31 research outputs found
Maspin and MCM2 immunoprofiling in salivary gland carcinomas
- Publication venue
- BioMed Central
- Publication date
- 01/01/2011
- Field of study
<p>Abstract</p> <p>Background</p> <p>The pathogenesis of salivary gland carcinomas is very complex and prognostic markers are difficult to find in these carcinomas of which the different subtypes have varying malignant potential. The study was conducted to examine the cellular distribution of maspin and MCM2 in salivary gland carcinomas and their value to predict lymph node metastasis.</p> <p>Materials and methods</p> <p>Fifty three paraffin blocks of different lesions (15 muco-epidermoid carcinoma, 14 adenoid cystic carcinoma, 3 epi-myoepithelial carcinoma, 5 salivary duct carcinoma, 5 malignant pleomorphic adenoma, 6 polymorphous low grade adenocarcinoma and 5 acinic cell carcinoma) were prepared for immunohistochemical staining with maspin and MCM2 antibodies. ANOVA and Pearson correlation tests were used for the statistical analysis of the results.</p> <p>Results</p> <p>All salivary gland carcinomas express maspin and MCM2 with variable cellular localization. There was a significant difference in the expression of each antibody between mucoepidermoid carcinoma, adenoid cystic carcinoma and polymorphous low grade adenocarcinoma. No association was found between examined markers and lymph node metastasis.</p> <p>Conclusions</p> <p>Salivary gland carcinomas express maspin and MCM2 with variable levels and cellular localization, consisting important markers of biological behavior in these tumors. The level of MCM2 expression can be used in the differential diagnosis of adenoid cystic carcinoma and polymorphous low grade adenocarcinoma. Further study with large sample size is recommended to assess their value in prediction of lymph node metastasis.</p
Analytical Study on Building a Comprehensive Big Data Management Maturity Framework
- Publication venue
- Regional Information Center for Science & Technology
- Publication date
- 02/01/2022
- Field of study
Harnessing big data in organizations today realizes benefits for competitive advantage. Generated profound insights are reflected in informed decision making, creating better business plans, and improved service delivery. Yet, organizations are still not recognizing how mature their big data management capabilities are. However, there is no structured approach to assess and build necessary capabilities for valuable big data utilizing, which draws a clear improvement pathway. Existing solutions lack a consistent perception of big data management capabilities, a reliable assessment, and a rigid improvement scheme. This paper contributes in building an analytical study on existing key works in assessing and building big data management capabilities. Drawing upon the results and gaps revealed from this analytical study, the main requirements for building a comprehensive big data management maturity framework are defined. This framework will enable organizations to assess and improve their current capabilities towards effective big data management.https://dorl.net/dor/ 20.1001.1.20088302.2022.20.1.13.
CORRELATION OF SARS-COV-2 EXPRESSION IN THE PLACENTA AND THE INCIDENCE OF PREECLAMPSIA
- Author
- Publication venue
- 'African Traditional Herbal Medicine Supporters Initiative (ATHMSI)'
- Publication date
- 22/12/2022
- Field of study
Background: The pandemic caused by SARS-CoV-2 also caused infection in some pregnant women. Some reports say this viral infection can show symptoms of preeclampsia.
Material and Methods: We analyzed 25 pregnant women with SARS-CoV-2 infection with 4 patients presenting with symptoms of preeclampsia. we performed routine blood analysis, renal function, liver function, and IHC examination to see the expression of viral proteins in the placenta.
