4 research outputs found
Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin
- Author
- Abbott Rachel
- Abbott Scott
- Akbani Rehan
- Aksoy B. Arman
- Aldape Kenneth
- Ally Adrian
- Amin Samirkumar
- Anastassiou Dimitris
- Auman J. Todd
- Baggerly Keith A.
- Balasundaram Miruna
- Balu Saianand
- Baylin Stephen B.
- Benz Christopher C.
- Benz Stephen C.
- Berman Benjamin P.
- Bernard Brady
- Bhatt Ami S.
- Birol Inanc
- Black Aaron D.
- Bodenheimer Tom
- Bootwalla Moiz S.
- Bowen Jay
- Bressler Ryan
- Bristow Christopher A.
- Brooks Angela N.
- Broom Bradley
- Buda Elizabeth
- Burton Robert
- Butterfield Yaron S.N.
- Byers Lauren A.
- Carlin Daniel
- Carter Scott L.
- Casasent Tod D.
- Chang Kyle
- Chanock Stephen
- Chen Zhong
- Cherniack Andrew D.
- Chin Lynda
- Cho Dong Yeon
- Cho Juok
- Chu Andy
- Chuah Eric
- Chun Hye Jung E.
- Cibulskis Kristian
- Ciriello Giovanni
- Cleland James
- Cline Melisssa
- Collisson Eric A.
- Craft Brian
- Creighton Chad J.
- Danilova Ludmila
- Davidsen Tanja
- Davis Caleb
- Dees Nathan D.
- Delehaunty Kim
- Demchok John A.
- Dhalla Noreen
- DiCara Daniel
- Ding Li
- Dinh Huyen
- Dobson Jason R.
- Dodda Deepti
- Doddapaneni Harsha Vardhan
- Donehower Lawrence
- Dooling David J.
- Dresdner Gideon
- Drummond Jennifer
- Eakin Andrea
- Edgerton Mary
- Eldred Jim M.
- Eley Greg
- Ellrott Kyle
- Fan Cheng
- Fei Suzanne
- Felau Ina
- Frazer Scott
- Freeman Samuel S.
- Frick Jessica
- Fronick Catrina C.
- Fulton Lucinda L.
- Fulton Robert
- Gabriel Stacey B.
- Gao Jianjiong
- Gastier-Foster Julie M.
- Gehlenborg Nils
- George Myra
- Getz Gad
- Gibbs Richard
- Goldman Mary
- Gonzalez-Perez Abel
- Gross Benjamin
- Guin Ranabir
- Gunaratne Preethi
- Hadjipanayis Angela
- Hamilton Mark P.
- Hamilton Stanley R.
- Han Leng
- Han Yi
- Harper Hollie A.
- Haseley Psalm
- Haussler David
- Hayes D. Neil
- Heiman David I.
- Helman Elena
- Helsel Carmen
- Herbrich Shelley M.
- Herman James G.
- Hinoue Toshinori
- Hirst Carrie
- Hirst Martin
- Hoadley Katherine A.
- Holt Robert A.
- Hoyle Alan P.
- Iype Lisa
- Jacobsen Anders
- Jeffreys Stuart R.
- Jensen Mark A.
- Jones Corbin D.
- Jones Steven J.M.
- Ju Zhenlin
- Jung Joonil
- Kahles Andre
- Kahn Ari
- Kalicki-Veizer Joelle
- Kalra Divya
- Kanchi Krishna Latha
- Kandoth Cyriac
- Kane David W.
- Kim Hoon
- Kim Jaegil
- Knijnenburg Theo
- Koboldt Daniel C.
- Kovar Christie
- Kramer Roger
- Kreisberg Richard
- Kucherlapati Raju
- Ladanyi Marc
- Laird Peter W.
- Lander Eric S.
- Larson David E.
- Lawrence Michael S.
- Lee Darlene
- Lee Eunjung
- Lee Semin
- Lee William
- Lehmann Kjong Van
- Leinonen Kalle
- Leiserson Max D.M.
- Leraas Kristen M.
- Lerner Seth
- Levine Douglas A.
- Lewis Lora
- Ley Timothy J.
- Li Haiyan I.
- Li Jun
- Li Wei
- Liang Han
- Lichtenberg Tara M.
