Searching journal content for articles similar to Freeman et al. 30 (3): 415.

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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...in cancer s, a comprehensive understanding 66 of somatic SV's scope and mechanisms is essential for uncovering key cancer mutations in 67 patient tumors. 68 69 However, despite the widespread clinical application of somatic SV detection methods based 70 on second-generation short-read sequencing...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...sequences and their association with expression quantitative trait loci (eQTLs) to form the most comprehensive resource of this type, accessible through the UCSC Genome Browser. If your GOI and/or candidate TF are known to be expressed in human cancer, two useful tools that are relevant are DepMap, which...
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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
...conducted as part of patient management.While short-read sequencing has greatly advanced our understanding of cancer susceptibility and progression, it faces several major challenges that have systematically excluded certain parts of the and certain types of variations from studies. Most notably, short...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
...integrated into the host cell (Huang et al. 2008). HPV integration is associated with changes in the sequence content of HPV, viral gene copy number, and epigenetic regulation of the viral (Groves et al. 2016; Warburton et al. 2018, 2021). Genomic and epigenomic changes can also occur in adjacent human...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge CB10 1SA, United Kingdom Corresponding author: ana.conesa@csic.esAbstractLong-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full...
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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
.... 2020). However, such methods provide incomplete information owing to the lack of informative polymorphisms found in >20% of individuals (Onozawa et al. 2015), quantitatively limited analysis of just a few CpG sites and one or two genomic loci with the potential for PCR bias, the requirement...
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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
...loci. More recently, careful analysis and categorization of clinical manifestations served as essential tools in recent discoveries where the same expansion mutations occurring at different genomic loci all resulted in benign adult familial myoclonic epilepsy (BAFME), also known as familial adult...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage s publicly available. Importantly, as the number of sequenced s increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior...
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Resource: Discordant calls across genotype discovery approaches elucidate variants with systematic errors
- Elizabeth G. Atkinson,
- Mykyta Artomov,
- Alexander A. Loboda,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Konrad J. Karczewski,
- Benjamin M. Neale,
- and Mark J. Daly
Genome Res. May 30, 2023 ; Published in Advance May 30, 2023, doi:10.1101/gr.277908.123
...platform biases (Fig. 2B). Finally, we used data from The 1000 Genomes Project (The 1000 Genomes Project Consortium 2012) as an independent public data set for testing the predictor. Exome sequences from 1393 samples (Supplemental Table S3) were used to create the variant call set following GATK best...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...) technologies continue to make whole- sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs...
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