Explanipedia

LCR-modules: a collection of workflows for cancer genome analysis Open

Kostiantyn Dreval, Laura K. Hilton, Bruno M. Grande, Krysta M. Coyle, Manuela Cruz , et al. · 2025

The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analys…

High-grade B-cell lymphoma, not otherwise specified: an LLMPP study Open

Brett Collinge, Laura K. Hilton, Jasper Wong, Waleed Alduaij, Susana Ben‐Neriah , et al. · 2025

Molecular characterization of high-grade B-cell lymphoma, not otherwise specified (HGBCL-NOS), is hindered by its rarity, evolving definition, and poor diagnostic reproducibility. To address this challenge, we analyzed 92 HGBCL-NOS tumors …

Somatic IRF4 mutations and thymic tropism in primary mediastinal large B-cell lymphoma Open

Shinya Rai, Gerben Duns, Fabian Frontzek, Jasper Wong, Yifan Yin , et al. · 2025

Disease-defining signatures in lymphomas, driven by intricate molecular mechanisms, have advanced molecular taxonomies, refined classification, and may guide clinical management; however, the role of these signatures in driving disease hal…

56 | GENOMIC ANALYSIS OF MATURE B‐CELL LYMPHOMAS Open

Kostiantyn Dreval, Margarito Martínez Cruz, Laura K. Hilton, Haya Shaalan, Meme Wijesinghe , et al. · 2025

High-grade B-cell lymphoma, not otherwise specified: an LLMPP study Open

Brett Collinge, Laura K. Hilton, Jasper Wong, Waleed Alduaij, Susana Ben‐Neriah , et al. · 2025

Molecular characterization of high-grade B-cell lymphoma, not otherwise specified (HGBCL-NOS), is hindered by its rarity, evolving definition, and poor diagnostic reproducibility. To address this challenge, we analyzed 92 HGBCL-NOS tumors …

Primary Central Nervous System Lymphoma Tumor Biopsies Show Heterogeneity in Gene Expression Profiles and Genetic Subtypes Open

Yuan Xiao Zhu, Jasper Wong, Talal Hilal, Alanna Maguire, Jon Ocal , et al. · 2024

Background Primary central nervous system lymphoma (PCNSL) is clinically challenging due to its location and small biopsy size, leading to a lack of comprehensive molecular and biologic description. We previously demonstrated that 91% of P…

Relapse Timing Is Associated With Distinct Evolutionary Dynamics in Diffuse Large B-Cell Lymphoma Open

Laura K. Hilton, Henry S. Ngu, Brett Collinge, Kostiantyn Dreval, Susana Ben‐Neriah , et al. · 2023

PURPOSE Diffuse large B-cell lymphoma (DLBCL) is cured in more than 60% of patients, but outcomes remain poor for patients experiencing disease progression or relapse (refractory or relapsed DLBCL [rrDLBCL]), particularly if these events o…

RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia Open

Md Rashedul Islam, Catherine E. Jenkins, Qi Cao, Jasper Wong, Misha Bilenky , et al. · 2023

Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns Open

Kostiantyn Dreval, Laura K. Hilton, Manuela Martins Cruz, Haya Shaalan, Susana Ben‐Neriah , et al. · 2023

Follicular lymphoma (FL) accounts for ∼20% of all new lymphoma cases. Increases in cytological grade are a feature of the clinical progression of this malignancy, and eventual histologic transformation (HT) to the aggressive diffuse large …

Relapse timing is associated with distinct evolutionary dynamics in DLBCL Open

Laura K. Hilton, Henry S. Ngu, Brett Collinge, Kostiantyn Dreval, Susana Ben‐Neriah , et al. · 2023

Diffuse large B-cell lymphoma (DLBCL) is cured in over 60% of patients, but outcomes are poor for patients with relapsed or refractory disease (rrDLBCL). Here, we performed whole genome/exome sequencing (WGS/WES) on tumors from 73 serially…

Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma Open

Nicole Thomas, Kostiantyn Dreval, Daniela S. Gerhard, Laura K. Hilton, Jeremy S. Abramson , et al. · 2022

Burkitt lymphoma (BL) accounts for most pediatric non-Hodgkin lymphomas, being less common but significantly more lethal when diagnosed in adults. Much of the knowledge of the genetics of BL thus far has originated from the study of pediat…

Super-enhancer hypermutation alters oncogene expression in B cell lymphoma Open

Élodie Bal, Rahul Kumar, Mohammad Hadigol, Antony B. Holmes, Laura K. Hilton , et al. · 2022

Elucidating the importance and regulation of key enhancers for human MEIS1 expression Open

Ping Xiang, Xining Yang, Leo Escano, Ishpreet Dhillon, Edith Schneider , et al. · 2022

Myeloid ecotropic virus insertion site 1 (MEIS1) is essential for normal hematopoiesis and is a critical factor in the pathogenesis of a large subset of acute myeloid leukemia (AML). Despite the clinical relevance of MEIS1, its regulation …

Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs Open

Alireza Lorzadeh, Colin A. Hammond, F. Wang, David J. H. F. Knapp, Jasper Wong , et al. · 2022

Additional file 2 of Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs Open

Alireza Lorzadeh, Charles E. Hammond, F. Wang, David J. H. F. Knapp, Jasper Wong , et al. · 2022

Additional file 2: Table S1 – S3. Table S1 – Table of primers and guide RNAs. Table S2 – total number and viability of HL60 cells. Related to Fig. 6D and E. Table S3 – Percentage of HL60 cells expressing CD11b+. Related to Fig. 6F.

Genetic Subgroups Inform on Pathobiology in Adult and Pediatric Burkitt Lymphoma Open

Nicole Thomas, Kostiantyn Dreval, Daniela S. Gerhard, Laura K. Hilton, Jeremy S. Abramson , et al. · 2021

Burkitt lymphoma (BL) accounts for the majority of pediatric non-Hodgkin lymphomas (NHL) and is relatively rare but significantly more lethal when diagnosed in adults. The global incidence is highest in Sub-Saharan Africa, where Epstein-Ba…

An Open-Source Toolkit That Powers the Genome-Wide Analysis of Mature B-Cell Lymphomas (GAMBL) Project Open

Kostiantyn Dreval, Bruno M. Grande, Helena Winata, Jasper Wong, Lakshay Sethi , et al. · 2021

Introduction: Genome- and transcriptome-wide analyses continue to enhance our understanding of the molecular pathogenesis of cancer. In lymphomas, this has enabled the identification of hundreds of recurrently mutated genes, highlighting g…

THE MUTATIONAL LANDSCAPE OF DOUBLE/TRIPLE‐HIT HIGH‐GRADE B‐CELL LYMPHOMA WITH BCL2 REARRANGEMENT (DH/TH‐BCL2) – AN LLMPP PROJECT Open

Brett Collinge, Laura K. Hilton, Jasper Wong, Susana Ben‐Neriah, Waleed Alduaij , et al. · 2021

Introduction: The poor outcome of high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangement (DH/TH) highlights the need for identifying specific targetable biology. Although a gene expression signature (DHITsig) shared by DH/T…

COPY NUMBER VARIATION ANALYSIS IDENTIFIES DISTINCT GENOMIC FEATURES IN ADULT BURKITT LYMPHOMA Open

Kostiantyn Dreval, Nicole Thomas, Daniela S. Gerhard, Laura K. Hilton, Jasper Wong , et al. · 2021

Introduction: Burkitt lymphoma (BL) is an aggressive B-cell non-Hodgkin lymphoma that disproportionately affects populations in malaria-endemic regions. Although BL is curable, age is associated with inferior clinical outcomes in most seri…

A pharmacological characterization of Cannabis sativa chemovar extracts Open

Alykhan Devsi, Brett Kiyota, Theophile Ouellette, Andrew P. Hegle, Ricardo E. Rivera-Acevedo , et al. · 2020

