BMC Bioinformatics, 2023 Background The spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational signatures can be found using non-negative matrix factorization (NMF).
Marta Pelizzola +2 more
doaj +1 more source
Deciphering Signatures of Mutational Processes Operative in Human Cancer
Cell Reports, 2013 The genome of a cancer cell carries somatic mutations that are the cumulative consequences of the DNA damage and repair processes operative during the cellular lineage between the fertilized egg and the cancer cell. Remarkably, these mutational processes
Ludmil B. Alexandrov +4 more
doaj +1 more source
Simultaneous evolutionary expansion and constraint of genomic heterogeneity in multifocal lung cancer. [PDF]
, 2017 Recent genomic analyses have revealed substantial tumor heterogeneity across various cancers. However, it remains unclear whether and how genomic heterogeneity is constrained during tumor evolution.
Bivona, Trever G +16 more
core +2 more sources
The landscape of viral associations in human cancers [PDF]
, 2020 Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and—for a subset—whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential ...
Alawi, Malik +14 more
core +3 more sources
Nodal marginal zone mutational signature [PDF]
Blood, 2016 In this issue of Blood , [Spina and coworkers][1] describe the nodal marginal zone lymphoma (NMZL) mutational signature, identifying family links with other marginal zone lymphoma types (NOTCH2, KLF2) and specific mutated genes (PTPRD).[1][2] ![Figure][3] Relative frequency of the ...
openaire +2 more sources
Blastic plasmacytoid dendritic cell neoplasm: Genomics mark epigenetic dysregulation as a primary therapeutic target [PDF]
, 2019 Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive hematologic malignancy for which there is still no effective B therapy.
Abate F. +30 more
core +2 more sources
Somatic mutation load of estrogen receptor-positive breast tumors predicts overall survival: an analysis of genome sequence data. [PDF]
, 2014 Breast cancer is one of the most commonly diagnosed cancers in women. While there are several effective therapies for breast cancer and important single gene prognostic/predictive markers, more than 40,000 women die from this disease every year.
Bainbridge, Matthew N +3 more
core +1 more source
Comparison of TCGA and GENIE genomic datasets for the detection of clinically actionable alterations in breast cancer. [PDF]
, 2019 Whole exome sequencing (WES), targeted gene panel sequencing and single nucleotide polymorphism (SNP) arrays are increasingly used for the identification of actionable alterations that are critical to cancer care.
Carpten, John D +4 more
core +3 more sources
Impact of cancer mutational signatures on transcription factor motifs in the human genome
BMC Medical Genomics, 2019 Background Somatic mutations in cancer genomes occur through a variety of molecular mechanisms, which contribute to different mutational patterns. To summarize these, mutational signatures have been defined using a large number of cancer genomes, and ...
Calvin Wing Yiu Chan +4 more
doaj +1 more source
ISOWN: accurate somatic mutation identification in the absence of normal tissue controls. [PDF]
, 2017 BackgroundA key step in cancer genome analysis is the identification of somatic mutations in the tumor. This is typically done by comparing the genome of the tumor to the reference genome sequence derived from a normal tissue taken from the same donor ...
Bartlett, John MS +5 more
core +1 more source