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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...to indicate expression status. For example, alleles that are not expressed, so called -alleles, are given the suffix “N.” A workshop (“W”) prefix may be used when the gene or lineage status is currently unclear.Classical MHC class II molecules act as peptide receptors that bind degraded protein segments...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
...validation of the semisupervised m6A caller. (A) Description of biological samples used for validation of fibertools. (B) Percentage of methylated adenines called by fibertools relative to all adenines in a whole--amplified (WGA) negative control as a function of the estimated precision reported...
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Method: Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries
- Matthew Wiens,
- Hossein Farahani,
- R. Wilder Scott,
- T. Michael Underhill,
- and Ali Bashashati
Genome Res. August 2024 34: 1196-1210; Published in Advance August 15, 2024, doi:10.1101/gr.277066.122
...with short variant-calling approaches to interrogate the unique haplotype state of individual cells (Fan et al. 2018; Poirion et al. 2018; Ding et al. 2019; Petti et al. 2019; Vu et al. 2019; Zhou et al. 2020; Lu et al. 2021). This pairing enables investigators to extract additional information from...
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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
...-ligation-based haplotype phasing and scaffolding, and adds support for multiple long-read data types. These enhancements allow Verkko2 to assemble all regions of a diploid human , including the short arms of the acrocentric chromosomes and both sex chromosomes. Together, these changes increase the number of telomere...
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Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
- Taishan Hu,
- Timothy L. Mosbruger,
- Nikolaos G. Tairis,
- Amalia Dinou,
- Pushkala Jayaraman,
- Mahdi Sarmady,
- Kingham Brewster,
- Yang Li,
- Tristan J. Hayeck,
- Jamie L. Duke,
- and Dimitri S. Monos
Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
...and assemblyThe next step in phasing the MHC sequences is to connect the locally phased blocks, mentioned above, to a fully phased reference-based haplotype scaffold. This scaffold is created by first calling SNPs across hg38 only at locations on the Infinium Omni2.5-8 array. This restrictive SNP calling...
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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
...has been enormous, and the flagship papers have been cited more than 10,000 times in clinical and basic research studies. The success of the project has been amplified by the use of diverse, high-quality, open-access data sets, and databases such as gnomAD (Koenig et al. 2024) and DECIPHER (Firth et...
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Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- Prashant S. Emani,
- Maya N. Geradi,
- Gamze Gürsoy,
- Monica R. Grasty,
- Andrew Miranker,
- and Mark B. Gerstein
Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
...of the query SNPs are found to match to pairs of haplotypes which may transition to other pairs for the next segment (Fig. 1B).Formally, we find the trajectories as sequences of reference haplotype pairs (for a diploid ) at each locus that best fit the observations: that is, for observed query SNPs at genomic...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...or if the changes are more complex. Units with unique features that occur only once in each haplotype in a given comparison can serve as unique landmarks we call anchors. This is the same approach we used above for DNA/POGO TE-containing units. For example, when a TE is inserted into the array, the combination...
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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
...-specific fashion where heterozygous V or J alleles permitted, with less V gene allele ambiguity than if relying on public databases for IgBLAST (1.5% ambiguous calls vs. 9.6%–23.8%). Our comprehensive list of alleles in both haplotypes reveals some that rarely or never produce productive transcripts, such as IGHV2...
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Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
- Luis F. Paulin,
- Jeremy Fan,
- Kieran O'Neill,
- Erin Pleasance,
- Vanessa L. Porter,
- Steven J.M. Jones,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
...(Smolka et al. 2024). Next, we included SVs from cuteSV (Jiang et al. 2022), Serverus (Keskus et al. 2024), and nanomonSV (Shiraishi et al. 2023). After calling SVs with each tool (cuteSV per sample, Sniffles2, Serverus, and nanomonSV in somatic mode), the SVs were merged into a multisample VCF, then all...

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