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Article
Open AccessBispecific BCMA/CD24 CAR-T cells control multiple myeloma growth
Anti-multiple myeloma B cell maturation antigen (BCMA)-specific chimeric antigen receptor (CAR) T-cell therapies represent a promising treatment strategy with high response rates in myeloma. However, durable c...
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Article
Open AccessExpression of integrin β-7 is epigenetically enhanced in multiple myeloma subgroups with high-risk cytogenetics
Oncogenic overexpression of integrin-β7 (ITGB7) in cases of high-risk multiple myeloma (MM) was reported to promote enhanced interactions between neoplastic plasma-B cells and stromal cells to develop cell-adhesi...
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Article
Open AccessThe spatio-temporal evolution of multiple myeloma from baseline to relapse-refractory states
Deciphering Multiple Myeloma evolution in the whole bone marrow is key to inform curative strategies. Here, we perform spatial-longitudinal whole-exome sequencing, including 140 samples collected from 24 Multi...
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Article
Open AccessStructural variants shape the genomic landscape and clinical outcome of multiple myeloma
Deciphering genomic architecture is key to identifying novel disease drivers and understanding the mechanisms underlying myeloma initiation and progression. In this work, using the CoMMpass dataset, we show th...
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Article
Plasma cells expression from smouldering myeloma to myeloma reveals the importance of the PRC2 complex, cell cycle progression, and the divergent evolutionary pathways within the different molecular subgroups
Sequencing studies have shed some light on the pathogenesis of progression from smouldering multiple myeloma (SMM) and symptomatic multiple myeloma (MM). Given the scarcity of smouldering samples, little data ...
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Article
Improving prognostic assignment in older adults with multiple myeloma using acquired genetic features, clonal hemopoiesis and telomere length
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Article
Open AccessFiNGS: high quality somatic mutations using filters for next generation sequencing
Somatic variant callers are used to find mutations in sequencing data from cancer samples. They are very sensitive and have high recall, but also may produce low precision data with a large proportion of false...
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Article
Open AccessAuthor Correction: Accelerated single cell seeding in relapsed multiple myeloma
A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-20978-y.
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Article
Open AccessThe molecular make up of smoldering myeloma highlights the evolutionary pathways leading to multiple myeloma
Smoldering myeloma (SMM) is associated with a high-risk of progression to myeloma (MM). We report the results of a study of 82 patients with both targeted sequencing that included a capture of the immunoglobul...
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Article
Open AccessThe functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma
Multiple Myeloma (MM) is a hematological malignancy with genomic heterogeneity and poor survival outcome. Apart from the central role of genetic lesions, epigenetic anomalies have been identified as drivers in...
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Article
Open AccessAccelerated single cell seeding in relapsed multiple myeloma
Multiple myeloma (MM) progression is characterized by the seeding of cancer cells in different anatomic sites. To characterize this evolutionary process, we interrogated, by whole genome sequencing, 25 samples...
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Article
Open AccessGenomic analysis of primary plasma cell leukemia reveals complex structural alterations and high-risk mutational patterns
Primary plasma cell leukemia (pPCL) is a rare and aggressive form of multiple myeloma (MM) that is characterized by the presence of ≥20% circulating plasma cells. Overall survival remains poor despite advances...
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Article
Open AccessTarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use
The study of cancer genomics continually matures as the number of patient samples sequenced increases. As more data is generated, oncogenic drivers for specific cancer types are discovered along with their ass...
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Article
Open AccessLoss of heterozygosity as a marker of homologous repair deficiency in multiple myeloma: a role for PARP inhibition?
PARP inhibitors can induce synthetic lethality in tumors characterized by homologous recombination deficiency (HRD), which can be detected by evaluating genome-wide loss of heterozygosity (LOH). Multiple myelo...
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Article
Open AccessDNAp: A Pipeline for DNA-seq Data Analysis
Next-generation sequencing is empowering genetic disease research. However, it also brings significant challenges for efficient and effective sequencing data analysis. We built a pipeline, called DNAp, for ana...
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Article
Open AccessEnhancing cancer clonality analysis with integrative genomics
It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural ...
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Article
Open AccessBridger: a new framework for de novo transcriptome assembly using RNA-seq data
We present a new de novo transcriptome assembler, Bridger, which takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers. When tested on dog, human, and mous...
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Article
Open AccessNew enumeration algorithm for protein structure comparison and classification
Protein structure comparison and classification is an effective method for exploring protein structure-function relations. This problem is computationally challenging. Many different computational approaches f...
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Chapter and Conference Paper
A Unified Adaptive Co-identification Framework for High-D Expression Data
High-throughput techniques are producing large-scale high-dimensional (e.g., 4D with genes vs timepoints vs conditions vs tissues) genome-wide gene expression data. This induces increasing demands for effectiv...