Results: we obtained 4 patients with confirmed SARS-CoV-2 infection by RT-PCR. In these 4 cases, none of the cases showed expression of the SARS-CoV-2 viral protein in the placenta, and all 4 mothers were declared dead after treatment, and 2 babies delivered out of these 4 cases died. In one case we had fetal death in pregnancy while in one case prematurity. 2 babies born to mothers with SARS-CoV-2 infection with preeclampsia were born in good condition. There were no babies infected with SARS-CoV-2
Conclusion: We conclude that SAR-CoV-2 infection in pregnant women with comorbidities can lead to a poor prognosis for both mother and baby. We cannot yet conclude whether SARS-CoV-2 infection can cause preeclampsia, but SARS-CoV-2 infection can exacerbate preeclampsia symptoms
Efficacy of ImageJ in the assessment of apoptosis
- Author
- Publication venue
- BioMed Central
- Publication date
- 01/01/2012
- Field of study
<p>Abstract</p> <p>Objective</p> <p>To verify the efficacy of ImageJ 1.43 n in determining the extent of apoptosis which is a complex and multistep process.</p> <p>Study Design</p> <p>Cisplatin in different concentrations was used to induce apoptosis in cultured Hep2 cells. Cell viability assay and nuclear image analysis of stained Hep2 cells were used to discriminate apoptotic cells and cells suspected to be undergoing apoptosis from control cells based on parameters such as nuclear area, circularity, perimeter and nuclear area factor (NAF), in association with visual morphology.</p> <p>Results</p> <p>Image analysis revealed a progressive and highly significant decrease in nuclear area factor detected in apoptotic cells and in cells suspected of undergoing apoptosis compared to the control cells (P-values < 0.01). Some of the other studied parameters showed also the same trend. This decrease was assumed to indicate DNA loss. Image analysis results correlated positively and significantly with the results obtained by cell viability assay (R = 0.958, P-value = 0.042). NAF was the most reliable parameter in assessment of apoptosis.</p> <p>Conclusion</p> <p>Nuclear area factor can be calculated using powerful free and open-source software. Consequently, a quantitative measure of apoptosis can be obtained that is linked to morphological changes. ImageJ 1.43 n may therefore provide a useful tool for the assessment and discrimination of apoptotic cells.</p> <p>Virtual slides</p> <p>The virtual slide(s) for this article can be found here:</p> <p><url>http://www.diagnosticpathology.diagnomx.eu/vs/5929043086367338</url></p
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- Author
- A Gordon Robertson
- Abdullah Kahraman
- Abel Gonzalez-Perez
- Adam A Margolin
- Adam Abeshouse
- Adam Grundhoff
- Adam J Struck
- Adam J Struck
- Adam J Wright
- Adam Lambert
- Adam P Butler
- Adam P Butler
- Adel El-Naggar
- Adnan M Nagrial
- Adrian Ally
