7 research outputs found
Pan-cancer analysis of whole genomes
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- Weisenberger
- Welch
- Wendl M. C. z
- wf Amary
- Whalley
- Wheeler
- wi Futreal
- Wigle
- Wilkerson M. D. v
- Williams
- Wilmott
- Wilson G. W. k
- Wilson R. K. z
- Wintersinger
- Wiznerowicz
- Wolf
- Wong
- Wong
- Woo
- Wood
- Wouters
- Wright
- Wright
- Wright A. J. k
- ws Ang
- Wu
- Wu
- Wu
- wv abg
- wz Hupp
- x Eils
- x Yung
- X. abp
- X. at
- X. bk
- X. cq
- X. ez
- X. ez
- X. fh
- X. fv
- X. fv
- X. fv
- X. fv
- X. k Mbabaali
- X. oi
- X. S. wd
- X. tc
- X. zv
- xb Danilova
- xb Felau
- xc Lovat
- xh Curley
- xh Fulton
- Xi
- Xia
- Xiang
- Xiong
- xo Abeshouse
- xp Benz
- xp Edwards
- xr Ghori
- xs Gundem
- Xue
- xv Luxton
- xw McDermott
- xy Visakorpi
- xz Whitaker
- Y. -E. ot
- Y. -J. k
- Y. -J. xn
- Y. abp
- Y. ae
- Y. ae
- Y. ae
- Y. ae
- Y. ai
- Y. aj
- Y. al
- Y. bk
- Y. dg
- Y. dy
- Y. ef
- Y. ep
- Y. ez
- Y. ff
- Y. fr
- Y. fv
- Y. fv
- Y. gl
- Y. hl
- Y. hq
- Y. hq
- Y. ia
- Y. kq
- Y. lw
- Y. nh
- Y. nk
- Y. nz
- Y. rg
- Y. rj
- Y. rm
- Y. S. jf
- Y. uz
- Y. vr
- Y. wt
- Y. yc
- ya Al-Ahmadie
- Yachida
- Yamaguchi
- Yamaguchi T. N. k
- Yamamoto
- Yamaue
- Yang
- Yang
- Yang
- Yang
- Yang
- Yao
- Yaspo
- Yates
- Yau
- yb Ally
- yd Cherniack
- yd Lai
- yd Schadendorf
- ye Auman
- ye Umbricht
- Yellapantula
- Yellapantula
- yh Bathe
- yj Baylin
- Yoon
- Yu
- Yu
- Yu
- Yuan
- Yugawa
- z ah
- Z. ej
- Z. ep
- Z. fr
- Z. hv
- Z. hy
- Z. jq
- Z. kt
- Z. oe
- Zaikova
- Zapatka
- zd Gershenwald
- Zenklusen
- Zeps
- zf Ghossein
- Zhang
- Zhang
- Zhang
- Zhang
- Zhang
- Zhang
- Zhang H. b
- Zhao
- Zheng
- Zhou
- Zhou
- Zhu
- Zhu
- zi zj
- zm Jayaseelan
- Zou
- Zou
- zt Kim
- zw Lewis
- Ó. A. th
- Ø. sk
- Publication venue
- Publication date
- 11/12/2019
- Field of study
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe
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An integrated map of genetic variation from 1,092 human genomes
- Author
- Abecasis GR
- Abecasis GR
- Abecasis GR
- Abecasis GR
- Abecasis GR
- Abecasis GR
- Abyzov A
- Abyzov A
- Abyzov A
- Albers CA
- Albrecht MW
- Albrecht MW
- Alkan C
- Alkan C
- Alkan C
- Altshuler DM
- Altshuler DM
- Altshuler DM
- Altshuler DM
- Altshuler DM
- Amstislavskiy VS
- Amstislavskiy VS
- Ananiev V
- Anderson P
- Angius A
- Auton A
- Auton A
- Awadalla P
- Awadalla P
- Ayub Q
- Bafna V
- Bafna V
- Bainbridge M
- Bainbridge M
- Bainbridge M
- Balasubramaniam S
- Balasubramaniam S
- Balasubramaniam S
- Balasubramaniam S
- Balasubramanian S
- Balasubramanian S
- Balasubramanian S
- Ball EV
- Banks E
- Banks E
- Baran Y
- Barker J
- Barnes B
- Barnes B
- Barnes KC
- Batzer MA
- Batzer MA
- Bauer M
- Beal K
- Beal K
- Bedoya G
- Beiswanger C
- Belaia Z
- Beloslyudtsev D
- Ben B
- Bentley DR
- Bentley DR
- Bentley DR
- Bentley DR
- Bentley DR
- Bhatia G
- Bigham A
- Blackwell T
- Bodmer W
- Borodina TA
- Bouk N
- Brooks LD
- Brooks LD
- Browning BL
- Burchard EG
- Burchard EG
- Burton J
- Busonero F
- Bustamante CD
- Bustamante CD
- Bustamante CD
- Bustamante CD
- Byrnes JK
- Cai H
- Cao H
- Carneiro MO
- Chakravarti A
- Chakravarti A
- Challis D
- Challis D
- Cheetham RK
- Cheetham RK
- Chen C
- Chen J
- Chen J
- Chen J
- Chen K
- Chen K
- Chen K
- Chen Y
- Chen Y
- Chinwalla A
- Chinwalla A
