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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...with lower proportions of phasing-informative reads.FocalSV achieves superior performance in complex somatic SV detection in cancer dataTo extend the evaluation to include SV detection beyond deletions and insertions, we analyzed additional SV types involving complex DNA rearrangements...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...repeats, and amplified gene arrays (e.g., rDNAs).The short arms of the human acrocentric chromosomes, whose base-level structure was first revealed by the T2T-CHM13 reference (Nurk et al. 2022), are most challenging to assemble owing to their long, tandemly repeated rDNA arrays and enrichment...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...ES or srGS was performed as described (Bowling et al. 2017, 2022; East et al. 2021; Hiatt et al. 2021). Briefly, whole blood genomic DNA was isolated using the QIAsymphony (Qiagen), and sequencing libraries were constructed by the HudsonAlpha Genomic Services Lab or the Clinical Services Laboratory, LLC...
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Resource: GenomeVIP: a cloud platform for genomic variant discovery and interpretation
- R. Jay Mashl,
- Adam D. Scott,
- Kuan-lin Huang,
- Matthew A. Wyczalkowski,
- Christopher J. Yoon,
- Beifang Niu,
- Erin DeNardo,
- Venkata D. Yellapantula,
- Robert E. Handsaker,
- Ken Chen,
- Daniel C. Koboldt,
- Kai Ye,
- David Fenyö,
- Benjamin J. Raphael,
- Michael C. Wendl,
- and Li Ding
Genome Res. August 2017 27: 1450-1459; Published in Advance May 18, 2017, doi:10.1101/gr.211656.116
.... An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Res 25: 918–925. Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, ZhangQ, Koboldt DC, XieM, KandothC, et al. 2014. Integrated analysis of germline and somatic...
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Method: Ancestry-agnostic estimation of DNA sample contamination from sequence reads
- Fan Zhang,
- Matthew Flickinger,
- Sarah A. Gagliano Taliun,
- InPSYght Psychiatric Genetics Consortium,
- Gonçalo R. Abecasis,
- Laura J. Scott,
- Steven A. McCaroll,
- Carlos N. Pato,
- Michael Boehnke,
- and Hyun Min Kang
Genome Res. February 2020 30: 185-194; Published in Advance January 24, 2020, doi:10.1101/gr.246934.118
...analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Res 25: 918–925. doi:10.1101/gr.176552.114 ↵Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, et al. 2018. Multiplexed droplet single-cell RNA...
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Method: HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
- Xian Fan,
- Mark Chaisson,
- Luay Nakhleh,
- and Ken Chen
Genome Res. May 2017 27: 793-800; Published in Advance January 19, 2017, doi:10.1101/gr.214767.116
...of variantFigure 1. Diagram of HySA for SV assembly and detection. (A). Abnormally aligned Illumina reads are extracted from a BAM file and aligned to a set of PacBio reads (light blue) generated from the same DNA sample. The cluster of reads associated with an SV is identified using a set of bipartite...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...variants, and deeper insights into the interplay between epigenetics and genomic variation. This mini-review provides a comprehensive overview of the latest developments in long-read DNA sequencing analysis, encompassing reference-based and de novo assembly approaches. We explore the entire workflow, from...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...continue to grow to massive scales, it will be invaluable for researchers to be equipped with tools and resources that facilitate scalable, efficient, and equitable analysis, including allele frequency information, which informs variant deleteriousness (Karczewski et al. 2017). In the service of this goal...
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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
...and sex. (B) Violin plots showing average read length, read N50, and average depth of coverage for all 100 samples. (C) DNA was extracted from cells grown from aliquots received from Coriell and sequenced using the R9.4.1 pore. Data were analyzed using both alignment- and assembly-based approaches...
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Method: Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
- Pratibha Jagannatha,
- Alexandra T. Tankka,
- Daniel A. Lorenz,
- Tao Yu,
- Brian A. Yee,
- Kristopher W. Brannan,
- Cathy J. Zhou,
- Jason G. Underwood,
- and Gene W. Yeo
Genome Res. November 2024 34: 2012-2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
...in Ribo-STAMP samples represents ribosome association with transcripts, and those in APOBEC1-only samples represent the editing profile of the enzyme alone. We generated PacBio-compatible long-read cDNA sequencing libraries from these cell lines induced with dox for 72 h and sequenced three replicates...
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