Partial versus Productive Immunoglobulin Heavy Locus Rearrangements in Chronic Lymphocytic Leukemia: Implications for B-Cell Receptor Stereotypy

Tsakou, Eugenia; Agathagelidis, Andreas; Boudjoghra, Myriam; Raff, Thorsten; Dagklis, Antonis; Chatzouli, Maria; Smilevska, Tatjana; Bourikas, George; Merle‐Béral, Hélène; Manioudaki-Kavallieratou, Eleni; Anagnostopoulos, Achilles; Brüggemann, Monika; Davi, Frédéric; Stamatopoulos, Kostas; Belessi, Chrysoula

doi:10.2119/molmed.2011.00216

Cited by 12 publications

(9 citation statements)

References 39 publications

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“…The IGHJ genes identified make up the IGHJ2, IGHJ4, and IGHJ5 families, are slightly smaller than human genes (Data S1; Lefranc et al, 2005), and contain functional RSSs, with the exception of the 2 IGHJ2 genes, which lack the conserved 5 0 -GAGCGTG-3 0 observed in human IGHJ gene heptamers (Figure 2D). All IGHJ4 and IGHJ5 genes retain the highly conserved WGXG amino acid (aa) motif, while IGHJ2 genes do not (Figure 2E), suggesting they are not functional (Tsakou et al, 2012). One intriguing observation was the IGHD-IGHJ-IGHD-IGHJ organization within the IGH locus.…”

Section: Sequencing and Assembly Of Erb Igh Locusmentioning

confidence: 99%

Genomic features of humoral immunity support tolerance model in Egyptian rousette bats

et al. 2021

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Section: Sequencing and Assembly Of Erb Igh Locusmentioning

confidence: 99%

Genomic features of humoral immunity support tolerance model in Egyptian rousette bats

et al. 2021

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“…In the past few months, the use of innovative tools for immunoglobulin genes analyses has been reported, such as the nanopore strategy, demonstrated as a good alternative for IGHV status assessment in CLL (24). Capture HTS has also been shown recenlty by the EuroClonalty group as an efficient means to assess clonalty in B-lineage lymphoproliferative disorders (25).…”

Section: Discussionmentioning

confidence: 99%

Reliable one-step assessment of IGHV mutational status and gene mutations in Chronic Lymphocytic Leukemia by capture-based high throughput sequencing

Bris

Thonier

Menard

et al. 2022

Preprint

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Proper management of chronic lymphocytic leukemia (CLL) patients requiring therapy relies on two important prognostic and theranostic molecular features: respectively, the mutational status of tumoral cells immunoglobulin heavy chain variable domain (IGHV) and the characteristics of TP53. Both these (immuno)genetic analyses require multiple time-consuming amplification and sequencing techniques by Sanger or HTS. The capture-HTS technology, allowing to select regions of interest, represents an attractive alternative and has already been applied for the detection of clonality in lymphoproliferative disorders. Here, a single-step capture design was developed to concomitantly investigate for IGHV and TP53. This was applied to a training retrospective (n=14) and a validation prospective (n=91) cohorts of CLL patients. The training cohort demonstrated the robustness of the method by comparison with the classical Sanger sequencing technology (100% identical results) for the IGHV mutational status. This consistency was confirmed for the first 59 patients of the validation cohort. Overall, the IGHV status of whole population (n=103) was accurately identified. Simultaneously, deletion or mutations of TP53 were identified from the same capture-library and HTS-sequencing run for each patient. This novel approach provides, in a single assay, useful answers about the molecular landscape of CLL patients, allowing for a documented choice of therapy.

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“…Table 3 reveals that the proposed tests identified more gene-sets than the CZZ test. It is interesting to notice that the proposed sphericity test has identified GO:0004527 and GO:0004869 as diseases-associated gene-sets in the MF category while they were missed by the CZZ test, and biologically these two gene-sets correspond to exonuclease activity and endopeptidase inhibitor activity, which have been recognized associated to the disease development of different types of leukemia recently (Shi et al [34], Tsakou et al [40]).…”

Section: Empirical Studymentioning

confidence: 99%

More powerful tests for sparse high-dimensional covariances matrices

Peng

Chen

Zhou

2016

Journal of Multivariate Analysis

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This paper considers improving the power of tests for the identity and sphericity hypotheses regarding high dimensional covariance matrices. The power improvement is achieved by employing the banding estimator for the covariance matrices, which leads to significant reduction in the variance of the test statistics in high dimension. Theoretical justification and simulation experiments are provided to ensure the validity of the proposed tests. The tests are used to analyze a dataset from an acute lymphoblastic leukemia gene expression study for an illustration.

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Partial versus Productive Immunoglobulin Heavy Locus Rearrangements in Chronic Lymphocytic Leukemia: Implications for B-Cell Receptor Stereotypy

Cited by 12 publications

References 39 publications

Genomic features of humoral immunity support tolerance model in Egyptian rousette bats

Genomic features of humoral immunity support tolerance model in Egyptian rousette bats

Reliable one-step assessment of IGHV mutational status and gene mutations in Chronic Lymphocytic Leukemia by capture-based high throughput sequencing

More powerful tests for sparse high-dimensional covariances matrices

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