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Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
- Wouter De Coster,
- Ida Höijer,
- Inge Bruggeman,
- Svenn D'Hert,
- Malin Melin,
- Adam Ameur,
- and Rosa Rademakers
Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
...adaptor ligation. Nat Biotechnol 38: 433–438. doi:10.1038/s41587-020-0407-5 ↵Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, et al. 2024. High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...We obtained unaligned HiFi LRS data for the HG002 individual from PacBio (https://downloads.pacbcloud.com/public/revio/2022Q4/). We obtained ONT R10 stereo duplex LRS data for HG002 from the Human Pangenomics Project (https://human-pangenomics.s3.amazonaws.com/index.html?prefix=submissions/0CB931D5-AE0C-4187...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...in this study have been submitted to the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under accession number PRJNA1196145. Sequencing data and complete IGH assemblies from samples HD1, HD2, MS1, and MS2 generated in this study have been submitted to the European Genome-phenome Archive...
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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
...(GWAS) catalog. This study effectively doubled the number of detected variants compared to short-read sequencing alone. Subsequent efforts have extended to additional diverse populations, such as the resequencing of 1000 Genomes Project samples using long reads that discovered extensive SVs missed...
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Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
- Sergey Aganezov,
- Sara Goodwin,
- Rachel M. Sherman,
- Fritz J. Sedlazeck,
- Gayatri Arun,
- Sonam Bhatia,
- Isac Lee,
- Melanie Kirsche,
- Robert Wappel,
- Melissa Kramer,
- Karen Kostroff,
- David L. Spector,
- Winston Timp,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
...decades. Prior to the completion of the Human Genome Project, only a small handful of oncogenes or tumor suppressors were known (Taparowsky et al. 1982; Li et al. 1997). Large-scale detection of cancer mutations began around the year 2000 after the initial sequencing of the human using either microarrays...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...-based enrichment strategies offered on the ONT platform provide faster, flexible, and more economical options to obtain very high coverage of large targets of interest. However, all approaches discussed in this section are less applicable for large projects that survey 100s of targets across 100s...
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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
...nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Res 34: 2061–2073. doi:10.1101/gr.279273.124 ↵Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pan Reference Consortium, Marschall T, Li H, Paten B. 2024. Pan...
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...a singleton approach with one additional diagnosis that was missed by SR-GS, a known likely pathogenic hemizygous stop-loss variant in IKBKG. Another larger effort from the Genomic Answers for Kids project sequenced 256 affected participants with diverse pediatric disorders, many of which remained undiagnosed...
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Research: A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
- Jesper Eisfeldt,
- Adam Ameur,
- Felix Lenner,
- Esmee Ten Berk de Boer,
- Marlene Ek,
- Josephine Wincent,
- Raquel Vaz,
- Jesper Ottosson,
- Tord Jonson,
- Sofie Ivarsson,
- Sofia Thunström,
- Alexandra Topa,
- Simon Stenberg,
- Anna Rohlin,
- Anna Sandestig,
- Margareta Nordling,
- Pia Palmebäck,
- Magnus Burstedt,
- Frida Nordin,
- Eva-Lena Stattin,
- Maria Sobol,
- Panagiotis Baliakas,
- Marie-Louise Bondeson,
- Ida Höijer,
- Kristine Bilgrav Saether,
- Lovisa Lovmar,
- Hans Ehrencrona,
- Malin Melin,
- Lars Feuk,
- and Anna Lindstrand
Genome Res. November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124
...sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Res (this issue) 34: 2061–2073. doi:10.1101/gr.279273.124 ↵Harvey WT, Ebert P, Ebler J, Audano PA, Munson KM, Hoekzema K, Porubsky D, Beck CR, Marschall T, Garimella K, et al. 2023. Whole...
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Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
...of variation (ratio of standard deviation to the mean TR joint allele size). Then we applied PCA based on the joint allele sizes. For 40/47 matching samples with SNP data from the 1000 Genomes Project (1000 Genomes Project Consortium 2015), we also performed PCA based on 30,544 randomly sampled common (minor...
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