[HTML][HTML] A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
C Xu - Computational and structural biotechnology journal, 2018 - Elsevier
Detection of somatic mutations holds great potential in cancer treatment and has been a
very active research field in the past few years, especially since the breakthrough of the next …
very active research field in the past few years, especially since the breakthrough of the next …
Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing
The advent of next-generation sequencing technologies has greatly promoted advances in
the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome …
the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome …
Pan-cancer analysis of the extent and consequences of intratumor heterogeneity
Intratumor heterogeneity (ITH) drives neoplastic progression and therapeutic resistance. We
used the bioinformatics tools' expanding ploidy and allele frequency on nested …
used the bioinformatics tools' expanding ploidy and allele frequency on nested …
Mutational landscape and significance across 12 major cancer types
Abstract The Cancer Genome Atlas (TCGA) has used the latest sequencing and analysis
methods to identify somatic variants across thousands of tumours. Here we present data and …
methods to identify somatic variants across thousands of tumours. Here we present data and …
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
Detection of somatic point substitutions is a key step in characterizing the cancer genome.
However, existing methods typically miss low-allelic-fraction mutations that occur in only a …
However, existing methods typically miss low-allelic-fraction mutations that occur in only a …
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen
receptor, progesterone receptor and ERBB2 gene amplification, represent approximately …
receptor, progesterone receptor and ERBB2 gene amplification, represent approximately …
Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution
The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has
never been rigorously tested. Because selection greatly affects the level of intratumor …
never been rigorously tested. Because selection greatly affects the level of intratumor …
A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal
A key constraint in genomic testing in oncology is that matched normal specimens are not
commonly obtained in clinical practice. Thus, while well-characterized genomic alterations …
commonly obtained in clinical practice. Thus, while well-characterized genomic alterations …
De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly
De novo somatic mutations in focal areas are well documented in diseases such as
neoplasia but are rarely reported in malformation of the developing brain …
neoplasia but are rarely reported in malformation of the developing brain …
MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data
Subclonal mutations reveal important features of the genetic architecture of tumors.
However, accurate detection of mutations in genetically heterogeneous tumor cell …
However, accurate detection of mutations in genetically heterogeneous tumor cell …