Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci

Genome Medicine

Volumn 7, Issue 1, 2015, Pages

  Dean, Jared ^a   Emerson, Ryan O ^a   Vignali, Marissa ^a   Sherwood, Anna M ^a   Rieder, Mark J ^a   Carlson, Christopher S ^b   Robins, Harlan S ^b  

^a ADAPTIVE BIOTECHNOLOGIES   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; T LYMPHOCYTE RECEPTOR; COMPLEMENTARITY DETERMINING REGION; LYMPHOCYTE ANTIGEN RECEPTOR;

ALLELE; ARTICLE; DNA SEQUENCE; GENE AMPLIFICATION; GENE DELETION; GENE LOCUS; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNE SYSTEM; MITOTIC RECOMBINATION; PRIORITY JOURNAL; ADULT; CHEMISTRY; COMPLEMENTARITY DETERMINING REGION; GENE REARRANGEMENT; GENETICS; IMMUNOLOGY; MALE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; POLYMERASE CHAIN REACTION; PROCEDURES; PSEUDOGENE; T LYMPHOCYTE;

ADULT; ALLELES; BASE SEQUENCE; COMPLEMENTARITY DETERMINING REGIONS; GENE REARRANGEMENT, BETA-CHAIN T-CELL ANTIGEN RECEPTOR; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MOLECULAR SEQUENCE ANNOTATION; POLYMERASE CHAIN REACTION; PSEUDOGENES; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; RECEPTORS, ANTIGEN, T-CELL, GAMMA-DELTA; SEQUENCE ANALYSIS, DNA; T-LYMPHOCYTES;

EID: 84947757122     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0238-z     Document Type: Article

References (19)

1. Davis MM, Bjorkman PJ. T-cell antigen receptor genes and T-cell recognition. Nature. 1988;334:395-402.
2. Ashwell JD, Weissman A. T-cell antigen receptor genes, gene products and coreceptors. In: Rich RR, editor. Clinical immunology, principles and practice. 2nd ed. London: Mosby International Limited; 2001. p. 5.1-5.19.
3. Janeway CASM, Travers P, Walport M. Immunobiology: the immune system in health and disease. 6th ed. New York: Garland Science; 2004.
4. Giudicelli V, Chaume D, Lefranc MP. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 2005;33:D256-261.
5. Wang Y, Jackson KJ, Sewell WA, Collins AM. Many human immunoglobulin heavy-chain IGHV gene polymorphisms have been reported in error. Immunol Cell Biol. 2008;86:111-5.
6. Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH. Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proc Natl Acad Sci U S A. 2015;112:E862-870.
7. Watson CT, Breden F. The immunoglobulin heavy chain locus: genetic variation, missing data, and implications for human disease. Genes Immun. 2012;13:363-73.
8. Robins HS, Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood. 2009;114:4099-107.
9. Miller JF, Sadelain M. The journey from discoveries in fundamental immunology to cancer immunotherapy. Cancer Cell. 2015;27:439-49.
10. Aifantis I, Buer J, von Boehmer H, Azogui O. Essential role of the pre-T cell receptor in allelic exclusion of the T cell receptor beta locus. Immunity. 1997;7:601-7.
11. Malissen M, Trucy J, Jouvin-Marche E, Cazenave PA, Scollay R, Malissen B. Regulation of TCR alpha and beta gene allelic exclusion during T-cell development. Immunol Today. 1992;13:315-22.
12. Nadel B, Tang A, Escuro G, Lugo G, Feeney AJ. Sequence of the spacer in the recombination signal sequence affects V(D)J rearrangement frequency and correlates with nonrandom Vkappa usage in vivo. J Exp Med. 1998;187:1495-503.
13. Feeney AJ, Tang A, Ogwaro KM. B-cell repertoire formation: role of the recombination signal sequence in non-random V segment utilization. Immunol Rev. 2000;175:59-69.
14. Oltz EM. Regulation of antigen receptor gene assembly in lymphocytes. Immunol Res. 2001;23:121-33.
15. Lefranc MP. IMGT® databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis. Leukemia. 2003;17:260-6.
16. Emerson R, DeWitt W, Vignali M, Gravley J, Desmarais C, Carlson C, et al. Immunosequencing reveals diagnostic signatures of chronic viral infection in T cell memory. bioarXiv. 2015. doi: http://dx.doi.org/10.1101/026567.
17. Carlson CS, Emerson RO, Sherwood AM, Desmarais C, Chung MW, Parsons JM, et al. Using synthetic templates to design an unbiased multiplex PCR assay. Nat Commun. 2013;4:2680.
18. Yousfi Monod M, Giudicelli V, Chaume D, Lefranc MP. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics. 2004;20 Suppl 1:i379-385.
19. Adams EJ, Gu S, Luoma AM. Human gamma delta T cells: evolution and ligand recognition. Cell Immunol. 2015;296:31-40.