Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.
BMC Genomics
; 15: 409, 2014 May 28.
Article
em En
| MEDLINE
| ID: mdl-24885090
ABSTRACT
BACKGROUND:
V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood.RESULTS:
We propose new algorithms that process high-throughput sequencing (HTS) data to extract unnamed V(D)J junctions and gather them into clones for quantification. This analysis is based on a seed heuristic and is fast and scalable because in the first phase, no alignment is performed with germline database sequences. The algorithms were applied to TR γ HTS data from a patient with acute lymphoblastic leukemia, and also on data simulating hypermutations. Our methods identified the main clone, as well as additional clones that were not identified with standard protocols.CONCLUSIONS:
The proposed algorithms provide new insight into the analysis of high-throughput sequencing data for leukemia, and also to the quantitative assessment of any immunological profile. The methods described here are implemented in a C++ open-source program called Vidjil.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Análise de Sequência de DNA
/
Leucemia-Linfoma Linfoblástico de Células Precursoras
/
Sequenciamento de Nucleotídeos em Larga Escala
/
Recombinação V(D)J
Tipo de estudo:
Diagnostic_studies
/
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
BMC Genomics
Assunto da revista:
GENETICA
Ano de publicação:
2014
Tipo de documento:
Article
País de afiliação:
França