ArticleProceedings of the National Academy of Sciences of the United States of America2015
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 48 citations in OpenAlex.
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- Association of antibody and T cell receptor repertoires in Trypanosoma cruzi infected rhesus macaques and host response to infection.Journal of biomedical science · 2025Article
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- StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling.PLoS computational biology · 2024Article
- Single-cell profiling reveals a memory B cell-like subtype of follicular lymphoma with increased transformation risk.Nature communications · 2022Article
- Vaccination History, Body Mass Index, Age, and Baseline Gene Expression Predict Influenza Vaccination Outcomes.Viruses · 2022Article
- Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing.Genomics, proteomics & bioinformatics · 2022Article
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- Rare t(X;14)(q28;q32) translocation reveals link between MTCP1 and chronic lymphocytic leukemia.Nature communications · 2021Article
- HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia.Journal of translational medicine · 2021Article
- Recurrent XPO1 mutations alter pathogenesis of chronic lymphocytic leukemia.Journal of hematology & oncology · 2021Article
- CRIS: complete reconstruction of immunoglobulinBioinformatics advances · 2021Article
- Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing.Frontiers in cell and developmental biology · 2020Review
- Pathogenic Citrulline-Multispecific B Cell Receptor Clades in Rheumatoid Arthritis.Arthritis & rheumatology (Hoboken, N.J.) · 2018Article
- Article
- Recovery of Immunoglobulin VJ Recombinations from Pancreatic Cancer Exome Files Strongly Correlates with Reduced Survival.Cancer microenvironment : official journal of the International Cancer Microenvironment Society · 2018Article
- ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.Genome biology · 2018Article
- Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification.Frontiers in immunology · 2018Article
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
Abstract
Immunoglobulins (Ig) are produced by B lymphocytes as secreted antibodies or as part of the B-cell receptor. There is tremendous diversity of potential Ig transcripts (>1 × 10(12)) as a result of hundreds of germ-line gene segments, random nucleotide incorporation during joining of gene segments into a complete transcript, and the process of somatic hypermutation at individual nucleotides. This recombination and mutation process takes place in the maturing B cell and is responsible for the diversity of potential epitope recognition. Cancers arising from mature B cells are characterized by clonal production of Ig heavy (IGH@) and light chain transcripts, although whether the sequence has undergone somatic hypermutation is dependent on the maturation stage at which the neoplastic clone arose. Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults and arises from a mature B cell with either mutated or unmutated IGH@ transcripts, the latter having worse prognosis and the assessment of which is routinely performed in the clinic. Currently, IGHV mutation status is assessed by Sanger sequencing and comparing the transcript to known germ-line genes. In this paper, we demonstrate that complete IGH@ V-D-J sequences can be computed from unselected RNA-seq reads with results equal or superior to the clinical procedure: in the only discordant case, the clinical transcript was out-of-frame. Therefore, a single RNA-seq assay can simultaneously yield gene expression profile, SNP and mutation information, as well as IGHV mutation status, and may one day be performed as a general test to capture multidimensional clinically relevant data in CLL.
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