- Wei-Hao Lee,
- Lechuan Li,
- Ruth Dannenfelser,
- and Vicky Yao
Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
...; 4Rice Synthetic Biology Institute, Rice University, Houston, Texas 77005, USA ↵5 These authors contributed equally to this work. Corresponding author: vy@rice.eduAbstractAs sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has...
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Method: Accurate assembly of circular RNAs with TERRACE
- Tasfia Zahin,
- Qian Shi,
- Xiaofei Carl Zang,
- and Mingfu Shao
Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
...to detect expressed circRNAs in cells. The RNA sequencing (RNA-seq) protocols that target on linear RNAs or mRNAs with poly(A) tails will neglect circRNAs (Kristensen et al. 2022). Tailored RNA-seq experiments have been designed for circRNAs, for example, using RNase R to digest linear RNAs and therefore...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...also examined two ONT assemblies generated with Flye (Kolmogorov et al. 2019), with different read length cutoffs (1 kb and 45 kb; the coverages are 400× and 100×). Briefly, we checked for each mRNA, the proportion of its sequence that is present in the assemblies (Supplemental Methods). The rationale...
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Method: DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly
- Ilari Scheinin,
- Daoud Sie,
- Henrik Bengtsson,
- Mark A. van de Wiel,
- Adam B. Olshen,
- Hinke F. van Thuijl,
- Hendrik F. van Essen,
- Paul P. Eijk,
- François Rustenburg,
- Gerrit A. Meijer,
- Jaap C. Reijneveld,
- Pieter Wesseling,
- Daniel Pinkel,
- Donna G. Albertson,
- and Bauke Ylstra
Genome Res. December 2014 24: 2022-2032; Published in Advance September 18, 2014, doi:10.1101/gr.175141.114
...in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due...
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