Search Results - "Breeze, Charles E"

A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies by Teschendorff, Andrew E, Breeze, Charles E, Zheng, Shijie C, Beck, Stephan

“…Intra-sample cellular heterogeneity presents numerous challenges to the identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While…”
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Identification of differentially methylated cell types in epigenome-wide association studies by Zheng, Shijie C., Breeze, Charles E., Beck, Stephan, Teschendorff, Andrew E.

“…An outstanding challenge of epigenome-wide association studies (EWASs) performed in complex tissues is the identification of the specific cell type(s)…”
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EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data by Teschendorff, Andrew E, Zhu, Tianyu, Breeze, Charles E, Beck, Stephan

“…Cell type heterogeneity presents a challenge to the interpretation of epigenome data, compounded by the difficulty in generating reliable single-cell DNA…”
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A mammalian methylation array for profiling methylation levels at conserved sequences by Arneson, Adriana, Haghani, Amin, Thompson, Michael J., Pellegrini, Matteo, Kwon, Soo Bin, Vu, Ha, Maciejewski, Emily, Yao, Mingjia, Li, Caesar Z., Lu, Ake T., Morselli, Marco, Rubbi, Liudmilla, Barnes, Bret, Hansen, Kasper D., Zhou, Wanding, Breeze, Charles E., Ernst, Jason, Horvath, Steve

“…Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe…”
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African ancestry-derived APOL1 risk genotypes show proximal epigenetic associations by Breeze, Charles E, Lin, Bridget M, Winkler, Cheryl A, Franceschini, Nora

“…Apolipoprotein L1 (APOL1) coding variants, termed G1 and G2, are established genetic risk factors for a growing spectrum of diseases, including kidney disease,…”
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Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations by Breeze, Charles E, Haugen, Eric, Reynolds, Alex, Teschendorff, Andrew, van Dongen, Jenny, Lan, Qing, Rothman, Nathaniel, Bourque, Guillaume, Dunham, Ian, Beck, Stephan, Stamatoyannopoulos, John, Franceschini, Nora, Berndt, Sonja I

“…Genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and…”
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Snoring and breathing pauses during sleep: interview survey of a United Kingdom population sample reveals a significant increase in the rates of sleep apnoea and obesity over the last 20 years - data from the UK sleep survey by Lechner, Matt, Breeze, Charles E., Ohayon, Maurice M., Kotecha, Bhik

“…(1) To determine the prevalence of snoring, breathing pauses during sleep and obstructive sleep apnoea syndrome in the United Kingdom (UK) and determine the…”
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FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases by Breeze, Charles E, Haugen, Eric, Gutierrez-Arcelus, María, Yao, Xiaozheng, Teschendorff, Andrew, Beck, Stephan, Dunham, Ian, Stamatoyannopoulos, John, Franceschini, Nora, Machiela, Mitchell J, Berndt, Sonja I

“…The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing…”
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Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution by Bartlett, Thomas E., Chindera, Kantaraja, McDermott, Jacqueline, Breeze, Charles E., Cooke, William R., Jones, Allison, Reisel, Daniel, Karegodar, Smita T., Arora, Rupali, Beck, Stephan, Menon, Usha, Dubeau, Louis, Widschwendter, Martin

“…The exact timing and contribution of epigenetic reprogramming to carcinogenesis are unclear. Women harbouring BRCA1/2 mutations demonstrate a 30–40-fold…”
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Diversity in EWAS: current state, challenges, and solutions by Breeze, Charles E, Wong, Jason Y. Y, Beck, Stephan, Berndt, Sonja I, Franceschini, Nora

“…Abstract Here, we report a lack of diversity in epigenome-wide association studies (EWAS) and DNA methylation (DNAm) data, discuss current challenges, and…”
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Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs by van Dongen, Jenny, Ehli, Erik A, Jansen, Rick, van Beijsterveldt, Catharina E M, Willemsen, Gonneke, Hottenga, Jouke J, Kallsen, Noah A, Peyton, Shanna A, Breeze, Charles E, Kluft, Cornelis, Heijmans, Bastiaan T, Bartels, Meike, Davies, Gareth E, Boomsma, Dorret I

“…DNA methylation arrays are widely used in epigenome-wide association studies and methylation quantitative trait locus (mQTL) studies. Here, we performed the…”
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eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data by Breeze, Charles E., Paul, Dirk S., van Dongen, Jenny, Butcher, Lee M., Ambrose, John C., Barrett, James E., Lowe, Robert, Rakyan, Vardhman K., Iotchkova, Valentina, Frontini, Mattia, Downes, Kate, Ouwehand, Willem H., Laperle, Jonathan, Jacques, Pierre-Étienne, Bourque, Guillaume, Bergmann, Anke K., Siebert, Reiner, Vellenga, Edo, Saeed, Sadia, Matarese, Filomena, Martens, Joost H.A., Stunnenberg, Hendrik G., Teschendorff, Andrew E., Herrero, Javier, Birney, Ewan, Dunham, Ian, Beck, Stephan

“…Epigenome-wide association studies (EWAS) provide an alternative approach for studying human disease through consideration of non-genetic variants such as…”
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Gender-neutral HPV vaccination in the UK, rising male oropharyngeal cancer rates, and lack of HPV awareness by Lechner, Matt, Jones, Oliver S, Breeze, Charles E, Gilson, Richard

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The missing diversity in human epigenomic studies by Breeze, Charles E., Beck, Stephan, Berndt, Sonja I., Franceschini, Nora

“…Recent work has highlighted a lack of diversity in genomic studies. However, less attention has been given to epigenomics. Here, we show that epigenomic…”
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eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data by Breeze, Charles E, Reynolds, Alex P, van Dongen, Jenny, Dunham, Ian, Lazar, John, Neph, Shane, Vierstra, Jeff, Bourque, Guillaume, Teschendorff, Andrew E, Stamatoyannopoulos, John A, Beck, Stephan

“…Abstract Summary The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over…”
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Early detection of HPV-associated oropharyngeal cancer by Lechner, Matt, Breeze, Charles E, O'Mahony, James F, Masterson, Liam

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A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution by Zhu, Tianyu, Liu, Jacklyn, Beck, Stephan, Pan, Sun, Capper, David, Lechner, Matt, Thirlwell, Chrissie, Breeze, Charles E., Teschendorff, Andrew E.

“…Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease…”
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HGF-rs12536657 and Ocular Biometric Parameters in Hyperopic Children, Emmetropic Adolescents, and Young Adults: A Multicenter Quantitative Trait Study by Patiño-García, Ana, Recalde, Sergio, Santos, J. L., Breeze, Charles E., Pueyo, Victoria, Noval, Susana, Galdós, Marta, Bonet-Farriol, Elvira, Barrio-Barrio, Jesús, Alfonso-Bartolozzi, Belén

“…Introduction. Even though ocular refractive state is highly heritable and under strong genetic control, the identification of susceptibility genes remains a…”
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EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI by Zheng, Shijie C, Breeze, Charles E, Beck, Stephan, Dong, Danyue, Zhu, Tianyu, Ma, Liangxiao, Ye, Wei, Zhang, Guoqing, Teschendorff, Andrew E

“…Abstract Summary It is well recognized that cell-type heterogeneity hampers the interpretation of Epigenome-Wide Association Studies (EWAS). Many tools have…”
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Cell Type-Specific Signal Analysis in Epigenome-Wide Association Studies by Breeze, Charles E

“…Hundreds of epigenome-wide association studies (EWAS) have been performed, successfully identifying replicated epigenomic signals in processes such as aging…”
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