RESUMO
The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling.
Assuntos
Modelos Genéticos , Receptores de Antígenos de Linfócitos B , Análise de Sequência de DNA/métodos , Teorema de Bayes , Biologia Computacional , Rearranjo Gênico do Linfócito B/genética , Humanos , Cadeias de Markov , Filogenia , Receptores de Antígenos de Linfócitos B/classificação , Receptores de Antígenos de Linfócitos B/genética , Receptores de Antígenos de Linfócitos B/imunologia , Hipermutação Somática de Imunoglobulina/genética , VacinasRESUMO
OBJECTIVE: To evaluate the efficiency of the BIOMED-2 PCR assay and its implication in the diagnosis of mature B-cell non-Hodgkin's lymphomas. METHODS: Clinical, morphological and immunohistochemical features of 72 cases of non-Hodgkin's lymphomas were studied, including 25 reactive lymphoid hyperplasia, 37 diffuse large B cell lymphomas (DLBCL) and 35 extranodal marginal zone lymphomas of mucosa associated lymphoid tissues (MALT lymphoma and in addition, 25 cases of reactive lymphoid hyperplasia were used as the controls). DNA was exacted from the paraffin embedded formalin fixed tissue blocks and the quality of DNA was assessed using the BIOMED-2 specimen control reaction. Adequate samples were then analyzed by BIOMED-2 for immunoglobulin heavy and kappa light chain rearrangements. RESULTS: Adequate DNA was obtained in 83 of 97 samples, including 60 mature B cell lymphomas and 23 reactive lymphoid hyperplasia. Clonal B-cell gene rearrangements were detected in 57 of 60 (95%) lymphomas. In contrast, clonal Ig gene rearrangements were not detected in any of the 23 cases of reactive lymphoid hyperplasia. CONCLUSION: BIOMED-2 assay is highly sensitive and specific for the detection of clonal B cell gene rearrangement using routine paraffin embedded formalin fixed specimens.
Assuntos
Rearranjo Gênico do Linfócito B/genética , Genes de Imunoglobulinas , Linfoma de Células B/genética , Linfoma Difuso de Grandes Células B/genética , Antígenos CD20/metabolismo , Antígenos CD79/metabolismo , DNA de Neoplasias/genética , Rearranjo Gênico de Cadeia Pesada de Linfócito B/genética , Rearranjo Gênico de Cadeia Leve de Linfócito B/genética , Humanos , Imunofenotipagem , Linfoma de Células B/imunologia , Linfoma de Células B/patologia , Linfoma de Zona Marginal Tipo Células B/genética , Linfoma de Zona Marginal Tipo Células B/imunologia , Linfoma de Zona Marginal Tipo Células B/patologia , Linfoma Difuso de Grandes Células B/imunologia , Linfoma Difuso de Grandes Células B/patologia , Inclusão em Parafina , Pseudolinfoma/genética , Pseudolinfoma/imunologia , Pseudolinfoma/patologia , Sensibilidade e EspecificidadeAssuntos
Linfoma de Burkitt/genética , Rearranjo Gênico do Linfócito B/genética , Rearranjo Gênico do Linfócito T/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Adolescente , Linfoma de Burkitt/etnologia , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Masculino , Neoplasia Residual , Leucemia-Linfoma Linfoblástico de Células Precursoras/etnologia , Fatores SocioeconômicosRESUMO
We studied 23 Polish children with precursor-B-ALL, using PCR-heteroduplex analysis and DNA sequencing, to determine the availability of Ig/TCR gene rearrangements as patient-specific MRD-RQ-PCR targets. We found IGH, IGK-Kde, incomplete TCRD, Vdelta2-Jalpha, TCRG and TCRB rearrangements in 83%, 39%, 61%, 35%, 61% and 13% of patients, respectively. Comparison of Ig/TCR gene rearrangements pattern (frequency and characteristics of rearrangements) in Polish patients with those reported for patients of other European nationalities did not show major differences. These results are the first promising step for further development of MRD study in Polish patients according to current diagnostic standards.