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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
..., the structural diversity of MHC genomic organization in macaques remains poorly understood owing to a lack of adequate genomic reference sequences. We used ultralong Oxford Nanopore and high-accuracy Pacific Biosciences (PacBio) HiFi sequences to fully assemble the ∼5.2-Mb M3 haplotype of an MHC...
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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
...characterize these complex regions to gain insight into the impact of genomic diversity on health and disease. Here we resolve the organization of complete major histocompatibility complex (MHC) class II regions in rhesus macaques by using a long-read sequencing strategy (Oxford Nanopore Technologies...
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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
...could utilize parental Illumina short-read data for phasing. For more details on near-complete assembly and assembly algorithms, we encourage the reader to follow the review of Li and Durbin (2024).In general, assemblers first produce continuous sequences built upon overlapping individual reads...
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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
...years has revolutionized our ability to catalog cancer risk variants and understand the genomic landscape of cancer. Early studies relied on targeted sequencing and microarrays to detect genomic and transcriptomic variations enriched in cancer patients, revealing, for example, the prevalence...
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Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
- Charles Cole,
- Ashley Byrne,
- Matthew Adams,
- Roger Volden,
- and Christopher Vollmers
Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
...within an individual's (HLA typing) is of central importance to establish compatibility of donor and recipient for organ and bone marrow transplantation.Currently, HLA typing is performed in clinical laboratories by amplifying the genomic DNA encoding these genes and sequencing the resulting amplicons...
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Research: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
- Claire Vandiedonck,
- Martin S. Taylor,
- Helen E. Lockstone,
- Katharine Plant,
- Jennifer M. Taylor,
- Caroline Durrant,
- John Broxholme,
- Benjamin P. Fairfax,
- and Julian C. Knight
Genome Res. July 2011 21: 1042-1054; Published in Advance May 31, 2011, doi:10.1101/gr.116681.110
...represented in COX than in PGF and QBL. Vandiedonck et al. 1050 Genome Research www..org applied the MHC array to MHC-homozygous individuals, but the custom array should also be informative when applied to heterozygous samples. Here it will be necessary to know the DNA sequence or relevant genotypic...
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Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
- Li Song,
- Gali Bai,
- X. Shirley Liu,
- Bo Li,
- and Heng Li
Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
...-IMGT/HLA Database. Nucleic Acids Res 48: D948–D955. Roe D, Kuang R. 2020. Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures. Front Immunol 11: 583013. Ruggeri L, Capanni M, Urbani E, Perruccio K, Shlomchik WD, Tosti A, Posati S, Rogaia D, Frassoni F...
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Method: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
- Zhoutao Chen,
- Long Pham,
- Tsai-Chin Wu,
- Guoya Mo,
- Yu Xia,
- Peter L. Chang,
- Devin Porter,
- Tan Phan,
- Huu Che,
- Hao Tran,
- Vikas Bansal,
- Justin Shaffer,
- Pedro Belda-Ferre,
- Greg Humphrey,
- Rob Knight,
- Pavel Pevzner,
- Son Pham,
- Yong Wang,
- and Ming Lei
Genome Res. June 2020 30: 898-909; Published in Advance June 15, 2020, doi:10.1101/gr.260380.119
...linked-reads. For the same complete NA12878 TELL-seq data set, Long Ranger analysis showed that ∼98.9% of heterozygous SNVs were phased with N50 phasing block size at only 4.2 Mb.View this table: In this window In a new window Table 3. Summary of TELL-seq phasing results on NA12878 and NA24385 samplesGenomic...
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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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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...-read data sets from homozygous human cell lines with coverage ranging from 0.1× to 10×. Our algorithm accurately estimates complete major histocompatibility complex (MHC) haplotype sequences with small edit distances from the ground-truth sequences, providing a significant advantage over existing methods...

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