Epidemiology of E. coli in Cystic Fibrosis Airways Demonstrates the Capacity for Persistent Infection but Not Patient-Patient Transmission Open

Conrad Izydorczyk, Barbara J. Waddell, Brett Edwards, Jasper Wong, Michael G. Surette , et al. · 2020

Escherichia coli is frequently isolated from the respiratory secretions of cystic fibrosis (CF) patients yet is not considered a classical CF pathogen. Accordingly, little is known about the natural history of this organism in the C…

TET2- and TET3- dependence of vitamin C-induced epigenomic alterations in acute myeloid leukemia Open

Jasper Wong · 2020

Neomorphic mutations in isocitrate dehydrogenase 1/2 (IDH1/2) and inactivating mutations in ten eleven translocation dioxygenase 2 (TET2) are frequent and mutually exclusive events in de novo acute myeloid leukemia (AML). IDH1/2 mutations …

Clinical Outcomes Associated With Escherichia coli Infections in Adults With Cystic Fibrosis: A Cohort Study Open

Brett Edwards, Ranjani Somayaji, Jasper Wong, Conrad Izydorczyk, Barbara J. Waddell , et al. · 2019

Background Analysis of “emerging” pathogens in cystic fibrosis (CF) lung disease has focused on unique pathogens that are rare in other human diseases or are drug resistant. Escherichia coli is recovered in the sputum of up to 25% of patie…

Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver Open

Avinash Thakur, Jasper Wong, Evan Y. Wang, Jeremy Lotto, Donghwan Kim , et al. · 2019

Cell‐fate determination is influenced by interactions between master transcription factors (TFs) and cis‐regulatory elements. Hepatocyte nuclear factor 4 alpha (HNF4A), a liver‐enriched TF, acts as a master controller in specification of h…

1481. Clinical Outcomes of Escherichia coli Infections in Cystic Fibrosis (CF) Patients Open

Brett Edwards, Jasper Wong, Ranjani Somayaji, Barbara J. Waddell, Doug Storey , et al. · 2018

BACKGROUND: Despite a growing interest in emerging pathogens in CF, research has largely overlooked commonplace organisms. Escherichia coli has been reported in up to 50% of CF respiratory samples, yet little is known about its clinical im…

bioSyntax: syntax highlighting for computational biology Open

Artem Babaian, Anicet Ebou, Alyssa Fegen, Jeffrey Kam, Gherman Novakovsky , et al. · 2018

Additional file 2: of bioSyntax: syntax highlighting for computational biology Open

Artem Babaian, Anicet Ebou, Alyssa Fegen, Jeffrey Kam, Gherman Novakovsky , et al. · 2018

Table S1. Biological class definitions and colour definitions for the default bioSyntax theme in hexadecimal (gedit, sublime, VSCode, and gvim), cterm (vim), and 8-bit ANSI escape character (less) colours. (XLS 186 kb)

bioSyntax: Syntax Highlighting For Computational Biology Open

Artem Babaian, Anicet Ebou, Alyssa Fegen, Jeffrey Kam, Gherman Novakovsky , et al. · 2017

Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information that is obfuscated by the complexity of the data structures.…

Prevalence and Outcomes of Achromobacter Species Infections in Adults with Cystic Fibrosis: a North American Cohort Study Open

Brett Edwards, Jasper Wong, Ranjani Somayaji, Barbara J. Waddell, Fiona Whelan , et al. · 2017

Achromobacter species are increasingly being detected in cystic fibrosis (CF) patients, with an unclear epidemiology and impact. We studied a cohort of patients attending a Canadian adult CF clinic who had positive sputum cultures for Achr…

Clinical Outcomes of Achromobacter Species in Adult Cystic Fibrosis Patients: A Cohort Study Open

Brett Edwards, Ranjani Somayaji, Jasper Wong, Harvey Rabin, Michael D. Parkins · 2016

Jasper Wong YOU? Author Swipe