Cargando…

Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA

MOTIVATION: Cancer is a complex disease that involves rapidly evolving cells, often forming multiple distinct clones. In order to effectively understand progression of a patient-specific tumor, one needs to comprehensively sample tumor DNA at multiple time points, ideally obtained through inexpensiv...

Descripción completa

Detalles Bibliográficos
Autores principales:	Gawroński, Alexander R, Lin, Yen-Yi, McConeghy, Brian, LeBihan, Stephane, Asghari, Hossein, Koçkan, Can, Orabi, Baraa, Adra, Nabil, Pili, Roberto, Collins, Colin C, Sahinalp, S Cenk, Hach, Faraz
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2019
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6468241/ https://www.ncbi.nlm.nih.gov/pubmed/30759232 http://dx.doi.org/10.1093/nar/gkz067

Ejemplares similares

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing
por: Orabi, Baraa, et al.
Publicado: (2022)

PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
por: Malikic, Salem, et al.
Publicado: (2019)

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications
por: Hach, Faraz, et al.
Publicado: (2014)

Dissect: detection and characterization of novel structural alterations in transcribed sequences
por: Yorukoglu, Deniz, et al.
Publicado: (2012)

Optimized high-throughput screening of non-coding variants identified from genome-wide association studies
por: Morova, Tunc, et al.
Publicado: (2022)

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
por: McPherson, Andrew, et al.
Publicado: (2012)

FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery
por: Piazza, Rocco, et al.
Publicado: (2012)

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing
por: Weirather, Jason L., et al.
Publicado: (2015)

USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products
por: Geu-Flores, Fernando, et al.
Publicado: (2007)

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
por: Hormozdiari, Fereydoun, et al.
Publicado: (2010)

Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments
por: Ebrahimi, Ghazal, et al.
Publicado: (2022)

Statistical algorithms improve accuracy of gene fusion detection
por: Hsieh, Gillian, et al.
Publicado: (2017)

Ubc9 fusion-directed SUMOylation identifies constitutive and inducible SUMOylation
por: Jakobs, Astrid, et al.
Publicado: (2007)

Programming sites of meiotic crossovers using Spo11 fusion proteins
por: Sarno, Roberta, et al.
Publicado: (2017)

Fusoselect: cell–cell fusion activity engineered by directed evolution of a retroviral glycoprotein
por: Merten, Christoph A., et al.
Publicado: (2006)

Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotyping
por: Turner, Daniel J., et al.
Publicado: (2008)

Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones
por: Dolphin, Colin T., et al.
Publicado: (2006)

rDNA-directed integration by an HIV-1 integrase—I-PpoI fusion protein
por: Schenkwein, Diana, et al.
Publicado: (2013)

Robustness of Massively Parallel Sequencing Platforms
por: Kavak, Pınar, et al.
Publicado: (2015)

A sensitive array-based assay for identifying multiple TMPRSS2:ERG fusion gene variants
por: Lu, Qing, et al.
Publicado: (2008)

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines
por: Asmann, Yan W., et al.
Publicado: (2011)

HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology
por: Shrestha, Raunak, et al.
Publicado: (2017)

Native gel electrophoresis of human telomerase distinguishes active complexes with or without dyskerin
por: Gardano, Laura, et al.
Publicado: (2012)

Binding of lac repressor-GFP fusion protein to lac operator sites inserted in the tobacco chloroplast genome examined by chromatin immunoprecipitation
por: Newell, Christine A., et al.
Publicado: (2010)

Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats
por: Gabsalilow, Lilia, et al.
Publicado: (2013)

ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data
por: Li, You, et al.
Publicado: (2017)

Hercules: a profile HMM-based hybrid error correction algorithm for long reads
por: Firtina, Can, et al.
Publicado: (2018)

Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor
por: Shu, Dan, et al.
Publicado: (2014)

Barcode fusion genetics-protein-fragment complementation assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery
por: Evans-Yamamoto, Daniel, et al.
Publicado: (2022)

Discovery and genotyping of novel sequence insertions in many sequenced individuals
por: Kavak, Pınar, et al.
Publicado: (2017)

NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision
por: Chuang, Trees-Juen, et al.
Publicado: (2016)

Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data
por: Liu, Silvia, et al.
Publicado: (2016)

Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification
por: Cain-Hom, Carol, et al.
Publicado: (2017)

Solid-phase translation and RNA–protein fusion: a novel approach for folding quality control and direct immobilization of proteins using anchored mRNA
por: Biyani, Manish, et al.
Publicado: (2006)

cDNA display: a novel screening method for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA–protein fusions
por: Yamaguchi, Junichi, et al.
Publicado: (2009)

An efficient genotyper and star-allele caller for pharmacogenomics
por: Hari, Ananth, et al.
Publicado: (2023)

Using a microfluidic device for 1 μl DNA microarray hybridization in 500 s
por: Wei, Cheng-Wey, et al.
Publicado: (2005)

An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments
por: Heyer, Erin E., et al.
Publicado: (2015)

Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network
por: Qin, Tingting, et al.
Publicado: (2014)

The synthetic integron: an in vivo genetic shuffling device
por: Bikard, David, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_dpv255546snh44md24snsdo99d