- Adrian Baez-Ortega
- Adrian Thorogood
- Adriana Salcedo
- Adrienne M Flanagan
- Ake Borg
- Akihiro Fujimoto
- Akihiro Suzuki
- Akinyemi I Ojesina
- Alain Viari
- Alan J Robertson
- Alan P Hoyle
- Alan Thompson
- Alasdair Stenhouse
- Alastair M Thompson
- Aldo Scarpa
- Alessandro Pastore
- Alex Buchanan
- Alex Buchanan
- Alexander Claviez
- Alexander J Lazar
- Alexander Martinez-Fundichely
- Alfonso Muñoz
- Alfonso Valencia
- Aliaksei Z Holik
- Alice Meng
- Alicia L Bruzos
- Allison Creason
- Allison P Heath
- Alvin Wei Tian Ng
- Alvis Brazma
- Amaro Taylor-Weiner
- Amber L Johns
- Amie Radenbaugh
- Amit G Deshwar
- Ana Dueso-Barroso
- Ana Mijalkovic Mijalkovic-Lazic
- Ana Milovanovic
- Ana Milovanovic
- Andre Kahles
- Andrea Haake
- Andrea Holbrook
- Andrea L Richardson
- Andrea Mafficini
- Andrea Ruzzenente
- Andreas Behren
- Andreas Rosenwald
- Andreia V Pinho
- Andrew Berchuck
- Andrew D Cherniack
- Andrew J Dunford
- Andrew J Mungall
- Andrew J Spillane
- Andrew Menzies
- Andrew Menzies
- Andrew P Barbour
- Andrew Tutt
- Andrew V Biankin
- Andrey Korshunov
- Andrés Lanzós
- Andy Cafferkey
- Andy G Lynch
- Angela Chou
- Angela N Brooks
- Angela Tam
- Angelica Ochoa
- Angelika N Christ
- Angelo P Dei Tos
- Anieta M Sieuwerts
- Anil K Sood
- Anita Langerød
- Anja Füllgrabe
- Anke K Bergmann
- Ann-Marie Patch
- Anna deFazio
- Anna Ehinger
- Anna Fitzgerald
- Anne Hamilton
- Anne Vincent-Salomon
- Anne Y Warren
- Anne-Lise Børresen-Dale
- Annegien Broeks
- Anthony DiBiase
- Anthony J Gill
- Anthony Ng
- Anthony R Green
- Antonia L Pritchard
- Antonio Pea
- Antonios Koures
- Aparna Prasad
- Apurva M Hegde
- Aquila Fatima
- Arcadi Navarro
- Arie B Brinkman
- Arif O Harmanci
- Arindam Maitra
- Armando Lopez-Guillermo
- Arndt Borkhardt
- Arnoud Boot
- Asger Hobolth
- Ashley Williams
- Ashton A Connor
- Atul J Butte
- Aurélien Chateigner
- Austin J Hepperla
- Axel Aretz
- Aya Sasaki-Oku
- Ayellet V Segre
- B F Francis Ouellette
- Bailey Matthew H
- Barbara Hutter
- Barbara Hutter
- Barbara Kremeyer
- Bartha M Knoppers
- Beifang Niu
- Beifang Niu
- Beifang Niu
- Benedikt Brors
- Benita Kiat Tee Tan
- Benjamin J Raphael
- Benjamin P Berman
- Benjamin Raeder
- Bernardo Rodriguez-Martin
- Bernhard Radlwimmer
- Bernice H Wong
- Beth Karlan
- Bin Tean Teh
- Bin Zhu
- Birgit Burkhardt
- Bishoy M Faltas
- Bodil Bjerkehagen
- Bogdan Czerniak
- Boris Winterhoff
- Borislav C Rusev
- Bradly G Wouters
- Brandi N Davis-Dusenbery
- Brian Craft
- Brian D O'Connor
- Brian Patrick O'Neill
- Brice Aminou
- Calvin Wing Yiu Chan
- Cameron M Soulette
- Carl Herrmann
- Carl Morrison
- Carlo Gambacorti-Passerini
- Carlos Caldas
- Carlos D Bustamante
- Carlos López-OtÃn
- Carlota Rubio-Perez
- Carmen Gomez
- Carolien H M van Deurzen
- Carolyn M Hutter
- Carolyn M Hutter
- Carrie Cibulskis
- Caterina Vicentini
- Catherine A Shang
- Catherine D Moser
- Catherine J Kennedy
- Catrina C Fronick