- Lin Jake
- Lin Ling
- Lin Pei
- Liu Wenbin
- Liu Yingchun
- Liu Yuexin
- Lopez-Bigas Nuria
- Lorenzi Philip L.
- Lu Charles
- Lu Yiling
- Luquette Lovelace J.
- Ma Singer
- Magrini Vincent J.
- Mahadeshwar Harshad S.
- Mardis Elaine R.
- Margolin Adam A.
- Marra Marco A.
- Mayo Michael
- McAllister Cynthia
- McGuire Sean E.
- McLellan Michael D.
- McMichael Joshua F.
- Melott James
- Meng Shaowu
- Meyerson Matthew
- Mieczkowski Piotr A.
- Miller Christopher A.
- Miller Martin L.
- Miller Michael
- Mills Gordon B.
- Moore Richard A.
- Morgan Margaret
- Morton Donna
- Mose Lisle E.
- Mungall Andrew J.
- Muzny Donna
- Ng Sam
- Nguyen Lam
- Niu Beifang
- Noble Michael S.
- Noushmehr Houtan
- O'Laughlin Michelle
- Ojesina Akinyemi I.
- Omberg Larsson
- Ozenberger Brad
- Pantazi Angeliki
- Parfenov Michael
- Park Peter J.
- Parker Joel S.
- Paull Evan
- Pedamallu Chandra Sekhar
- Perou Charles M.
- Pihl Todd
- Pohl Craig
- Pot David
- Protopopov Alexei
- Przytycka Teresa
- Radenbaugh Amie
- Ramirez Nilsa C.
- Ramirez Ricardo
- Raphael Benjamin J.
- Reid Jeffrey
- Ren Xiaojia
- Reva Boris
- Reynolds Sheila M.
- Rhie Suhn K.
- Roach Jeffrey
- Robertson A. Gordon
- Rovira Hector
- Ryan Michael
- Rätsch Gunnar
- Saksena Gordon
- Salama Sofie
- Sander Chris
- Santoso Netty
- Schein Jacqueline E.
- Schmidt Heather
- Schultz Nikolaus
- Schumacher Steven E.
- Seidman Jonathan
- Senbabaoglu Yasin
- Seth Sahil
- Sharpe Samantha
- Shen Hui
- Shen Ronglai
- Sheth Margi
- Shi Yan
- Shmulevich Ilya
- Silva Grace O.
- Simons Janae V.
- Sinha Rileen
- Sipahimalani Payal
- Smith Scott M.
- Sofia Heidi J.
- Sokolov Artem
- Soloway Mathew G.
- Song Xingzhi
- Sougnez Carrie
- Spellman Paul
- Staudt Louis
- Stewart Chip
- Stojanov Petar
- Stuart Joshua M.
- Su Xiaoping
- Sumer S. Onur
- Sun Yichao
- Swatloski Teresa
- Tabak Barbara
- Tam Angela
- Tamborero David
- Tan Donghui
- Tang Jiabin
- Tarnuzzer Roy
- Taylor Barry S.
- Thiessen Nina
- Thorsson Vesteinn
- Triche Timothy
- Uzunangelov Vladislav
- Van Den Berg David J.
- Van Waes Carter
- Van't Veer Laura J.
- Vandin Fabio
- Varhol Richard J.
- Vaske Charles J.
- Veluvolu Umadevi
- Verhaak Roeland
- Voet Doug
- Walker Jason
- Wallis John W.
- Waltman Peter
- Wan Yunhu
- Wang Min
- Wang Wenyi
- Wang Zhining
- Waring Scot
- Weinhold Nils
- Weinstein John N.
- Weisenberger Daniel J.
- Wendl Michael C.
- Wheeler David
- Wilkerson Matthew D.
- Wilson Richard K.
- Wise Lisa
- Wolf Denise M.
- Wong Andrew
- Wu Chang Jiun
- Wu Chia Chin
- Wu Hsin Ta
- Wu Junyuan
- Wylie Todd
- Xi Liu
- Xi Ruibin
- Xia Zheng
- Xu Andrew W.
- Yang Da
- Yang Liming
- Yang Lixing
- Yang Tai Hsien Ou
- Yang Yang
- Yao Jun
- Yao Rong
- Yau Christina
- Ye Kai
- Yoshihara Kosuke
- Yuan Yuan
- Yung Alfred K.
