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Method: Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
- Paul J. Norman,
- Steven J. Norberg,
- Lisbeth A. Guethlein,
- Neda Nemat-Gorgani,
- Thomas Royce,
- Emily E. Wroblewski,
- Tamsen Dunn,
- Tobias Mann,
- Claudia Alicata,
- Jill A. Hollenbach,
- Weihua Chang,
- Melissa Shults Won,
- Kevin L. Gunderson,
- Laurent Abi-Rached,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2017 27: 813-823; Published in Advance March 30, 2017, doi:10.1101/gr.213538.116
...-like receptors (KIR) of natural killer (NK) cells (Moretta et al. 1996; Parham and Moffett 2013). Contrasting with HLA class I, the highly polymorphic HLA class II molecules, HLA-DR, HLA-DQ, and HLA-DP are dedicated to adaptive immunity (Germain 1994). Also encoded byMHC region genes are components...
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Article: Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes
- Paul J. Norman,
- Laurent Abi-Rached,
- Ketevan Gendzekhadze,
- John A. Hammond,
- Achim K. Moesta,
- Deepti Sharma,
- Thorsten Graef,
- Karina L. McQueen,
- Lisbeth A. Guethlein,
- Christine V.F. Carrington,
- Dasdayanee Chandanayingyong,
- Yih-Hsin Chang,
- Catalina Crespí,
- Güher Saruhan-Direskeneli,
- Kamran Hameed,
- Giorgi Kamkamidze,
- Kwadwo A. Koram,
- Zulay Layrisse,
- Nuria Matamoros,
- Joan Milà,
- Myoung Hee Park,
- Ramasamy M. Pitchappan,
- D. Dan Ramdath,
- Ming-Yuh Shiau,
- Henry A.F. Stephens,
- Siske Struik,
- Dolly Tyan,
- David H. Verity,
- Robert W. Vaughan,
- Ronald W. Davis,
- Patricia A. Fraser,
- Eleanor M. Riley,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2009 19: 757-769; doi:10.1101/gr.085738.108
...and on the telomeric side by FCAR, the gene encoding the receptor for immunoglobulin A that is expressed on phagocytic cells. Human KIR haplotypes vary in gene content, having between seven and 15 genes (Uhrberg et al. 1997). Each KIR haplotype is divided into two parts by three conserved framework regions...
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LETTER: Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates
- Jennifer G. Sambrook,
- Arman Bashirova,
- Sophie Palmer,
- Sarah Sims,
- John Trowsdale,
- Laurent Abi-Rached,
- Peter Parham,
- Mary Carrington,
- and Stephan Beck
Genome Res. January 2005 15: 25-35; doi:10.1101/gr.2381205
...) are encoded within the Leukocyte Receptor Complex (LRC) on chromosome 19q13.4. Here we report the comparative genomic analysis of single KIR haplotypes in two other primates. In the common chimpanzee ( Pan troglodytes ), seven KIR genes ( ptKIRnewI, ptKIRnewII, ptKIR2DL5, ptKIRnewIII, ptKIR3DP1, ptKIR2DL4, ptKIR...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...variations in the 52 haplotypes analyzed.In this study, we developed an improved structural KIR annoTator (SKIRT) method for high-resolution allelic and CNV identification of KIR genes. This method accurately annotates complete haplotypes, gene copy numbers, and structural variations. Our study on long...
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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
...optimization to assign reads and determine genotypes. This has been used in pharmacogenetics with tools like Cypiripi (Numanagić et al. 2015) and ALDY (Numanagić et al. 2018; Hari et al. 2023), HLA typing using OptiType (Szolek et al. 2014), killer cell IG-like receptor (KIR) genotyping with Geny (Zhou et al...
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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
...for macaque killer-cell immunoglobulin-like receptors (KIR) gene clusters (Bruijnesteijn et al. 2021). The assembly of the full MHC genomic region from a homozygous macaque provides unequivocal confirmation that this cy0333 haplotype reference is an accurate ∼5.2-Mb end-to-end layout of the MHC M3 haplotype...
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Resource: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- Valerie A. Schneider,
- Tina Graves-Lindsay,
- Kerstin Howe,
- Nathan Bouk,
- Hsiu-Chuan Chen,
- Paul A. Kitts,
- Terence D. Murphy,
- Kim D. Pruitt,
- Françoise Thibaud-Nissen,
- Derek Albracht,
- Robert S. Fulton,
- Milinn Kremitzki,
- Vincent Magrini,
- Chris Markovic,
- Sean McGrath,
- Karyn Meltz Steinberg,
- Kate Auger,
- William Chow,
- Joanna Collins,
- Glenn Harden,
- Timothy Hubbard,
- Sarah Pelan,
- Jared T. Simpson,
- Glen Threadgold,
- James Torrance,
- Jonathan M. Wood,
- Laura Clarke,
- Sergey Koren,
- Matthew Boitano,
- Paul Peluso,
- Heng Li,
- Chen-Shan Chin,
- Adam M. Phillippy,
- Richard Durbin,
- Richard K. Wilson,
- Paul Flicek,
- Evan E. Eichler,
- and Deanna M. Church
Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
...1 (Dennis et al. 2012; Steinberg et al. 2014), or on Chromosome X, with the single haplotype represented in RP11 (Mueller et al. 2013).We also retiled several genomic loci associated with immune responses (IGK, IGH, LRC-KIR, and the cytokine cluster on 17q) with CHM1 clones, replacing...
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LETTER: Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- Deyou Zheng,
- Adam Frankish,
- Robert Baertsch,
- Philipp Kapranov,
- Alexandre Reymond,
- Siew Woh Choo,
- Yontao Lu,
- France Denoeud,
- Stylianos E. Antonarakis,
- Michael Snyder,
- Yijun Ruan,
- Chia-Lin Wei,
- Thomas R. Gingeras,
- Roderic Guigó,
- Jennifer Harrow,
- and Mark B. Gerstein
Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
...and pseudogene members of the KIR and LILR gene families in ENm007, a task that proved problematic for all computational methods ( Guigó et al. 2006 ; Harrow et al. 2006 ). View larger version: In this window In a new window Figure 9. Complexity in pseudogene annotation—insertion of one pseudogene into another...
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LETTER: Genetic Divergence of the Rhesus Macaque Major Histocompatibility Complex
- Riza Daza-Vamenta,
- Gustavo Glusman,
- Lee Rowen,
- Brandon Guthrie,
- and Daniel E. Geraghty
Genome Res. August 2004 14: 1501-1515; doi:10.1101/gr.2134504
...important to a particular CTL response, but also concerning the interaction of class I with the innate immune response ( Colonna 1996 ). An essential component of the latter response is the interaction between the killer cell Ig-like receptors (KIR) and their MHC class I ligands. In humans, specific class I...
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LETTER: The Genomic Sequence and Comparative Analysis of the Rat Major Histocompatibility Complex
- Peter Hurt,
- Lutz Walter,
- Ralf Sudbrak,
- Sven Klages,
- Ines Müller,
- Takashi Shiina,
- Hidetoshi Inoko,
- Hans Lehrach,
- Eberhard Günther,
- Richard Reinhardt,
- and Heinz Himmelbauer
Genome Res. April 2004 14: 631-639; doi:10.1101/gr.1987704
...Ig-like receptor (KIR) genes ( Naper et al. 1999 ; Hoelsbrekken et al. 2003 ), similar to the mouse, but at variance with human. Our sequence of the second telomeric class I gene cluster RT1-N (position 2273–3059 kb) has revealed 16 class Ib genes, most of them potentially expressed and concentrated...

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