- Chad J Creighton
- Chandra Sekhar Pedamallu
- Chang Li
- Charles David Imbusch
- Charles M Perou
- Charles Saller
- Charles Short
- Charlie E Massie
- Chawalit Pairojkul
- Chen Hong
- Chen Ye
- Cheng-Zhong Zhang
- Chin-Lee Wu
- Chip Stewart
- Chip Stewart
- Chip Stewart
- Choon Kiat Ong
- Chris Lawerenz
- Chris Mitchell
- Chris Sander
- Christian von Mering
- Christiane Buchholz
- Christina K Yung
- Christina K Yung
- Christina Yau
- Christine A Iacobuzio-Donahue
- Christine Chomienne
- Christine Desmedt
- Christine P'ng
- Christof von Kalle
- Christoph Borst
- Christoph Plass
- Christopher A Miller
- Christopher Benz
- Christopher J Scarlett
- Christopher J Yoon
- Christopher K Wong
- Christopher M Lalansingh
- Christopher M Lalansingh
- Christopher Ogden
- Christopher S Foster
- Christopher Umbricht
- Christopher W Toon
- Christos Sotiriou
- Cindy Bell
- Cinzia Cantù
- Ciyue Shen
- Claes Wadelius
- Clare Verrill
- Clarissa Gerhauser
- Claudia Calabrese
- Claudio Bassi
- Claudio Luchini
- Claudiu Farcas
- Clemency Jolly
- Colin A Purdie
- Colin A Semple
- Colin C Collins
- Colin S Cooper
- Conrad R Leonard
- Constance H Li
- Corbin D Jones
- Craig Shriver
- Cristina López
- Cyriac Kandoth
- Cyril Fisher
- D Neil Hayes
- Dai-Ying Wu
- Daiming Fan
- Daisuke Komura
- Dale W Garsed
- Daniel A Leongamornlert
- Daniel Baumhoer
- Daniel Hübschmann
- Daniel J Turner
- Daniel J Weisenberger
- Daniel M Berney
- Daniel Rosebrock
- Daniel S Brewer
- Daniela S Gerhard
- Danielle Pasternack
- Darell Bigner
- Dariush Etemadmoghadam
- Darlene Lee
- Darrin F Taylor
- Dave Larson
- David A Wheeler
- David A Wheeler
- David C Wedge
- David Craft
- David D L Bowtell
- David E Neal
- David Haan
- David Haussler
- David Haussler
- David Hedley
- David Huntsman
- David I Heiman
- David J Adams
- David J Van Den Berg
- David K Chang
- David K Miller
- David Khoo
- David Mutch
- David N Louis
- David Nicol
- David Ocana
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- David R Jones
- David Scott
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- David Torrents
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- David Vicente
- Davide Antonello
- Declan Cahill
- Denis Larsimont
- Denis Yuen
- Denise Brooks
- Deniz DemircioÄŸlu
- Dennis C Sgroi
- Dennis Karsch
- Dennis T Maglinte
- Dennis Wigle
- Derek W Wright
- Dianne E Chadwick
- Dido Lenze
- Dieter Kube
- Dieter Weichenhan
- Dilip D Giri
- Dimitri Livitz
- Dimitri Livitz
- Dimple Chakravarty
- Ding
- Dirk Schadendorf
- Dmitry A Gordenin
- Dominik Glodzik
- Don Chalmers
- Dong Guanlan
- Dongbing Liu
- Donghoon Lee
- Donghui Tan
- Donna M Muzny
- Dorthe Grabau
- Douglas A Levine
- Douglas F Easton
- Douglas Voet
- Duncan Beardsmore
- Dursi Lewis Jonathan
- Edward W Rowe
- Eigo Shimizu
- Ekta Khurana
- Elaine R Mardis
- Electron Kebebew
- Elena Piñeiro-Yáñez
- Elena Provenzano
- Elias Campo
- Elisabet Barrera
