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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
...) Alignment of PacBio HiFi reads from healthy donor 1 (HD1) onto the hg38 reference . The top IGV track shows PacBio HiFi reads grouped by origin: centromeric (H1.1) and telomeric (H1.2) side of the duplication in haplotype 1 (H1), and haplotype 2 (H2). The middle track shows a single ultra-long ONT read...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...Guanapo population. High-molecular-weight genomic DNA from the YY male was sequenced on the Pacific Biosciences platform, and both Y haplotypes were reconstructed by Trio binning. By mapping of male specific SNPs and RADseq sequences, we identify a single male specific-region of ∼5 Mb length at the distal...
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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 assemblies concatenated together using again Chromap but allowing for multimapping reads (-q 0) to avoid discarding information in regions identical between two haplotypes. We also identified telomeric sequences with tidk v.0.2.31 (https://github.com/tolkit/telomeric-identifier) and where...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...of the cy0333 MHC M3 haplotype of MCM full genomic region. The MHC full genomic region is defined as everything from the telomeric gene GABBR1 to the centromeric gene KIFC1, as per the method of Shiina et al. (2017). Gene content is separated into putatively expressed genes on the left line and noncoding...
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Method: Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples
- Sergey Aganezov and
- Benjamin J. Raphael
Genome Res. September 2020 30: 1274-1290; Published in Advance September 4, 2020, doi:10.1101/gr.256701.119
...’s reconstructions of clone- and haplotype-specific karyotypes will aid further studies of the role of intra-tumor heterogeneity in cancer development and response to treatment. RCK is freely available as open source software.The somatic mutations that drive cancer development range across all genomic scales, from...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...for a CfxA2 beta-lactamase gene. We find clear recombination blocks for these AMR gene haplotypes, showcasing devider's ability to unveil evolutionary signals for heterogeneous mixtures.The presence of highly similar genomic sequences within a single organism or a group of organisms is common in biological...
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Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
- Lucinda C. Xiao,
- Ayush Semwal,
- Brianna St John,
- Kathleen Zeglinski,
- Shian Su,
- James Lancaster,
- Shifeng Xue,
- Bruno Reversade,
- Matthew E. Ritchie,
- Frédérique Magdinier,
- Marnie E. Blewitt,
- and Quentin Gouil
Genome Res. April 2026 36: 827-848; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
...incompletely understood despite their relevance to facioscapulohumeral muscular dystrophy (FSHD). Current FSHD molecular testing relies on complex, multistep and low-resolution assays, which aim to identify contractions on permissive haplotypes (FSHD type 1) or epigenetic reactivation due to pathogenic...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...G gene body methylation of the lower-expressed allele. This suggests that epigenetically regulated ASE is likely a previously overlooked mechanism facilitating plant infection. Overall, our study reveals how dikaryotism uniquely shapes key eukaryotic features.Telomere-to-telomere (T2T) and haplotype...
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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
...to phenotype in population-scale and rare disease studies, as well as in cancer. Recent developments in sequencing throughput and computational methods, such as pan graphs and haplotype-resolved assemblies, are paving the way for the future inclusion of long-read sequencing in clinical cohort studies...
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Method: Telomere-to-telomere assembly by preserving contained reads
- Sudhanva Shyam Kamath,
- Mehak Bindra,
- Debnath Pal,
- and Chirag Jain
Genome Res. November 2024 34: 1908-1918; Published in Advance October 15, 2024, doi:10.1101/gr.279311.124
..., we achieved a twofold increase in the contig NG50 and the number of haplotype-resolved T2T contigs compared to hifiasm.Building high-quality haplotype-resolved de novo assemblies remains a principal challenge in genomics research. The Telomere-to-Telomere (T2T) Consortium's assembly of the CHM13...

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