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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...or close to the core MHC genes in T. cristatus, although we note that precise localization of Class III is beyond the scope of the present article.Diversity of MHC sequences in newtsThe MHC gene family frequently undergoes rapid expansions and contractions, leading to variation in gene content and blurred...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...in MHC, such as HLA-A, -B, -C, -DR, -DP, and -DQ are highly polymorphic among human populations, which is maintained by balancing selection (DeGiorgio et al. 2014; Meyer et al. 2018). Many HLA alleles (Marsh et al. 2010), or subgroups distinguished by gene sequences, were reported to be associated...
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Resource: Assembly and analysis of 100 full MHC haplotypes from the Danish population
- Jacob M. Jensen,
- Palle Villesen,
- Rune M. Friborg,
- The Danish Pan-Genome Consortium,
- Thomas Mailund,
- Søren Besenbacher,
- and Mikkel H. Schierup
Genome Res. September 2017 27: 1597-1607; Published in Advance August 3, 2017, doi:10.1101/gr.218891.116
....1038/nature23264. Norman PJ, Norberg SJ, Guethlein LA, Nemat-Gorgani N, Royce TE, Wroblewski EE, Mann T, Dunn T, Alicata C, Hollenbach JA, et al. 2017. Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II. Genome Res 27: 813...
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LETTER: Ancient haplotypes of the HLA Class II region
- Christopher K. Raymond,
- Arnold Kas,
- Marcia Paddock,
- Ruolan Qiu,
- Yang Zhou,
- Sandhya Subramanian,
- Jean Chang,
- Anthony Palmieri,
- Eric Haugen,
- Rajinder Kaul,
- and Maynard V. Olson
Genome Res. September 2005 15: 1250-1257; doi:10.1101/gr.3554305
.... 1998 . Large-scale sequence comparisons reveal unusually high levels of variation in the HLA-DQB1 locus in the class II region of the human MHC. J. Mol. Biol. 282 : 71 -97. ↵ Hughes, A.L. and Nei, M. 1989 . Nucleotide substitution at major histocompatibility complex class II loci: Evidence...
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LETTER: MHC-Linked Olfactory Receptor Loci Exhibit Polymorphism and Contribute to Extended HLA/OR-Haplotypes
- Anke Ehlers,
- Stephan Beck,
- Simon A. Forbes,
- John Trowsdale,
- Armin Volz,
- Ruth Younger,
- and Andreas Ziegler
Genome Res. December 1, 2000 10: 1968-1978; doi:10.1101/gr.120400
...MHC-Linked Olfactory Receptor Loci Exhibit Polymorphism and Contribute to Extended HLA/OR-Haplotypes Anke Ehlers 1 , Stephan Beck 2 , Simon A. Forbes 3 , John Trowsdale 3 , Armin Volz 1 , Ruth Younger 2 , and Andreas Ziegler...
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LETTER: Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region
- Naoya Yuhki,
- Thomas Beck,
- Robert M. Stephens,
- Yoko Nishigaki,
- Kymberly Newmann,
- and Stephen J. O'Brien
Genome Res. June 2003 13: 1169-1179; Published in Advance May 12, 2003, doi:10.1101/gr.976103
...class II MHC includes 44 genes (31 predicted to be expressed) which display DNA sequence homology and ordered gene synteny with human HLA and mouse H2, in extended class II and centromere proximal regions ( DM to DO ) of the classical class II region. However, remarkable genomic alterations...
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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
.... 2008b), and clonal selection, without confounding effects such as HLA polymorphisms and other genetic differences that occur in studies of human samples. Results High-throughput TCR sequencing reveals patterns of CDR3 sequence sharing among mice To investigate TCR publicness in a repertoire-wide manner...
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RESOURCE: Complete MHC Haplotype Sequencing for Common Disease Gene Mapping
- C. Andrew Stewart,
- Roger Horton,
- Richard J.N. Allcock,
- Jennifer L. Ashurst,
- Alexey M. Atrazhev,
- Penny Coggill,
- Ian Dunham,
- Simon Forbes,
- Karen Halls,
- Joanna M.M. Howson,
- Sean J. Humphray,
- Sarah Hunt,
- Andrew J. Mungall,
- Kazutoyo Osoegawa,
- Sophie Palmer,
- Anne N. Roberts,
- Jane Rogers,
- Sarah Sims,
- Yu Wang,
- Laurens G. Wilming,
- John F. Elliott,
- Pieter J. de Jong,
- Stephen Sawcer,
- John A. Todd,
- John Trowsdale,
- and Stephan Beck
Genome Res. June 2004 14: 1176-1187; Published in Advance May 12, 2004, doi:10.1101/gr.2188104
..., S.A., Trowsdale, J., Volz, A., Younger, R., and Ziegler, A. 2000 . MHC-linked olfactory receptor loci exhibit polymorphism and contribute to extended HLA/OR-haplotypes. Genome Res. 10 : 1968 –1978. ↵ Ewing, B. and Green, P. 1998 . Base-calling of automated sequencer traces using phred. II. Error...
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REPORT: MHC Class II Pseudogene and Genomic Signature of a 32-kb Cosmid in the House Finch (Carpodacus mexicanus)
- Christopher M. Hess,
- Joe Gasper,
- Hopi E. Hoekstra,
- Christopher E. Hill,
- and Scott V. Edwards
Genome Res. May 1, 2000 10: 613-623; doi:10.1101/gr.10.5.613
..., the values of Θ for exon 3 are similar to those of exon 2 (Table 1 ). Moreover, these values are somewhat higher than the neutral Θ found in other vertebrates such as humans. For example, Grimsley et al. (1998) found Θ values of 0.0262 for HLA-H , an Mhc pseudogene linked to the highly polymorphic HLA-A gene...
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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
...expression. Cis control of MHC gene expression in LCLs and primary cells To further test whether variation in expression could be attributed to haplotypic effects, we investigated the three most significant differentially expressed genes—ZFP57, HLA-DQA2, and HLA-DQB2 (Table 1). ZFP57 encodes a zinc finger...
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