- Christoforides A
- Christoforides A
- Church D
- Church D
- Churchhouse C
- Clark AG
- Clark AG
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- Clarke D
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- Clarke L
- Clarke L
- Clarke L
- Clarke L
- Clarke L
- Clarke L
- Clemm NC
- Coffey AJ
- Cohen R
- Coin LJM
- Colonna V
- Colonna V
- Cook C
- Cooper DN
- Cox T
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- Craig DW
- Craig DW
- Craig DW
- Craig DW
- Craig DW
- Cucca F
- Cunningham F
- Cunningham F
- Daly MJ
- Danecek P
- Danecek P
- Davies CJ
- De la Vega FM
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- Degenhardt J
- del Angel G
- del Angel G
- del Angel G
- del Angel G
- Delaneau O
- DePristo MA
- DePristo MA
- DePristo MA
- Dermitzakis ET
- Dermitzakis ET
- Devine SE
- Devine SE
- Ding L
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- Dinh H
- Donnelly P
- Dooling D
- Dooling D
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- Duncanson A
- Dunn M
- Durbin RM
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- Dutil J
- Eberle M
- Eberle M
- Eichler EE
- Eichler EE
- Eichler EE
- Evani US
- Evani US
- Fang L
- Fang X
- Felsenfeld AL
- Flicek P
- Flicek P
- Flicek P
- Flicek P
- Flicek P
- Flicek P
- Flicek P
- Fowler G
- Frankish A
- Fu Y
- Fu Y
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- Fuchsberger C
- Fulton L
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- Fulton R
- Fulton R
- Gabriel SB
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- Garcia-Montero A
- Garner J
- Garrison EP
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- Genovese G
- Genovese G
- Gerstein MB
- Gerstein MB
- Gerstein MB
- Gerstein MB
- Gharani N
- Gibbs RA
- Gibbs RA
- Gibbs RA
- Gibbs RA
- Gibbs RA
- Gibbs RA
- Gibbs RA
- Gignoux CR
- Gignoux CR
- Gollub J
- Gottipati S
- Gravel S
- Gravel S
- Gravel S
- Green ED
- Green ED
- Griffin L
- Griffin L
- Grocock R
- Grossman SR
- Guo X
- Guo X
- Guo X
- Guo X
- Gupta N
- Gupta N
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- Gupta-Hinch A
- Guyer MS
- Habegger L
- Habegger L
- Hajirasouliha I
- Hajirasouliha I
- Hale W
- Halperin E
- Handsaker RE
- Handsaker RE
- Handsaker RE
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- Harmanci AO
- Harmanci AO
- Harrow J
- Hartl C
- Hartl C
- Hartl C
- Haussler D
- Haussler D
- Hefferon T
- Henn B
- Hernandez RD
- Herrero J
- Herrero J
- Herwig R
- Hodgkinson A
- Hodgkinson A
- Homer N
- Homer N
- Homer N
- Hormozdiari F
- Hormozdiari F
- Howie B
- Hsieh C-H
- Hsieh C-H
- Huang N
- Humphray S
- Humphray S
- Humphray S
- Humphray S
- Hurles ME
- Hurles ME
- Hurles ME
- Iqbal Z
- Iqbal Z
- Izatt T
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- Izatt T
- James T
- Jian M
- Jiang H
- Jin H
- Jin H
- Jin M
- Jin M
- Jin X
- Jin X
- Jones C
- Jones D
- Jorde L
- Jorde L
- Jostins L
- Jun G
- Kahn S
- Kahn S
- Kahn S
- Kalra D
- Kang HM
- Kang HM
- Kang HM
- Katzman SJ
- Kaye JS
- Keane TM
- Keane TM
- Keane TM
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- Keinan A
- Keinan A
- Kelman G
- Kenny EE
- Kent A
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- Kerasidou A
- Khurana E
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- Khurana E
- Kidd JM
- Kim KC