- Zack Travis
- Zeng Dong
- Zenklusen Jean Claude
- Zhang Hailei
- Zhang Jianhua
- Zhang Jiashan
- Zhang Nianxiang
- Zhang Qunyuan
- Zhang Wei
- Zhao Wei
- Zheng Siyuan
- Zhu Jing
- Zmuda Erik
- Zou Lihua
- Publication venue
- Publication date
- 01/01/2014
- Field of study
Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies
ADMANI:Annotated digital mammograms and associated non-image datasets
- Author
- Al-Qershi Osamah
- Brotchie Peter
- Carneiro Gustavo
- Chen Yuanhong
- Elliott Michael S.
- Fox Samantha K.
- Frazer Helen M.L.
- Hill Brendan
- Hopper John L.
- Karthik Ravishankar
- Kunicki Katrina M.
- Kwok Chun Fung
- Li Shuai
- Lippey Jocelyn F.
- Makalic Enes
- McCarthy Davis J.
- Nguyen Tuong L.
- Peña-Solorzano Carlos A.
- Ralalage Prabhathi Basnayake
- Schmidt Daniel F.
- Tang Jennifer S.N.
- Wang Chong
- Publication venue
- 'Radiological Society of North America (RSNA)'
- Publication date
- 21/12/2022
- Field of study
Direct observation of the dead-cone effect in quantum chromodynamics
- Author
- Acharya S.
- Acharya S.
- Acharya Shreyasi
- Adamova D.
- Adamova D.
- Adamova Dagmar
- Adler A.
- Adler A.
- Adler Alexander
- Adolfsson J.
- Adolfsson J.
- Adolfsson Jonatan
- Aglieri Rinella G.
- Aglieri Rinella G.
- Aglieri Rinella Gianluca
- Agnello M.
- Agnello M.
- Agnello Michelangelo
- Agrawal N.
- Agrawal N.
- Agrawal Neelima
- Ahammed Z.
- Ahammed Z.
- Ahammed Zubayer
- Ahmad S.
- Ahmad S.
- Ahmad Shakeel
- Ahn S.U.
- Ahn S.U.
- Ahn Sang Un
- Ahuja I.
- Ahuja I.
- Ahuja Ishaan
- Akbar Z.
- Akbar Z.
- Akbar Zaenal
- Akindinov A.
- Akindinov A.
- Akindinov Alexander
- Al-Turany M.
- Al-Turany M.
- Al-turany Mohammad
- Alam S.N.
- Alam S.N.
- Alam Sk Noor
- Alarcon Do Passo Suaide Alexandre
- Aleksandrov D.
- Aleksandrov D.
- Aleksandrov Dmitry
- Alessandro B.
- Alessandro B.
- Alessandro Bruno
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- Alfanda Haidar Mas'ud
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- Alfaro Molina R.
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- Zherebchevskii Vladimir
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- Publication venue
- Publication date
- 10/06/2021
- Field of study
At particle collider experiments, elementary particle interactions with large momentum transfer produce quarks and gluons (known as partons) whose evolution is governed by the strong force, as described by the theory of quantum chromodynamics (QCD) [1]. The vacuum is not transparent to the partons and induces gluon radiation and quark pair production in a process that can be described as a parton shower [2]. Studying the pattern of the parton shower is one of the key experimental tools in understanding the properties of QCD. This pattern is expected to depend on the mass of the initiating parton, through a phenomenon known as the dead-cone effect, which predicts a suppression of the gluon spectrum emitted by a heavy quark of mass m and energy E, within a cone of angular size m/E around the emitter [3]. A direct observation of the dead-cone effect in QCD has not been possible until now, due to the challenge of reconstructing the cascading quarks and gluons from the experimentally accessible bound hadronic states. Here we show the first direct observation of the QCD dead-cone by using new iterative declustering techniques [4, 5] to reconstruct the parton shower of charm quarks. This result confirms a fundamental feature of QCD, which is derived more generally from its origin as a gauge quantum field theory. Furthermore, the measurement of a dead-cone angle constitutes the first direct experimental observation of the non-zero mass of the charm quark, which is a fundamental constant in the standard model of particle physics.The direct measurement of the QCD dead cone in charm quark fragmentation is reported, using iterative declustering of jets tagged with a fully reconstructed charmed