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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
..., and limitations introduced by cloning or PCR amplification, which affected previous technologies such as Sanger sequencing, Illumina, and 454. A key advantage of LRS is the ability to generate long reads, ranging from ∼20 kb to >1 Mb. Although initial versions of LRS had high error rates (12% to 20%), the latest...
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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
...31) is also required to capture sufficient mutated bases in low TF samples. This is particularly important for patients with early stage cancer and for samples and tumor types with low tumor mutational burden. In theory, NanoRCS lowers throughput capacity by sequencing the same molecule in a single...
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Method: Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
- Lin Lyu,
- Xue Li,
- Ru Feng,
- Xin Zhou,
- Tuhin K. Guha,
- Xiaofei Yu,
- Guo Qiang Chen,
- Yufeng Yao,
- Bing Su,
- Duowu Zou,
- Michael P. Snyder,
- and Lei Chen
Genome Res. March 2023 33: 401-411; Published in Advance March 27, 2023, doi:10.1101/gr.277178.122
...optimization and application.Spatial transcriptomic (ST) sequencing has revolutionized the biological research field. This class of technologies combine the strength of two pillars of modern biological research: sequencing and imaging. One form of ST mapping works by capturing the messenger RNA from...
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Method: Genomic loci susceptible to systematic sequencing bias in clinical whole genomes
- Timothy M. Freeman,
- Genomics England Research Consortium,
- Dennis Wang,
- and Jason Harris
Genome Res. March 2020 30: 415-426; Published in Advance March 10, 2020, doi:10.1101/gr.255349.119
...its application to five small whole sequencing (WGS) noncancer cohorts, to detect how common these systematic biases are and the extent to which they affect different genomic regions and to gauge whether the systematic bias predictions from our method are supported by gold-standard reference data...
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Methods: Decoding Randomly Ordered DNA Arrays
- Kevin L. Gunderson,
- Semyon Kruglyak,
- Michael S. Graige,
- Francisco Garcia,
- Bahram G. Kermani,
- Chanfeng Zhao,
- Diping Che,
- Todd Dickinson,
- Eliza Wickham,
- Jim Bierle,
- Dennis Doucet,
- Monika Milewski,
- Robert Yang,
- Chris Siegmund,
- Juergen Haas,
- Lixin Zhou,
- Arnold Oliphant,
- Jian-Bing Fan,
- Steven Barnard,
- and Mark S. Chee
Genome Res. May 2004 14: 870-877; Published in Advance April 12, 2004, doi:10.1101/gr.2255804
...of a large collection of DNA-linked objects through the use of hybridization, and have applied it to the manufacture of randomly assembled arrays of beads in wells. Once the algorithm has been used to determine the identity of each bead, the microarray can be used in a wide variety of applications, including...
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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
...CTP integration matched perfectly with the reference , whereas the 5′ end sequence without dmCTP integration showed several C→T mismatches due to considerable C→T conversion. To evaluate the accuracy and performance of GPS alignment, we randomly generated one million pair-end reads from the reference human...
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Research: Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
- Zoe June Assaf,
- Susanne Tilk,
- Jane Park,
- Mark L. Siegal,
- and Dmitri A. Petrov
Genome Res. December 2017 27: 1988-2000; Published in Advance October 27, 2017, doi:10.1101/gr.219956.116
...events, while the use of neutral sequences eliminates the confounding effects of natural selection. Unfortunately, these divergence-based methods can be compromised by the assumption that a genomic region is truly neutral and by the fact that even neutral regions can be subject to other selective forces...
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Method: Optimizing sparse sequencing of single cells for highly multiplex copy number profiling
- Timour Baslan,
- Jude Kendall,
- Brian Ward,
- Hilary Cox,
- Anthony Leotta,
- Linda Rodgers,
- Michael Riggs,
- Sean D'Italia,
- Guoli Sun,
- Mao Yong,
- Kristy Miskimen,
- Hannah Gilmore,
- Michael Saborowski,
- Nevenka Dimitrova,
- Alexander Krasnitz,
- Lyndsay Harris,
- Michael Wigler,
- and James Hicks
Genome Res. May 2015 25: 714-724; Published in Advance April 9, 2015, doi:10.1101/gr.188060.114
...that are available. Fortunately, copy number analysis requires only sparse sequence coverage, yet it can distinguish subpopulations and provides deep insights into genetic heterogeneity. Thus, in theory, coupling sparse sequencing withmolecular barcoding approaches offers a means to profile many cells together...
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Research: Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles
- Tannistha Nandi,
- Matthew T.G. Holden,
- Xavier Didelot,
- Kurosh Mehershahi,
- Justin A. Boddey,
- Ifor Beacham,
- Ian Peak,
- John Harting,
- Primo Baybayan,
- Yan Guo,
- Susana Wang,
- Lee Chee How,
- Bernice Sim,
- Angela Essex-Lopresti,
- Mitali Sarkar-Tyson,
- Michelle Nelson,
- Sophie Smither,
- Catherine Ong,
- Lay Tin Aw,
- Chua Hui Hoon,
- Stephen Michell,
- David J. Studholme,
- Richard Titball,
- Swaine L. Chen,
- Julian Parkhill,
- and Patrick Tan
Genome Res. January 2015 25: 129-141; Published in Advance September 18, 2014, doi:10.1101/gr.177543.114
..., we predicted 84,846 high quality SNPs in the WGS panel compared to the K96243 reference (Chr I: 43,829 and Chr II: 41,017). We validated the technical accuracy of the WGS data by Sanger sequencing of 50 randomly selected SNPs. Of the predicted SNPs, all 50 were confirmed by Sanger sequencing. Whole...
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Method: Reconstructing complex regions of genomes using long-read sequencing technology
- John Huddleston,
- Swati Ranade,
- Maika Malig,
- Francesca Antonacci,
- Mark Chaisson,
- Lawrence Hon,
- Peter H. Sudmant,
- Tina A. Graves,
- Can Alkan,
- Megan Y. Dennis,
- Richard K. Wilson,
- Stephen W. Turner,
- Jonas Korlach,
- and Evan E. Eichler
Genome Res. April 2014 24: 688-696; Published in Advance January 13, 2014, doi:10.1101/gr.168450.113
...problem for the de novo assembly of s (Alkan et al. 2011b; Church et al. 2011; Salzberg et al. 2012). Finishing of the human and mouse s involved selecting large-insert BAC clones and subjecting them to capillary-based shotgun sequence and assembly (English et al. 2012). Sanger-based assembly of large...

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