Structural variant calling: the long and the short of it

M Mahmoud, N Gobet, DI Cruz-Dávalos, N Mounier… - Genome biology, 2019 - Springer
Recent research into structural variants (SVs) has established their importance to medicine
and molecular biology, elucidating their role in various diseases, regulation of gene …

Current status of structural variation studies in plants

Y Yuan, PE Bayer, J Batley… - Plant Biotechnology …, 2021 - Wiley Online Library
Structural variations (SVs) including gene presence/absence variations and copy number
variations are a common feature of genomes in plants and, together with single nucleotide …

Mechanisms and therapeutic implications of hypermutation in gliomas

M Touat, YY Li, AN Boynton, LF Spurr, JB Iorgulescu… - Nature, 2020 - nature.com
A high tumour mutational burden (hypermutation) is observed in some gliomas,,,–; however,
the mechanisms by which hypermutation develops and whether it predicts the response to …

Genetic and transcriptional evolution alters cancer cell line drug response

U Ben-David, B Siranosian, G Ha, H Tang, Y Oren… - Nature, 2018 - nature.com
Human cancer cell lines are the workhorse of cancer research. Although cell lines are
known to evolve in culture, the extent of the resultant genetic and transcriptional …

Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

B Chapuy, C Stewart, AJ Dunford, J Kim, A Kamburov… - Nature medicine, 2018 - nature.com
Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is
a clinically and genetically heterogeneous disease that is further classified into …

Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly

F Zink, SN Stacey, GL Norddahl… - Blood, The Journal …, 2017 - ashpublications.org
Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is
derived from a single dominant hematopoietic stem cell lineage. Somatic mutations in …

Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software

DL Cameron, L Di Stefano, AT Papenfuss - Nature communications, 2019 - nature.com
In recent years, many software packages for identifying structural variants (SVs) using whole-
genome sequencing data have been released. When published, a new method is commonly …

[HTML][HTML] Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

S Raghavan, PS Winter, AW Navia, HL Williams… - Cell, 2021 - cell.com
Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma
(PDAC), but our understanding of their drivers, stability, and relationship to therapeutic …

Validation of OncoPanel: a targeted next-generation sequencing assay for the detection of somatic variants in cancer

EP Garcia, A Minkovsky, Y Jia… - … of Pathology and …, 2017 - meridian.allenpress.com
Context.—The analysis of somatic mutations across multiple genes in cancer specimens
may be used to aid clinical decision making. The analytical validation of targeted next …

Targetable genetic features of primary testicular and primary central nervous system lymphomas

B Chapuy, MGM Roemer, C Stewart… - Blood, The Journal …, 2016 - ashpublications.org
Primary central nervous system lymphomas (PCNSLs) and primary testicular lymphomas
(PTLs) are extranodal large B-cell lymphomas (LBCLs) with inferior responses to current …