- Elisabetta Sereni
- Elizabeth A Musgrove
- Elizabeth L Appelbaum
- Elizabeth L Christie
- Elli Papaemmanuil
- Ellrott Kyle
- Emilie Lalonde
- Eoghan Harrington
- Eric Chuah
- Eric Green
- Eric Lander
- Eric Minwei Liu
- Eric Z Ma
- Eric Z Ma
- Erik Garrison
- Erik Larsson
- Erik Mayer
- Erik N Bergstrom
- Erin Curley
- Ermin Hodzic
- Erwin G Van Meir
- Esa Pitkänen
- Esther Rheinbay
- Esther Rheinbay
- Eun Pyo Hong
- Eunjung Alice Lee
- Eva G Alvarez
- Eva Hellstrom-Lindberg
- Ewan Birney
- F Germán RodrÃguez-González
- Fabien C Lamaze
- Fabien Calvo
- Fabio C P Navarro
- Faiyaz Notta
- Fan Yang
- Fan Zhang
- Faraz Hach
- Faraz Hach
- Faridah Mbabaali
- Fatima Al-Shahrour
- Federico Abascal
- Fei-Fei Liu
- Felicity Newell
- Fenglin Liu
- Fernanda Amary
- Ferran Muiños
- Florian Markowetz
- Fouad Yousif
- Francesc Muyas
- Francesco Favero
- Francisco M De La Vega
- Francisco Sanchez-Vega
- Fraser R Duthie
- Fred Sweep
- Freddie C Hamdy
- Fruzsina Molnár-Gábor
- Fumie Hosoda
- G Petur Nielsen
- G Steven Bova
- Gad Getz
- Gad Getz
- Gad Getz
- Gaetan MacGrogan
- Gaetano Finocchiaro
- Gary D Bader
- Gavin Ha
- Gavin W Wilson
- Genta Nagae
- Geoff Macintyre
- George B Hanna
- George L Mihaiescu
- Georgia Escaramis
- Georgina V Long
- Gerd Nettekoven
- German M Demidov
- German Ott
- Gerrit K Hooijer
- Gerstein Mark B
- Gert G Van den Eynden
- Getz Gad
- Ghislaine Scelo
- Giada Bonizzato
- Giampaolo Tortora
- Gilles Romieu
- Gilles Thomas
- Giovanni Marchegiani
- Gisela Mir Arnau
- Giuseppe Malleo
- Gloria M Petersen
- Gordon B Mills
- Gordon B Mills
- Gordon Saksena
- Gordon Saksena
- Gordon Saksena
- Grace Tiao
- Grace Tiao
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- Grant Sanders
- Gu Kong
- Guanming Wu
- Guido Reifenberger
- Guido Sauter
- Guillaume Bourque
- Gulietta M Pupo
- Gun Ho Jang
- Gunes Gundem
- Gunnar Rätsch
- Gurnit Atwal
- Hailei Zhang
- Haiyan Irene Li
- Han Liang
- Hana Susak
- Hans Binder
- Hans Lehrach
- Hans-Jörg Warnatz
- Hardeep K Nahal-Bose
- Hark Kyun Kim
- HarshaVardhan Doddapaneni
- Hartmut Juhl
- Harvey Pass
- Hayley C Whitaker
- Hayley J Luxton
- Hazel Burke
- Heather K Schmidt
- Heather Thorne
- Hee Jin Lee
- Heidi J Sofia
- Heidi Sofia
- Helen Davies
- Helena Kilpinen
- Helene Kretzmer
- Heng Xiong
- Henk G Stunnenberg
- Henrik Hornshøj
- Henry Lee-Six
- Hideki Ohdan
- Hidenori Ojima
- Hidewaki Nakagawa
- Hikmat Al-Ahmadie
- Hilda A Pickett
- Hirofumi Rokutan
- Hirokazu Taniguchi
- Hiroki Yamaue
- Hiroko Tanaka
- Hiromi Nakamura
- Hiroshi Aikata
- Hiroto Katoh
- Hiroyuki Aburatani
- Hitoshi Katai
- Hitoshi Nakagama
- Hojabr Kakavand
- Holger Sültmann
- Holmfridur Hilmarsdottir
- Hong Su
- Hong Xue
- Hong Xue
- Hongtu Zhu
- Hongwei Zhang
- Hongxin Zhang
- Hsiao-Wei Chen
- Huanming Yang
- Hugh Barr
- Hui Shen
- Husen M Umer
- Huy Q Dinh
- Hyung-Lae Kim
- Hyung-Lae Kim
- Hyung-Yong Kim
- Hyunghwan Kim
