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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...alignments is a key strength of our aligner.DiscussionIn this paper, we describe Moni-align, the first short-read pan aligner based on the r-index. The r-index has advantages over graph-based indexes because it can be constructed without a costly multiple alignment step and fully preserves the sequences...
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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
...) or 59 (Miyatake et al. 2022a) RE loci in small retrospective cohorts of 37 and 22 patients, respectively. Alternatively, short-read sequencing (SR-GS) is emerging as a potential replacement for exome sequencing in rare disorders. This shift is driven by recognition of the gains achievable in diagnostic...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...repertoire, we combined sequencing of the germline IG loci with single-cell transcriptome sequencing of B cells from the same donor. Sequencing and assembly of the germline IG loci captured the IGH locus in a single fully phased contig where the maternal and paternal contributions to the germline V, D, and J...
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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
...-read sequencing, enabling the generation of highly accurate assemblies without the need for short-read polishing.This method has several important limitations. First, adaptive sampling relies on matching the first approximately 200 bases of each read to the IGH reference (Loose et al. 2016), so truly novel...
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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
.... These collaborative efforts have yielded invaluable insights into the molecular mechanisms underlying cancer initiation, progression, and metastasis, uncovering recurring patterns of genomic alterations, novel cancer genes, and pathways. Consequently, short-read sequencing for both tumor and germline is routinely...
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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
...are amplified and size-selected to maintain the target length. The amplicons are then prepared for long-read sequencing. (Created with BioRender; https://www.biorender.com/)While many long-read capture methods use the same probes that would be used for short-read approaches, there is evidence that fewer probes...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...and the cells’ innate immune response (Russell et al. 2019). The value of long reads for both DNA and RNA sequencing was demonstrated by a study of the human adaptive immune system's response to MMR vaccination. ONT sequencing was used to characterize both the transcriptome of single B cells and relevant loci...
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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
...). Briefly, Paragraph genotypes SVs by constructing localized sequence graphs containing the reference allele and the candidate SV allele and performs a localized realignment of paired-end short reads to the graph. The genotype is then determined based on the coverage of reads uniquely supporting...
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Research: Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
- Hyunchul Jung,
- Jung Kyoon Choi,
- and Eunjung Alice Lee
Genome Res. August 2018 28: 1136-1146; Published in Advance July 3, 2018, doi:10.1101/gr.231837.117
...allele with exon skipping caused by a somatic L1 insertion shown in A. The esophageal cancer sample had eight heterozygous SNVs in MOV10. For each of the eight SNV loci, the number of reads with a reference allele and an alternative allele is shown for both whole- sequencing (DNA) and RNA-sequencing data...
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Research: Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background
- Ingegerd Elvers,
- Jason Turner-Maier,
- Ross Swofford,
- Michele Koltookian,
- Jeremy Johnson,
- Chip Stewart,
- Cheng-Zhong Zhang,
- Steven E. Schumacher,
- Rameen Beroukhim,
- Mara Rosenberg,
- Rachael Thomas,
- Evan Mauceli,
- Gad Getz,
- Federica Di Palma,
- Jaime F. Modiano,
- Matthew Breen,
- Kerstin Lindblad-Toh,
- and Jessica Alföldi
Genome Res. November 2015 25: 1634-1645; Published in Advance September 16, 2015, doi:10.1101/gr.194449.115
...and average mutations per breed and immunophenotype are indicated. (B) Exome libraries were sequenced and variants were called with MuTect, a caller adapted for cancer data, and IndeLocator. Somatic variants were annotated using SnpEff. MuSiC was used for identification of significantly mutated genes...
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