ArticleScientific reports2017
Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 20 citations in OpenAlex.
- Protocol for identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data.STAR protocols · 2026Article
- BCL2 promoter region mutations are an independent marker of BCL2 level in lymphoid malignancies.NPJ genomic medicine · 2026Article
- Development and validation of a gene expression signature to predict early events in patients with follicular lymphoma.Blood advances · 2025Article
- A core driver gene set identified based on geMER reveals its potential driver mechanism in pan-cancer.NPJ precision oncology · 2025Article
- CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer.BMC genomics · 2025Article
- FOXD2 regulations IQGAP3 mediated CaThe Kaohsiung journal of medical sciences · 2023Article
- Article
- Identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data.iScience · 2023Article
- Article
- abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis.BMC bioinformatics · 2022Article
- Integrating whole genome sequencing, methylation, gene expression, topological associated domain information in regulatory mutation prediction: A study of follicular lymphoma.Computational and structural biotechnology journal · 2022Article
- Article
- Detection of new drivers of frequent B-cell lymphoid neoplasms using an integrated analysis of whole genomes.PloS one · 2021Article
- Novel Mutation Hotspots within Non-Coding Regulatory Regions of the Chronic Lymphocytic Leukemia Genome.Scientific reports · 2020Article
- IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.Computational and structural biotechnology journal · 2020Article
- Exploring the potential effect of paricalcitol on markers of inflammation in de novo renal transplant recipients.PloS one · 2020Article
- BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts.Frontiers in genetics · 2019Article
- Identification of Single Nucleotide Non-coding Driver Mutations in Cancer.Frontiers in genetics · 2018Review
- Article
- New developments in the pathology of malignant lymphoma: a review of the literature published from May to August 2017.Journal of hematopathology · 2017Review
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The contribution of mutations in regulatory regions to tumorigenesis has been the subject of many recent studies. We propose a new framework for integrative analysis of genome-wide sequencing data by considering diverse genetic information. This approach is applied to study follicular lymphoma (FL), a disease for which little is known about the contribution of regulatory gene mutations. Results from a test FL cohort revealed three novel highly recurrent regulatory mutation blocks near important genes implicated in FL, BCL6 and BCL2. Similar findings were detected in a validation FL cohort. We also found transcription factors (TF) whose binding may be disturbed by these mutations in FL: disruption of FOX TF family near the BCL6 promoter may result in reduced BCL6 expression, which then increases BCL2 expression over that caused by BCL2 gene translocation. Knockdown experiments of two TF hits (FOXD2 or FOXD3) were performed in human B lymphocytes verifying that they modulate BCL6/BCL2 according to the computationally predicted effects of the SNVs on TF binding. Overall, our proposed integrative analysis facilitates non-coding driver identification and the new findings may enhance the understanding of FL.
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