ArticleBMC genomics2014
Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 66 citations in OpenAlex.
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- Genomic fusion breakpoints for DNA-based measurable residual disease monitoring in pediatric acute lymphoblastic leukemia.Leukemia · 2026Article
- Feasibility of IG and TCR rearrangements quantification in ctDNA for monitoring clinical response in pediatric lymphomas.Frontiers in genetics · 2026Article
- Human Autosomal Recessive DNA Polymerase Delta 3 Deficiency Presenting as Omenn Syndrome.Journal of clinical immunology · 2023Article
- Vidjil add-on for MRD quantification of samples processed using the EuroClonality-NGS protocol.EJHaem · 2023Article
- A current and future perspective on T cell receptor repertoire profiling.Frontiers in genetics · 2023Review
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Quality Control for IG /TR Marker Identification and MRD Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Review
- One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Article
- Tools for fundamental analysis functions of TCR repertoires: a systematic comparison.Briefings in bioinformatics · 2020Article
- Computational approaches to therapeutic antibody design: established methods and emerging trends.Briefings in bioinformatics · 2020Review
- Identifying IGH disease clones for MRD monitoring in childhood B-cell acute lymphoblastic leukemia using RNA-Seq.Leukemia · 2020Article
- Clinical utility of target capture-based panel sequencing in hematological malignancies: A multicenter feasibility study.Cancer science · 2020Article
- Article
- Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy.International journal of molecular sciences · 2020Review
- Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL.Blood cancer journal · 2019Article
- Article
Corrections and comments
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Authors and funding
10 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundV(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.
resultsWe 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.
conclusionsThe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.