Cargando…

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors

Identifying somatic mutations is critical for cancer genome characterization and for prioritizing patient treatment. DNA whole exome sequencing (DNA-WES) is currently the most popular technology; however, this yields low sensitivity in low purity tumors. RNA sequencing (RNA-seq) covers the expressed...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wilkerson, Matthew D., Cabanski, Christopher R., Sun, Wei, Hoadley, Katherine A., Walter, Vonn, Mose, Lisle E., Troester, Melissa A., Hammerman, Peter S., Parker, Joel S., Perou, Charles M., Hayes, D. Neil
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2014
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117748/ https://www.ncbi.nlm.nih.gov/pubmed/24970867 http://dx.doi.org/10.1093/nar/gku489

Ejemplares similares

BlackOPs: increasing confidence in variant detection through mappability filtering
por: Cabanski, Christopher R., et al.
Publicado: (2013)

SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples
por: Kimes, Patrick K., et al.
Publicado: (2014)

ABRA: improved coding indel detection via assembly-based realignment
por: Mose, Lisle E., et al.
Publicado: (2014)

SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling
por: Silva, Grace O., et al.
Publicado: (2017)

Prediction of Toxicant-Specific Gene Expression Signatures after Chemotherapeutic Treatment of Breast Cell Lines
por: Troester, Melissa A., et al.
Publicado: (2004)

DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing
por: Bhattacharya, Arjun, et al.
Publicado: (2021)

High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs
por: Panda, Amaresh C., et al.
Publicado: (2017)

High-salt transcription from enzymatically gapped promoters nets higher yields and purity of transcribed RNAs
por: MalagodaPathiranage, Kithmie, et al.
Publicado: (2023)

Improved indel detection in DNA and RNA via realignment with ABRA2
por: Mose, Lisle E, et al.
Publicado: (2019)

Genomic characterization of rare molecular subclasses of hepatocellular carcinoma
por: Damrauer, Jeffrey S., et al.
Publicado: (2021)

Virus expression detection reveals RNA-sequencing contamination in TCGA
por: Selitsky, Sara R., et al.
Publicado: (2020)

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data
por: Cabanski, Christopher R, et al.
Publicado: (2012)

Translating transcriptomic findings from cancer model systems to humans through joint dimension reduction
por: Price, Brandon A., et al.
Publicado: (2023)

A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus
por: Aucelli, Tiziana, et al.
Publicado: (2006)

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling
por: Zhao, Wei, et al.
Publicado: (2014)

Targeted single molecule mutation detection with massively parallel sequencing
por: Gregory, Mark T., et al.
Publicado: (2016)

A random mutation capture assay to detect genomic point mutations in mouse tissue
por: Wright, Jocelyn H., et al.
Publicado: (2011)

Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria
por: Mengiste, Amanuella A, et al.
Publicado: (2023)

Determinants of DNA yield and purity collected with buccal cell samples
por: van Wieren-de Wijer, D. B. M. A., et al.
Publicado: (2009)

Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens
por: Yost, Shawn E., et al.
Publicado: (2012)

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
por: Wang, Kai, et al.
Publicado: (2010)

Differential Pathogenesis of Lung Adenocarcinoma Subtypes Involving Sequence Mutations, Copy Number, Chromosomal Instability, and Methylation
por: Wilkerson, Matthew D., et al.
Publicado: (2012)

Identification of mRNA isoform switching in breast cancer
por: Zhao, Wei, et al.
Publicado: (2016)

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations
por: Hoffmann, Christian, et al.
Publicado: (2007)

Gene expression patterns associated with p53 status in breast cancer
por: Troester, Melissa A, et al.
Publicado: (2006)

A dual gene-specific mutator system installs all transition mutations at similar frequencies in vivo
por: Seo, Daeje, et al.
Publicado: (2023)

Classifying cells with Scasat, a single-cell ATAC-seq analysis tool
por: Baker, Syed Murtuza, et al.
Publicado: (2019)

Understanding mutational effects in digenic diseases
por: Gazzo, Andrea, et al.
Publicado: (2017)

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions
por: Betts, Matthew J., et al.
Publicado: (2015)

Potential Tumor Suppressor Role for the c-Myb Oncogene in Luminal Breast Cancer
por: Thorner, Aaron R., et al.
Publicado: (2010)

Identification of single-point mutations in mycobacterial 16S rRNA sequences by confocal single-molecule fluorescence spectroscopy
por: Marmé, Nicole, et al.
Publicado: (2006)

Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning
por: Tabone, Tania, et al.
Publicado: (2006)

Ice-COLD-PCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations
por: Milbury, Coren A., et al.
Publicado: (2011)

Predicting the functional impact of protein mutations: application to cancer genomics
por: Reva, Boris, et al.
Publicado: (2011)

Maximizing signal-to-noise ratio in the random mutation capture assay
por: Poovathingal, Suresh Kumar, et al.
Publicado: (2012)

Directed adenovirus evolution using engineered mutator viral polymerases
por: Uil, Taco G., et al.
Publicado: (2011)

Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ
por: Mignardi, Marco, et al.
Publicado: (2015)

Oligo targeting for profiling drug resistance mutations in the parasitic trypanosomatids
por: Altmann, Simone, et al.
Publicado: (2022)

Fast chromatin immunoprecipitation assay
por: Nelson, Joel D., et al.
Publicado: (2006)

Stable gene expression for normalisation and single-sample scoring
por: Bhuva, Dharmesh D, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_eot06o5hrl40g305hv26lf41kb