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- Kimelman M
- Kingsbury Z
- Knoppers BM
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- Ko A
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- Ko A
- Koboldt DC
- Koboldt DC
- Kolb-Kokocinski A
- Konkel MK
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- Korbel JO
- Korbel JO
- Korbel JO
- Kovar C
- Kovar C
- Kovar C
- Kulesha E
- Kural D
- Kural D
- Kurdoglu AA
- Kurdoglu AA
- Kurdoglu AA
- Lacroute P
- Lacroute P
- Lander ES
- Lander ES
- Lander ES
- Lappalainen T
- Lappalainen T
- Lee C
- Lee C
- Lee C
- Lee S
- Lee W-P
- Lee W-P
- Lehrach H
- Lehrach H
- Leinonen R
- Leinonen R
- Lek M
- Lek M
- Leong WF
- Leong WF
- Lewis L
- Lewis L
- Li G
- Li G
- Li G
- Li H
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- Li J
- Li Q
- Li Y
- Li Y
- Li Y
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- Li Y
- Li Z
- Li Z
- Lienhard M
- Lienhard M
- Lihm J
- Lihm J
- Lin H
- Lindsay SJ
- Liu B
- Liu C
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- Liu X
- Lopez J
- Lu J
- Lu J
- Lu Y
- Lunter G
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- Luo R
- Luo R
- Lyons R
- Ma X
- MacArthur DG
- MacArthur DG
- MacArthur DG
- Makarov V
- Makarov V
- Makarov V
- Maples BK
- Marchini JL
- Mardis ER
- Mardis ER
- Mardis ER
- Mardis ER
- Maroo A
- Maroo A
- Marth GT
- Marth GT
- Marth GT
- Marth GT
- Marth GT
- Martinez-Cruzado JC
- Maschio A
- Mathias R
- Mathieson I
- McCarroll SA
- McCarroll SA
- McCarthy S
- McCarthy S
- McCarthy S
- McCarthy S
- McEwen JE
- McLaren WM
- McLaren WM
- McLaren WM
- McLellan MD
- McLellan MD
- McVean GA
- McVean GA
- McVean GA
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- McVean GA
- Meric P
- Mertes F
- Michaelson JJ
- Michelson LP
- Michelson LP
- Mills RE
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- Ming CZ
- Moreno-Estrada A
- Moreno-Estrada A
- Mu XJ
- Mu XJ
- Mu XJ
- Murray L
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- Zheng-Bradley X
- Zheng-Bradley X
- Zheng-Bradley X
- Zheng-Bradley X
- Zheng-Bradley X
- Zhou Y
- Zhu H
- Zhu H
- Zhu J
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2012
- Field of study
By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations
Coupling Krebs cycle metabolites to signalling in immunity and cancer
- Author
- A Littlewood-Evans
- A Michelucci
- A Ooi
- A Rasola
- A Salminen
- AC Ariza
- ACR Epstein
- AK Jha
- AL Doedens
- AM Intlekofer
- AM Intlekofer
- AP Hollander
- AR Grassian
- B Delage
- B Jiang
- B Nota
- B Németh
- BA McFadden
- C Bardella
- C Brigati
- C Chesnelong
- C Frezza
- C Peyssonnaux
- C Schneider
- CG Lee
- CH Chang
- CJ Hall
- CS Benn
- CT Hensley
- D Bhuniya
- D Hamel
- D He
- D Ye
- DJ Brat
- DK Finlay
- DW Parsons
- E Quickelberghe Van
- EA Maher
- EA Mills
- EA Struys
- EH Kobayashi
- EL Mills
- EL Mills
- EL Mills
- EL Pearce
- ER Mardis
- ET Chouchani
- ET Chouchani
- EV Dang
- F Li
- F Wang
- G Allegri
- GD Lewis
- GE Gibson
- GL Semenza
- GL Semenza
- GM Tannahill
- GM Tannahill
- H Noushmehr
- H Suzuki
- H Tarhonskaya
- H Yan
- HH Luan
- HZ Shi
- IP Tomlinson
- J Adam
- J An
- J Brück
- J Du
- J Folbergrová
- J Meiser
- J Naujoks
- J Pan
- J Park
- J Zhang
- J Zhang
- JA Diepen van
- JA Losman
- JH Shin
- JL Izquierdo-Garcia
- JM Weiss
- JO Williams
- JR Sherwin