- Ian J Davis
- Ian Welch
- Ignacio Vázquez-GarcÃa
- Ignaty Leshchiner
- Ignaty Leshchiner
- Ignaty Leshchiner
- Iker Reyes-Salazar
- Ilinca Lungu
- Ilse Rooman
- Ilya Shmulevich
- Iman Sarrafi
- Iman Sarrafi
- Ina Felau
- Ioana Cutcutache
- Irene Papatheodorou
- Irinel Popescu
- Iris Pauporté
- Iris Selander
- Isabelle Treilleux
- Isidro Cortés-Ciriano
- Ivan Borozan
- Ivana Cataldo
- Ivica Letunic
- Ivica Letunic
- Ivo Buchhalter
- Ivo Buchhalter
- Ivo G Gut
- Ivo G Gut
- Ivon Harliwong
- Izar Villasante
- Iñigo Martincorena
- J Lynn Fink
- J Robert O'Neill
- J Todd Auman
- Jaclyn Smith
- Jacqueline Boultwood
- Jacqueline E Schein
- Jaegil Kim
- Jake June-Koo Lee
- Jakob Skou Pedersen
- Jakob Skou Pedersen
- James E Haber
- James G Kench
- James Gossage
- James S Wilmott
- Jan Komorowski
- Jan O Korbel
- Janae V Simons
- Jane E Brock
- Janet S Graham
- Janet S Rader
- Jared T Simpson
- Jared T Simpson
- Jason Huse
- Jaswinder S Samra
- Javier Bartolome
- Javier Bartolomé Rodriguez
- Javier Temes
- Jean C Zenklusen
- Jean Y Yang
- Jean-Rémi Trotta
- Jeffrey A Wintersinger
- Jeffrey Boyd
- Jeffrey E Gershenwald
- Jeffrey Marks
- Jeffrey Roach
- Jenna Eagles
- Jennifer L Jennings
- Jeong-Yeon Lee
- Jeremiah A Wala
- Jeremiah A Wala
- Jeremy Chien
- Jeremy Johns
- Jerome Myers
- Jesper Lagergren
- Jessica I Hoell
- Jessica K Miller
- Ji Wan Park
- Jia Liu
- Jian Wang
- Jianhong Hu
- Jianjiong Gao
- Jianmin Wu
- Jiashan Zhang
- Jiayin Wang
- Jiayin Wang
- Jieming Chen
- Jihoon Kim
- Jill Barnholtz-Sloan
- Jillian A Hung
- Jing Zhang
- Jingchun Zhu
- Joachim Weischenfeldt
- Joachim Weischenfeldt
- Joan Frigola
- Joana Carlevaro-Fita
- Jocelyne Jacquemier
- Joel S Parker
- Johan Staaf
- Johann S De Bono
- Johanna Bertl
- Johannes Werner
- Johannes Werner
- John A Demchok
- John A Foekens
- John Bartlett
- John Busanovich
- John D McPherson
- John F Thompson
- John Letaw
- John N Weinstein
- John N Weinstein
- John R McPherson
- John V Pearson
- John W M Martens
- Jon G Jonasson
- Jon W Teague
- Jon W Teague
- Jonas Demeulemeester
- Jonathan Barenboim
- Jonathan Cebon
- Jonathan D Kay
- Jonathan Göke
- Jonathan Hinton
- Jonathan Hinton
- Jonathan Nicholson
- Jonathan R Stretch
- Jonathan Spring
- Jonathan Warrell
- Jong K Kim
- Jongsun Jung
- Jongsun Jung
- Jongwhi H Hong
- Joong-Won Park
- Jordi Deu-Pons
- Jorge Reis-Filho
- Jorge Zamora
- Jorunn E Eyfjord
- Jos Jonkers
- Jose I Martin-Subero
- Jose M C Tubio
- Jose M G Izarzugaza
- Josep L L Gelpi
- Josep L L Gelpi
- Joshua Armenia
- Joshua M Stuart
- Joshua M Stuart
- Joshy George
- José MarÃa Heredia-Genestar
- Joy C Jayaseelan
- Juergen Eils
- Juhee Lee
- Jules N A Kerssemakers
- Julia Markowski
- Julia Richter
- Julian M Hess
- Julian M Hess
- Julian M Hess
- Juliann Shih
- Julie Livingstone
- Julie M Wilson
- Jun Li
- Jun Yu
- Jung Kyoon Choi
- Junjun Zhang
- Junjun Zhang
- Juok Cho
- Juris Viksna
