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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
...are reduced by the consensus of multiple (≥3) repeats. NanoRCS offers a precise, multimodal nanopore sequencing-based strategy for cfDNA sequencing through the accurate identification of tumor-informed SNVs along with CNAs and fragmentation length patterns in cfDNA (Fig. 1D).View larger version...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
- Jonas A. Gustafson,
- Sophia B. Gibson,
- Nikhita Damaraju,
- Miranda P.G. Zalusky,
- Kendra Hoekzema,
- David Twesigomwe,
- Lei Yang,
- Anthony A. Snead,
- Phillip A. Richmond,
- Wouter De Coster,
- Nathan D. Olson,
- Andrea Guarracino,
- Qiuhui Li,
- Angela L. Miller,
- Joy Goffena,
- Zachary B. Anderson,
- Sophie H.R. Storz,
- Sydney A. Ward,
- Maisha Sinha,
- Claudia Gonzaga-Jauregui,
- Wayne E. Clarke,
- Anna O. Basile,
- André Corvelo,
- Catherine Reeves,
- Adrienne Helland,
- Rajeeva Lochan Musunuri,
- Mahler Revsine,
- Karynne E. Patterson,
- Cate R. Paschal,
- Christina Zakarian,
- Sara Goodwin,
- Tanner D. Jensen,
- Esther Robb,
- The 1000 Genomes ONT Sequencing Consortium,
- University of Washington Center for Rare Disease Research (UW-CRDR),
- Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
- William Richard McCombie,
- Fritz J. Sedlazeck,
- Justin M. Zook,
- Stephen B. Montgomery,
- Erik Garrison,
- Mikhail Kolmogorov,
- Michael C. Schatz,
- Richard N. McLaughlin, Jr.,
- Harriet Dashnow,
- Michael C. Zody,
- Matt Loose,
- Miten Jain,
- Evan E. Eichler,
- and Danny E. Miller
Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
...sequencing-based map of normal patterns of human genetic variation for filtering and prioritizing candidate disease-causing variants (International HapMap Consortium 2005; The 1000 Genomes Project Consortium 2015; Byrska-Bishop et al. 2022). The impact of 1KGP on our understanding of human genetic diversity...
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Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
..., and other fields (Desai et al. 2020; Merritt et al. 2020; Brady et al. 2021; Butler et al. 2021; Jerby-Arnon et al. 2021; Pelka et al. 2021; Rao et al. 2021; Rendeiro et al. 2021). Existing spatial gene expression platforms operate at a range of plex and with diverse profiling strategies. Sequencing-based...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
.... Bioinformatics strategies, challenges, and opportunities for next generation sequencing-based HLA genotyping. Transfus Med Hemother 46: 312–325. doi:10.1159/000502487 ↵Klitz W, Maiers M, Spellman S, Baxter-Lowe LA, Schmeckpeper B, Williams TM, Fernandez-Viña M. 2003. New HLA haplotype frequency reference...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...Haplotype-resolved and population genomics of the threatened garden dormouse in Europe Paige A. Byerly1,2,16, Alina von Thaden1,2,16, Evgeny Leushkin1,3, Leon Hilgers1,3, Shenglin Liu1,3, Sven Winter4,5, Tilman Schell1,3, Charlotte Gerheim1,3, Alexander Ben Hamadou1,3, Carola Greve1,3, Christian...
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Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
..., California 94720, USA; 6Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA ↵7 Present address: Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA Corresponding authors: jbanfield@berkeley.edu, meren@uchicago.eduAbstractGenomes...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA; 5Centre de Recherche en Biologie cellulaire...
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Research: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements
- Luisa Berná,
- Pablo Marquez,
- Andrés Cabrera,
- Gonzalo Greif,
- María E. Francia,
- and Carlos Robello
Genome Res. May 2021 31: 823-833; Published in Advance April 27, 2021, doi:10.1101/gr.262832.120
...characterization of four novel Neospora caninum strains. Parasitol Res 118: 3535–3542. doi:10.1007/s00436-019-06474-9 ↵Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. 2012. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics...
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Resource: Recompleting the Caenorhabditis elegans genome
- Jun Yoshimura,
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Idan Gabdank,
- Lamia Wahba,
- Cheryl L. Smith,
- Mark L. Edgley,
- Ann E. Rougvie,
- Andrew Z. Fire,
- Shinichi Morishita,
- and Erich M. Schwarz
Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
...encoded unchanged products in VC2010; moreover, we predicted ≥53 new genes in VC2010. The recompleted of C. elegans should be a valuable resource for genetics, genomics, and systems biology.The usefulness of model organisms in modern biology partly comes from their having reference assemblies...
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