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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...Splice exhibits excellent reproducibility across cDNA input and PCR cycle differences and is able to identify and quantitate transcripts that differed by a single base. Of the 193 BRCA1 and 72 BRCA2 variants profiled, 89% (237/265) had no publicly available RNA splicing data. Complete or near complete impact...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...). By looking at the mutations through -wide “breadth”, the limited number of equivalents becomes less restrictive, enabling the identification of tumor fractions (TFs) ∼100 times lower compared to targeted “depth” in SNV analysis (Zviran et al. 2020). Genome-wide cfDNA can also reveal tumor-specific copy...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
..., Mandell JB, Gulsuner S, King MC. 2021. CRISPR-Cas9/long-read sequencing approach to identify cryptic variants in BRCA1 and other tumour suppressor genes. J Med Genet 58: 850–852. doi:10.1136/jmedgenet-2020-107320 ↵Zeng T, Li YI. 2022. Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol...
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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
...of SIRT1 in modulating breast cancer immunity. Although SIRT1 is not explicitly listed as a key player in the breast cancer pathway according to the KEGG database (absent from hsa05224), it is recognized as a tumor suppressor owing to its protective role against DNA damage and oxidative stress...
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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...Gs are indicated. (E) Locus of the promoter and regulatory region of SPI1 with DNA methylation and gene expression levels before and after 9 mo of HC treatment. Yellow shading indicates DNA methylation levels, blue shading indicates significant DMRs, and gray shading denotes gene expression levels.Genomic context...
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Method: Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations
- John F. Thompson,
- Jeffrey G. Reifenberger,
- Eldar Giladi,
- Kristen Kerouac,
- Jaime Gill,
- Erik Hansen,
- Avak Kahvejian,
- Philipp Kapranov,
- Travis Knope,
- Doron Lipson,
- Kathleen E. Steinmann,
- and Patrice M. Milos
Genome Res. February 2012 22: 340-345; Published in Advance July 15, 2011, doi:10.1101/gr.122192.111
...-molecule sequencing. Gene isolation, amplification, or ligation is not necessary. Accurate and low-cost detection of DNA sequence variants is demonstrated for the BRCA1 gene. Disease-causing mutations as well as common variants from well-characterized samples are identified. Single-molecule sequencing generates very...
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Research: Gene essentiality in cancer cell lines is modified by the sex chromosomes
- Shahar Shohat,
- Ethel Vol,
- and Sagiv Shifman
Genome Res. November/December 2022 32: 1993-2002; Published in Advance November 23, 2022, doi:10.1101/gr.276488.121
...misclassified cell lines) (Supplemental Table S1).To infer the presence of the Y Chromosome, we used the DNA copy number of all genes on the Y Chromosome (relative to all other genes) and the expression of Y-linked genes. Classification based on the Y Chromosome DNA copy number (Fig. 1A) was in high agreement...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
...hypomethylation, DNA hypermethylation of CpG islands (CGIs) is a well-defined feature of cancer cells and is believed to be the main cause of aberrant gene repression (Baylin and Jones 2016). CGIs are key regulatory genomic regions of a few hundred base pairs in size characterized by high frequency of Cp...
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Research: DDX54 regulates transcriptome dynamics during DNA damage response
- Miha Milek,
- Koshi Imami,
- Neelanjan Mukherjee,
- Francesca De Bortoli,
- Ulrike Zinnall,
- Orsalia Hazapis,
- Christian Trahan,
- Marlene Oeffinger,
- Florian Heyd,
- Uwe Ohler,
- Matthias Selbach,
- and Markus Landthaler
Genome Res. August 2017 27: 1344-1359; Published in Advance June 8, 2017, doi:10.1101/gr.218438.116
...induction (Fig. 6D). These results suggest that DDX54 promotes cell survival upon DNA damage. As a potent regulator of the gene expression during the DDR, DDX54 has the potential to be important for tumor biology. To address this, we analyzed The Cancer Genome Atlas (TCGA) mRNA-seq data (Sebestyén et al...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...such as the breast cancer susceptibility gene BRCA1 (Tapia et al. 2008) supports the notion that tumor suppressors are frequently inactivated by DNA methylation at CpG islands and promoters. Genome-scale methods including MeDIP-seq (Ruike et al. 2010) and CHARM (Irizarry et al. 2009) have confirmed global...

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