18 papers · ranked by Valyu relevance
Mary Goldman, Junjun Zhang, Nuno A. Fonseca, Isidro Cortés-Ciriano + 20 more
The Pan-Cancer Analysis of Whole Genomes (PCAWG) project has generated, to our knowledge, the largest whole-genome cancer sequencing resource to date. Here we provide a user’s guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper: The ICGC Data Portal…
Christina K. Yung, Brian D. O’Connor, Sergei Yakneen, Junjun Zhang + 109 more
The International Cancer Genome Consortium (ICGC)’s Pan-Cancer Analysis of Whole Genomes (PCAWG) project aimed to categorize somatic and germline variations in both coding and non-coding regions in over 2,800 cancer patients. To provide this dataset to the research working groups for downstream analysis, the PCAWG…
Justin P. Whalley, Ivo Buchhalter, Esther Rheinbay, Keiran M. Raine + 19 more
Working with cancer whole genomes sequenced over a period of many years in different sequencing centres requires a validated framework to compare the quality of these sequences. The Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC), a project a cohort of over 2800 donors…
Mary J. Goldman, Junjun Zhang, Nuno A. Fonseca, Isidro Cortés-Ciriano + 20 more
'Isidro Cortés-Ciriano' 'Qian Xiang' 'Brian Craft' 'Elena Piñeiro-Yáñez' 'Brian D. O’Connor' 'Wojciech Bazant' 'Elisabet Barrera' 'Alfonso Muñoz-Pomer' 'Robert Petryszak' 'Anja Füllgrabe' 'Fatima Al-Shahrour' 'Maria Keays' 'David Haussler' 'John N. Weinstein' 'Wolfgang Huber' 'Alfonso Valencia' 'Peter J. Park' 'Irene…
Simona Giunta
Cancer is underlined by genetic changes. In an unprecedented international effort, the Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) sequenced the tumors of over two thousand five hundred patients across 38 different cancer types, as…
Ziyu Tao, Shixiang Wang, Chenxu Wu, Tao Wu + 8 more
Copy number alterations (CNAs) are a predominant source of genetic alterations in human cancer and play an important role in cancer progression. However comprehensive understanding of the mutational processes and signatures of CNA is still lacking. Here we developed a mechanism-agnostic method to categorize CNA based…
Marc Zapatka, Ivan Borozan, Daniel S. Brewer, Murat Iskar + 9 more
'Adam Grundhoff' 'Malik Alawi' 'Nikita Desai' 'Holger Sültmann' 'Holger Moch' '' 'Colin S. Cooper' 'Roland Eils' 'Vincent Ferretti' 'Peter Lichter' ''] Correction to: Nature Genetics 10.1038/s41588-019-0558-9, published online 05 February 2020. In the published version of this paper, the members of the Pan-Cancer…
Sergei Yakneen, Sebastian M. Waszak, Michael Gertz, Jan O. Korbel
We present Butler, a computational framework developed in the context of the international Pan-cancer Analysis of Whole Genomes (PCAWG)1 project to overcome the challenges of orchestrating analyses of thousands of human genomes on the cloud. Butler operates equally well on public and academic clouds. This highly…
Vinayak Bhandari, Constance H. Li, Robert G. Bristow, Paul C. Boutros
'Paul C. Boutros' ''] Correction to: Nature Communications 10.1038/s41467-019-14052-x, published online 05 February 2020 In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium were listed in the Supplementary Information; however, these members should have…
Yiyun Rao, Nabeel Ahmed, Justin Pritchard, Edward P. O’Brien
Background Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutations might be enriched in cancer has been explored in several recent studies. However, none of these…
Saptarshi Chakraborty, Zoe Guan, Colin B. Begg, Ronglai Shen
Statistical inference on the cancer-site specificities of collective ultra-rare whole genome somatic mutations is an open problem. Traditional statistical methods cannot handle wholegenome mutation data due to their ultra-high-dimensionality and extreme data sparsity – e.g., >30 million unique variants are observed in…
Stella Pranoto, Hsing-Chieh Wu, Chun-Yen Chu
Porcine circovirus (PCV) comprises four distinct species, namely, PCV1-4, with considerable differences between them, resulting in limited crossprotection. PCV2 inflicts substantial economic losses on the swine industry. PCV3 was found to have been circulating before its discovery in 2015. PCV3 is suspected of having a…
Authors not listed
Polyethylene glycols (PEGs), a major class of water-soluble polymers (WSPs), are widely used in diverse applications which may lead to their release into the environment. This work investigates the reaction of PEGs with photochemically produced hydroxyl radicals (•OH), an important environmental oxidant, and assesses…
Paige M. Whelpley, Jose L. Zepeda, William S. Schjerven, Sara M Rocus + 1 more
Phenoxy ring-substituted isopropyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH(CH3)2, where R is 2-(3-methoxyphenoxy), 2-(4-methoxyphenoxy), 3-(4-methoxyphenoxy), 3-(4-methylphenoxy), 4-(4-bromophenoxy), 4-(4-fluorophenoxy), 2-(4-chlorophenoxy), 3-(4-chlorophenoxy), 4-(3-chlorophenoxy), 4-(4-chlorophenoxy)…
Anne-Charlotte Dubbelman, Bo van Wieringen, Lesley Roman Arias, Michael van Vliet + 3 more
Matrix effect limits the accuracy of quantitation of the otherwise popular metabolomics technique liquid chromatography coupled to mass spectrometry (LC-MS). The gold standard to correct for this phenomenon, whereby compounds co-eluting with the analyte-of-interest cause ionization enhancement or suppression, is to…
Authors not listed
Polyethylene glycol (PEG) plays a central role in nanomedicine, providing essential properties such as the stealth effect. However, the emergence of anti-PEG antibodies (APAs) increasingly undermines these benefits, raising concerns about safety and efficiency. This creates an urgent need for PEG alternatives.…
Guang‐Zhong Yin, José Luis Díaz Palencia, De‐Yi Wang
A novel fully bio-based Poly (Glycerol-Itaconic acid) (PGI) was designed and highly efficiently synthesized by solvent-free polycondensation. The Poly (ethylene glycol) (PEG) was used as the phase change materials (PCM) working substance and encapsulated by the sustainable PGI supporter. PEG chains were tightly…
Shiming Yuan, J. Alme, D. Röhrich, Matthias Rudolph Richter + 6 more
'Magnus Rentsch Ersdal' 'P. Giubilato' 'G. Aglieri Rinella' 'A. Velure' 'M. Lupi' 'J. Schambach'] Abstract—A Large Ion Collider Experiment (ALICE) is one of the four major experiments conducted at the CERN Large Hadron Collider (LHC). The ALICE detector is currently undergoing an upgrade for the upcoming Run 3 at the…