- Justin P Whalley
- Jyoti Nangalia
- Jörg Tost
- Jüri Reimand
- K Vijay Raghavan
- Kadir C Akdemir
- Kai Ye
- Kai Ye
- Kai Ye
- Kaixian Yu
- Kami Chiotti
- Kamna Ramakrishnan
- Kaoru Nakano
- Karen McCune
- Karen Mungall
- Karen Smith-McCune
- Karin A Oien
- Karin S Kassahn
- Karine Jegalian
- Karolina Czajka
- Karsten Rippe
- Katalin Karaszi
- Katarzyna O Sikora
- Katayoon Kasaian
- Katayoon Kasaian
- Katherine A Hoadley
- Kathleen H Burns
- Kathleen Marchal
- Kathryn Alsop
- Katia Nones
- Kazuaki Chayama
- Kazuhiro Maejima
- Kazuhiro Ohi
- Ke Yuan
- Keiran M Raine
- Keiran M Raine
- Keith A Boroevich
- Kelso Sean
- Ken Chen
- Ken Chen
- Ken Dutton-Regester
- Kenji Tatsuno
- Kenneth Aldape
- Keren Isaev
- Kerstin Haase
- Keun Soo Ahn
- Keunchil Park
- Kevin J Dawson
- Kevin Thai
- Kiejung Park
- Kin Chan
- Kiran Kumar
- Kirsten Kübler
- Kiyo Shimizu
- Kjong-Van Lehmann
- Klev Diamanti
- Koji Arihiro
- Koo Jeong Kang
- Kortine Kleinheinz
- Kortine Kleinheinz
- Kristian Cibulskis
- Kuan-Lin Huang
- Kui Wu
- Kunihito Gotoh
- Kwun M Fong
- Kyle Covington
- Kyle Covington
- Kyle Ellrott
- Kyle Ellrott
- Kyle Ellrott
- L Van't Veer
- Lara Jerman
- Lara Urban
- Lars Feuerbach
- Larsson Omberg
- Laura Planko
- Laurence B Lovat
- Laurent Arnould
- Lauri A Aaltonen
- Lawrence E Heisler
- Layla Oesper
- Lee E Timms
- Lei Song
- Leigh B Thorne
- Leng Han
- Leonidas Salichos
- Leslie Cope
- Leszek J Klimczak
- Levi Garraway
- Lewis Jonathan Dursi
- Lewis Jonathan Dursi
- Lewis R Roberts
- Li Ding
- Li Ding
- Li Ding
- Li Shantao
- Liang Wen-Wei
- Liangtao Zheng
- Lieven P C Verbeke
- Lihua Zou
- Liis Uusküla-Reimand
- Liliana Greger
- Liming Yang
- Lin Li
- Lina Sieverling
- Lina Wadi
- Lincoln D Stein
- Linda Mileshkin
- Linghua Wang
- LiRehan Akbani
- Lisa Lype
- Lisa Mirabello
- Lisle E Mose
- Liu Xi
- Liu Xi
- Lixing Yang
- Lora Lewis
- Lorenz H P Trümper
- Loretta M S Lau
- Lori Boice
- Loris Mularoni
- Lorraine A Chantrill
- Louis Letourneau
- Luc Dirix
- Luca Landoni
- Luca Malcovati
- Lucas Lochovsky
- Lucila Ohno-Machado
- Lucinda A Fulton
- Lucy Matthews
- Lucy Stebbings
- Lucy Stebbings
- Lucy Yates
- Ludmil B Alexandrov
- Ludmila Danilova
- Luisa Mantovani-Löffler
- Luke Marsden
- Maciej Wiznerowicz
- Malcolm Brock
- Malcolm J Moore
- Malene Juul
- Malik Alawi
- Mamoru Kato
- Manasa Ramakrishna
- Manaswi Gupta
- Manolis Kellis
- Manuel Prinz
- Mara Rosenberg
- Marat D Kazanov
- Marc D Perry
- Marc D Perry
- Marc J van de Vijver
- Marc Zapatka
- Marcel Kool
- Marcel Smid
- Marcin Imielinski
- Marco A Marra
- Marco Miotto
- Marcus Bosenberg
- Marek Cmero
- Maria Elisabeth Goebler
- Maria Keays
- Maria O'Donovan
- Maria Scardoni
- Maria Vittoria Davi
- Marie-Laure Yaspo
- Marina Pajic
- Mario Berrios
- Mario Cazzola
- Marius Rohde
- Mark A Rubin
- Mark B Gerstein
- Mark B Gerstein
- Mark H Wright
- Mark Lathrop
- Mark P Hamilton
- Mark Phillips
- Mark Pinese