- JS Isaacs
- JV Lee
- JY Chen
- K Sellers
- K Yen
- KE Wellen
- L Dang
- L Dang
- L Peruzzotti-Jametti
- L Valls-Lacalle
- L Valls-Lacalle
- L Xie
- L Zhang
- L Zheng
- LB Sullivan
- LF Yousif
- M Bambouskova
- M Blatnik
- M Carbonneau
- M Duran
- M El Azzouny
- M Jamal Uddin
- M Kohlhauer
- M Kranendijk
- M Kranendijk
- M Okabe
- M Peng
- M Sasaki
- M Sciacovelli
- M Sciacovelli
- M Topçu
- M Xiao
- M Yang
- MA Selak
- MC Vissers
- MD Kornberg
- ME Figueroa
- MJ Kerins
- MM Blewett
- MP Murphy
- MS Brennan
- MSHY Sugimoto
- N Osinalde
- N Sadagopan
- N Ternette
- NJ MacIver
- O Yogev
- P Bénit
- P Geubelle
- P Rustin
- P Wang
- P Wang
- PA Tyrakis
- PA Tyrakis
- PE Pergola
- PH Maxwell
- PL Sulkowski
- PS Ward
- R Chowdhury
- R El-Khoury
- R Rzem
- R Saito
- RA Chalmers
- RA Smith
- RA Smith
- RD Guzy
- RJ Arts
- S Angiari
- S Feng
- S Frede
- S Inoue
- S Joshi
- S Kim
- S Nair
- S Saeed
- S Sivanand
- S Turcan
- S Zhao
- SB Hatch
- SC Cheng
- SK Kurdistani
- SM Nadtochiy
- SR Jean
- T Brabletz
- T Cordes
- T Hagen
- T Laukka
- T Maes
- T Rubic
- T Watanabe
- T Xu
- TI Johnson
- TL Yeh
- TW Fan
- V Lampropoulou
- W He
- W Lei
- W Mi
- W Wu
- W Xu
- W Zhang
- WA Flavahan
- WM Linehan
- WW Ackermann
- X Mu
- Y Jiang
- Y Li
- Y Wang
- YP Cheon
- Z Jin
- Z Xie
- Z Yang
- Z Zhang
- ZJ Reitman
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Search for subsolar-mass black hole binaries in the second part of Advanced LIGO’s and Advanced Virgo’s third observing run
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- Antelis JM
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- Arellano FEP
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- Barsuglia M
- Barta D
- Bartlett J
- Barton MA
- Bartos I
- Basak S
- Bassiri R
- Basti A
- Bawaj M
- Bayley JC
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- Bedakihale VM
- Beirnaert F
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- Belahcene I
- Bell AS
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- Blackburn JK
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- Publication venue
- 'Oxford University Press (OUP)'
- Publication date
- 28/02/2023
- Field of study
Model-based Cross-correlation Search for Gravitational Waves from the Low-mass X-Ray Binary Scorpius X-1 in LIGO O3 Data
- Author
- Abbott R
- Abe H
- Acernese F
- Ackley K
- Adhicary S
- Adhikari N
- Adhikari RX
- Adkins VK
- Adya VB
- Affeldt C
- Agarwal D
- Agathos M
- Aguiar OD
- Aiello L
- Ain A
- Ajith P
- Akutsu T
- Albanesi S
- Alfaidi RA
- Allocca A
- Alléné C
- Altin PA
- Amato A
- Anand S
- Ananyeva A
- Anderson SB
- Anderson WG
- Ando M
- Andrade T
- Andres N
- Andrić T
- Andrés-Carcasona M
- Ansoldi S
- Antelis JM
- Antier S
- Apostolatos T
- Appavuravther EZ
- Appert S
- Apple SK
- Arai K
- Araya A
- Araya MC
- Areeda JS
- Aritomi N
- Arnaud N
- Arogeti M
- Aronson SM
- Arène M
- Asada H
- Ashton G
- Aso Y
- Assiduo M
- Aston SM
- Astone P
- Aubin F
- AultONeal K
- Babak S
- Badaracco F
- Badger C
- Bae S
- Bae Y
- Bagnasco S
- Bai Y
- Baier JG
- Baird J
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- Barsuglia M
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- Bartlett J
- Barton MA
- Bartos I
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- Bawaj M
- Bayley JC
- Bazzan M
- Bedakihale VM
- Beirnaert F
