IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains

Lefranc, Marie‐Paule; Pommié, Christelle; Kaas, Quentin; Duprat, Élodie; Bosc, Nathalie; Guiraudou, Delphine; Jean, C. Manson; Ruiz, Manuel; Piedade, Isabelle da; Rouard, Mathieu; Foulquier, Elodie; Thouvenin, Valérie; Lefranc, Gérard

doi:10.1016/j.dci.2004.07.003

Cited by 449 publications

(370 citation statements)

References 52 publications

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“…In the current study, oxidation of Met 256 (immunogenetics (IMGT) [8] database (Http://imgt.cines.fr): CH2-15.1) and Met432 (IMGT: CH3-107) of a recombinant fully human monoclonal antibody after exposure to light was investigated and compared with chemically induced oxidation using tBHP. Met 256 and Met432 were located in the CH2-CH3 interface in close proximity [8,9] and were the focus of this study.…”

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confidence: 99%

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Mass spectrometry analysis of photo-induced methionine oxidation of a recombinant human monoclonal antibody

Liu

Gaza-Bulseco

Zhou

2009

J. Am. Soc. Mass Spectrom.

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Oxidation of methionine (Met) residues of a recombinant fully human monoclonal antibody after exposure to light was investigated and compared with chemically induced oxidation using tert-butyl-hydroperoxide (tBHP). Met256 and Met432 in the Fc region in the samples exposed to light or incubated with tBHP were oxidized. The Fc mass spectra of the antibody exposed to light showed mainly peaks with a molecular weight (MW) increase of 32 Da, however the sample treated with tBHP showed peaks with increase of only 16 Da. These results suggested that either oxidation of one Met residue (either Met256 or Met432) catalyzed the oxidation of the second Met residue on the same heavy chain (HC) or Met residues of one HC were preferentially oxidized when the antibody was exposed to light, while Met256 and Met432 were randomly oxidized when the antibody was incubated with tBHP. (J Am Soc Mass Spectrom 2009, 20, 525-528)

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confidence: 99%

“…Met 256 and Met432 were located in the CH2-CH3 interface in close proximity [8,9] and were the focus of this study.…”

mentioning

confidence: 99%

Mass spectrometry analysis of photo-induced methionine oxidation of a recombinant human monoclonal antibody

Liu

Gaza-Bulseco

Zhou

2009

J. Am. Soc. Mass Spectrom.

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“…The specific reverse primer was located in the C region of TCR-b chain covering both C region alleles (CP1: GCACCTCCTTCCCATTCAC; aa 43-45.4 according to IMGT unique numbering for C-DOMAIN 24 ). To improve the sensitivity of PCR, a nested reverse primer located upstream of the CP1 primer was designed (CP2: CACAGCGACCT CGGGTGG; located at aa 1-6).…”

Section: Designing Of Degenerate Primermentioning

confidence: 99%

“…To improve the sensitivity of PCR, a nested reverse primer located upstream of the CP1 primer was designed (CP2: CACAGCGACCT CGGGTGG; located at aa 1-6). 24 All primers were designed by DNAMAN 5.2.10 and synthesized by MWG (Ebersberg, Germany).…”

Section: Designing Of Degenerate Primermentioning

confidence: 99%

High throughput analysis of TCR-β rearrangement and gene expression in single T cells

Zhou

Srivastava

Grummel

et al. 2006

Laboratory Investigation

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Analysis of T-cell receptor beta chain (TCR-b) rearrangement is essential to investigate T-cell responses in human autoimmune diseases, infection and cancer. Since the TCR-b locus contains 55 variable (V) region gene segments, multiple assays have been necessary to determine TCR-b rearrangements of individual T cells. We established a seminested rtPCR method for single T-cell analysis with two sets of degenerate primers covering 76 and 24% of the TCR-Vb genes, respectively. The specificity of the approach was validated by screening cDNAs obtained from T-cell clones (TCC) with defined TCR-b rearrangement. We applied the method successfully to profile TCR-b rearrangement of single T cells sorted from body fluids or dissected tissue. Concomitant analysis of other gene transcripts allowed determining phenotype and function of TCR-b-defined single T cells. Our fast, cost-efficient and high throughput approach will facilitate studies on T-cell responses in human diseases.

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“…In VBASE, alignments are annotated according to the structural criteria defined by Chothia [24][25][26] and the CDRs are defined by Kabat et al 27 In IMGT, sequences are annotated and CDRs/FRs defined according to the IMGT unique numbering system. 28 Since investigators may use either IMGT or VBASE to help classify a V H sequence as GL (no somatic mutations, no affinity maturation), mutated and affinity matured (AM; evidence of having undergone affinity maturation) or mutated but nonaffinity matured (NAM), it is important to establish the nature of any differences that may arise from the two resources when identical sequences are examined.…”

Section: Introductionmentioning

confidence: 99%

Analysis of VH gene sequences using two web-based immunogenetics resources gives different results, but the affinity maturation status of chronic lymphocytic leukaemia clones as assessed from either of the resulting data sets has no prognostic significance

et al. 2005

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Some cellular and molecular features of chronic lymphocytic leukaemia (CLL) cells that are associated with prognosis may reflect the context within which their progenitors encountered antigen. It follows that the nature of antigen drive in CLL could influence the clinical course and we were prompted to assess the impact, if any, of affinity maturation (an antigen-driven process) on prognosis. Statistical models for assessing affinity maturation status are typically applied to V H gene sequence data analysed using a web-based resource like IMGT or VBASE. Since these resources differ with respect to some key relevant features, we evaluated a cohort of CLL cases by applying statistical models to V H data derived from both IMGT and VBASE. Important differences between the resulting data sets became apparent. These resulted from database variance and because IMGT and VBASE define complementarity-determining and framework regions (CDRs, FRs) in different ways. Thus, the numbers of mutations identified and their distribution between CDRs/FRs varied between the data sets for the majority of clones. Consequently, two different but overlapping sets of cases with evidence of affinity maturation were defined. Notwithstanding their differences, no significant associations of affinity maturation status with CD38 expression, p53 functional status or survival were identifiable in either data set.

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IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains

Cited by 449 publications

References 52 publications

Mass spectrometry analysis of photo-induced methionine oxidation of a recombinant human monoclonal antibody

Mass spectrometry analysis of photo-induced methionine oxidation of a recombinant human monoclonal antibody

High throughput analysis of TCR-β rearrangement and gene expression in single T cells

Analysis of VH gene sequences using two web-based immunogenetics resources gives different results, but the affinity maturation status of chronic lymphocytic leukaemia clones as assessed from either of the resulting data sets has no prognostic significance

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