hadron.In particle collider experiments, elementary particle interactions with large momentum transfer produce quarks and gluons (known as partons) whose evolution is governed by the strong force, as described by the theory of quantum chromodynamics (QCD). These partons subsequently emit further partons in a process that can be described as a parton shower which culminates in the formation of detectable hadrons. Studying the pattern of the parton shower is one of the key experimental tools for testing QCD. This pattern is expected to depend on the mass of the initiating parton, through a phenomenon known as the dead-cone effect, which predicts a suppression of the gluon spectrum emitted by a heavy quark of mass mQ and energy E, within a cone of angular size mQ/E around the emitter. Previously, a direct observation of the dead-cone effect in QCD had not been possible, owing to the challenge of reconstructing the cascading quarks and gluons from the experimentally accessible hadrons. We report the direct observation of the QCD dead cone by using new iterative declustering techniques to reconstruct the parton shower of charm quarks. This result confirms a fundamental feature of QCD. Furthermore, the measurement of a dead-cone angle constitutes a direct experimental observation of the non-zero mass of the charm quark, which is a fundamental constant in the standard model of particle physics
Whole-genome sequencing reveals host factors underlying critical COVID-19
- Author
- Abd Elghafar Mohamed S.
- Abdel-Aziz Mahmoud
- Abdelrazik Marwa
- Abdollahi Hamed
- Abdullah T.
- Abecasis Goncalo
- Abedalthagafi M.
- Abel Lynn
- Abernathy C.
- Abraheem Azmeralde
- Abul-Husn Noura S.
- Acquilini D.
- Adams C.
- Adams Emma L.
- Adams K.
- Adamsara Alireza
- Adanini Olurenke
- Adeleye O.
- Adra D.
- Afilalo J.
- Afilalo M.
- Afolabi D.
- Afrasiabi Z.
- Agasou A.
- Agrawal Shruti
- Agüero D.
- Ahmad N.
- Ahmadi Saeideh
- Ahmed A.
- Ahmed Cecilia
- Akeroyd L.
- Akhtar M.N.
- Akinkugbe O.
- Aksentijevich Alexandra
- Al-Afghani H.
- Al-Awdah L.
- Alaamery M.
- Alahmadey Z.Z.
- Alaverdian D.
- Alavere H.
- Albader A.
- Albaiceta G.M.
- Albakri J.K.
- AlBardis H.
- Albeladi M.
- Albesher N.
- Albrich W.
- AlDhawi N.
- Aldridge J.
- Aleagha Afshar Etemadi
- Alexander Peter.
- Alfonso J.
- Alghamdi B.
- Alghamdi J.
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- Ali Altaf
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- Aliannejad Rasoul
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- Åsvold Bjørn Olav
- Publication venue
- Publication date
- 01/01/2022
- Field of study
Altres ajuts: Department of Health and Social Care (DHSC); Illumina; LifeArc; Medical Research Council (MRC); UKRI; Sepsis Research (the Fiona Elizabeth Agnew Trust); the Intensive Care Society, Wellcome Trust Senior Research Fellowship (223164/Z/21/Z); BBSRC Institute Program Support Grant to the Roslin Institute (BBS/E/D/20002172, BBS/E/D/10002070, BBS/E/D/30002275); UKRI grants (MC_PC_20004, MC_PC_19025, MC_PC_1905, MRNO2995X/1); UK Research and Innovation (MC_PC_20029); the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z); the Edinburgh Clinical Academic Track (ECAT) programme; the National Institute for Health Research, the Wellcome Trust; the MRC; Cancer Research UK; the DHSC; NHS England; the Smilow family; the National Center for Advancing Translational Sciences of the National Institutes of Health (CTSA award number UL1TR001878); the Perelman School of Medicine at the University of Pennsylvania; National Institute on Aging (NIA U01AG009740); the National Institute on Aging (RC2 AG036495, RC4 AG039029); the Common Fund of the Office of the Director of the National Institutes of Health; NCI; NHGRI; NHLBI; NIDA; NIMH; NINDS.Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care or hospitalization after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease