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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
..., J, and C gene segments may affect the antibody repertoire of a given individual, representing the potential of future precision medicine based on individual variation (Kidd et al. 2016; Kenter et al. 2021; Peres et al. 2023).In the work presented here, we generated full-length single-cell antibody...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...The pig pan provides insights into the roles of coding structural variations in genetic diversity and adaptation Zhengcao Li1, Xiaohong Liu1, Chen Wang1, Zhenyang Li1, Bo Jiang1, Ruifeng Zhang1, Lu Tong1, Youping Qu1, Sheng He1, Haifan Chen1, Yafei Mao2, Qingnan Li1, Torsten Pook3, Yu Wu1, Yanjun...
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Method: Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs
- Sara Silva Pereira,
- Aitor Casas-Sánchez,
- Lee R. Haines,
- Moses Ogugo,
- Kihara Absolomon,
- Mandy Sanders,
- Steve Kemp,
- Álvaro Acosta-Serrano,
- Harry Noyes,
- Matthew Berriman,
- and Andrew P. Jackson
Genome Res. September 2018 28: 1383-1394; Published in Advance July 13, 2018, doi:10.1101/gr.234146.118
...a form of developmental regulation that may be exploitable in vaccine design.Further research will also be needed to understand population variation in the VAP. We had expected to see a strong geographical signature in the VSG repertoire, based on other organisms (e.g., var diversity in natural P...
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Method: Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations
- Rachael J.M. Bashford-Rogers,
- Anne L. Palser,
- Brian J. Huntly,
- Richard Rance,
- George S. Vassiliou,
- George A. Follows,
- and Paul Kellam
Genome Res. November 2013 23: 1874-1884; Published in Advance June 6, 2013, doi:10.1101/gr.154815.113
...-mediated variation contributes significantly to the diversification of the mature B-cell repertoire (Brezinschek et al. 1995; Dorner et al. 1998; Weinstein et al. 2009; Batrak et al. 2011). The diversification and selection dynamics of BCR repertoires in healthy individuals and those with infection, autoimmunity...
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Research: T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity
- Asaf Madi,
- Eric Shifrut,
- Shlomit Reich-Zeliger,
- Hilah Gal,
- Katharine Best,
- Wilfred Ndifon,
- Benjamin Chain,
- Irun R. Cohen,
- and Nir Friedman
Genome Res. October 2014 24: 1603-1612; Published in Advance July 14, 2014, doi:10.1101/gr.170753.113
...antigens subsequent to any bias in nt recombination in the thymus. Shared autoreactivity is not limited to T-cell CDR3-types; there also appears to be an enrichment in self-reactive, autoantibodies present frombirth in thehealthy human antibody repertoire. We have previously found that humans, during...
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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
...antibody repertoire and susceptibility to infectious and autoimmune diseases. However, repetitive sequences and complex structural variation pose significant challenges for large-scale characterization. Here, we introduce a method that combines Oxford Nanopore Technologies ultra-long sequencing...
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Method: Gene prediction in the immunoglobulin loci
- Vikram Sirupurapu,
- Yana Safonova,
- and Pavel A. Pevzner
Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
...@ucsd.eduAbstractThe V(D)J recombination process rearranges the variable (V), diversity (D), and joining (J) genes in the immunoglobulin (IG) loci to generate antibody repertoires. Annotation of these loci across various species and predicting the V, D, and J genes (IG genes) are critical for studies of the adaptive...
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ARTICLE: Comparative Genomics of Gene Expression in the Parasitic and Free-Living Nematodes Strongyloides stercoralis and Caenorhabditis elegans
- Makedonka Mitreva,
- James P. McCarter,
- John Martin,
- Mike Dante,
- Todd Wylie,
- Brandi Chiapelli,
- Deana Pape,
- Sandra W. Clifton,
- Thomas B. Nutman,
- and Robert H. Waterston
Genome Res. February 2004 14: 209-220; doi:10.1101/gr.1524804
...of Washington, Seattle, Washington 98195, USA Abstract Although developmental timing of gene expression is used to infer potential gene function, studies have yet to correlate this information between species. We analyzed 10,921 ESTs in 3311 clusters from first- and infective third-stage larva (L1, L...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...regression models. Biometrika 71: 1–10. doi:10.1093/biomet/71.1.1 ↵Avnir Y, Watson CT, Glanville J, Peterson EC, Tallarico AS, Bennett AS, Qin K, Fu Y, Huang CY, Beigel JH, et al. 2016. IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies...
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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
...-Y, Beigel JH, et al. 2016. IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity. Sci Rep 6: 20842. doi:10.1038/srep20842 ↵Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, Chudakov DM. 2015. Mi...
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