- Bejger M
- Belahcene I
- Bell AS
- Benedetto V
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- Benoit W
- Bentley JD
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- Bersanetti D
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- Vidyant S
- Viets AD
- Vijaykumar A
- Villa-Ortega V
- Vinet J-Y
- Virtuoso A
- Vitale S
- Vivanco FH
- Vocca H
- von Reis ERG
- von Wrangel JSA
- Vorvick C
- Vyatchanin SP
- Wade LE
- Wade M
- Wagner KJ
- Walet RC
- Walker M
- Wallace GS
- Wallace L
- Wang J
- Wang JZ
- Wang WH
- Ward RL
- Warner J
- Was M
- Washimi T
- Washington NY
- Watada K
- Watarai D
- Watchi J
- Wayt KE
- Weaver B
- Weaving CR
- Webster SA
- Weinert M
- Weinstein AJ
- Weiss R
- Weller CM
- Weller RA
- Wellmann F
- Wen L
- Wette K
- Weßels P
- Whelan JT
- White DD
- Whiting BF
- Whittle C
- Wilk OS
- Wilken D
- Williams CE
- Williams D
- Williams MJ
- Williamson AR
- Willis JL
- Willke B
- Wipf CC
- Woan G
- Woehler J
- Wofford JK
- Wojtowicz IA
- Wong D
- Wong ICF
- Wright M
- Wu C
- Wu DS
- Wu H
- Wysocki DM
- Xiao L
- Yadav N
- Yamada T
- Yamamoto H
- Yamamoto K
- Yamamoto T
- Yamashita K
- Yamazaki R
- Yang FW
- Yang KZ
- Yang L
- Yang Y
- Yang Y
- Yang Y-C
- Yap MJ
- Yeeles DW
- Yeh S-W
- Yelikar AB
- Yokoyama J
- Yokozawa T
- Yoo J
- Yoshioka T
- Yu H
- Yu H
- Yuzurihara H
- Zadrożny A
- Zanolin M
- Zeidler S
- Zelenova T
- Zendri J-P
- Zevin M
- Zhan M
- Zhang H
- Zhang J
- Zhang L
- Zhang R
- Zhang T
- Zhang Y
- Zhao C
- Zhao G
- Zhao Y
- Zhao Y
- Zheng Y
- Zhou R
- Zhu XJ
- Zhu Z-H
- Zimmerman AB
- Zucker ME
- Zweizig J
- Publication venue
- 'American Astronomical Society'
- Publication date
- 01/01/2022
- Field of study
We present the results of a model-based search for continuous gravitational waves from the low-mass X-ray binary Scorpius X-1 using LIGO detector data from the third observing run of Advanced LIGO and Advanced Virgo. This is a semicoherent search that uses details of the signal model to coherently combine data separated by less than a specified coherence time, which can be adjusted to balance sensitivity with computing cost. The search covered a range of gravitational-wave frequencies from 25 to 1600 Hz, as well as ranges in orbital speed, frequency, and phase determined from observational constraints. No significant detection candidates were found, and upper limits were set as a function of frequency. The most stringent limits, between 100 and 200 Hz, correspond to an amplitude h0 of about 10−25 when marginalized isotropically over the unknown inclination angle of the neutron star's rotation axis, or less than 4 × 10−26 assuming the optimal orientation. The sensitivity of this search is now probing amplitudes predicted by models of torque balance equilibrium. For the usual conservative model assuming accretion at the surface of the neutron star, our isotropically marginalized upper limits are close to the predicted amplitude from about 70 to 100 Hz; the limits assuming that the neutron star spin is aligned with the most likely orbital angular momentum are below the conservative torque balance predictions from 40 to 200 Hz. Assuming a broader range of accretion models, our direct limits on gravitational-wave amplitude delve into the relevant parameter space over a wide range of frequencies, to 500 Hz or more