- Mark Shackleton
- Markus B Schilhabel
- Markus Kreuz
- Markus Loeffler
- Markus Ringnér
- Marta Aymerich
- Marta Gut
- Marta Paczkowska
- Marta Tojo
- Martin Hansmann
- Martin L Ferguson
- Martin Peifer
- Mary J Goldman
- Masakazu Yamamoto
- Masaki Ueno
- Masashi Fujita
- Masashi Fukayama
- Matteo Fassan
- Matthew A Field
- Matthew A Reyna
- Matthew D Wilkerson
- Matthew Eldridge
- Matthew G Cordes
- Matthew G Soloway
- Matthew H Bailey
- Matthew H Bailey
- Matthew H Bailey
- Matthew J Anderson
- Matthew Meyerson
- Matthew R Huska
- Matthew Ringel
- Matthew W Fittall
- Matthias Bieg
- Matthias Bieg
- Matthias Schlesner
- Matthias Schlesner
- Mattia Bosio
- Maxime Tarabichi
- Maximillian G Marin
- Mayuko Furuta
- Mei Huang
- Melpomeni Kasapi
- Meyerson William U
- Mi Ni Huang
- Mia Nastic
- Michael A Hollingsworth
- Michael Birrer
- Michael C Heinold
- Michael C Heinold
- Michael C Quinn
- Michael C Wendl
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- Xuemei Luo
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- Yi Huang
- Yi Huang
- Yifei Men
- Yiling Lu
- Yilong Li
- Yingyan Yu
- Yiwen Chen
- Yogesh Kumar
- Yogesh Kumar
- Yoke-Eng Chiew
- Yong Hou
- Yong Zhou
- Yong-Jie Lu
- Yongzhan Nie
- Yosef E Maruvka
- Yosef E Maruvka
- Yoshiiku Kawakami
- Young Seok Ju
- Youngchoon Woo
- Youngil Koh
- Youngwook Kim
- Youyong Lu
- Yu Fan
- Yu Fan
- Yu Fan
- Yu-Jia Shiah
- Yuan Ji
- Yuan Yuan
- Yuichi Shiraishi
- Yulia Newton
- Yulia Rubanova
- Yumeng Wang
- Yupeng Cun
- Yussanne Ma
- Zachary Heins
- Zechen Chong
- Zechen Chong
- Zemin Zhang
- Zhaohong Chen
- Zhenggang Wu
- Zhenggang Wu
- Zhining Wang
- Zhongming Zhao
- Ziao Lin
- Zsofia Kote-Jarai
- Ólafur Andri Stefánsson
- Øystein Garred
- Publication venue
- Nature Communications
- Publication date
- 01/01/2020
- Field of study
Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
- Author
- Aanniz Tarek
- Abar Aden Elmi
- Abbad Anass
- Abdelfattah May
- Abdelhamid W.
- Abdella Saro
- Abdellah Faouzi
- Abdelmjid El Oualid
- Abdelmoula Fatma
- Abdelmoulah F.
- Abderrahmane Maaroufi
- Abderrazak Rfaki
- Abdillahi Idil Salah
- Abdissa Alemseged
- Abdo I.
- Abdoelraheem Mohamed Hassan
- Abe Haruka
- Abebe Markos
- Abechi Priscilla
- Abera Adugna
- Abi Rachid
- Abias Abe G.
- Abichu Getachew
- Abid N.
- Abid Nabil
- Abid Salma
- Abilio Nuro
- Abimbola Sharon
- Abo Shama Noura M
- Abosede O.
- Aboubaker Mohamed Houmed
- Abouelhoda Mohamed
- Abouelnaga S.
- Abualas Elamin
- Abubeker Ramalia Chabi
- Abuelenein Ehab Abdelkader
- Abuzaid Nadir
- Abworo Edward O.
- Ada Diosdado Odjama Nseng
- Addidle Michael
- Adegbola Richard
- Adegnika Akim A.
- Adegnika Ayola Akim
- Adel Abd Monaem
- Adeniji Johnson A.
- Adepetun Tomiwa
- Adesegun A.
- Adesuyi Omoare
- Adetifa Ifedayo M. O.
- Adewumi Olubusuyi M.
- Adewumi Oluwatimilehin
- Adewumi Praise
- Adeyemi Kayode T.
- Adhikari Bishwo N.
- Adil El Hamouchi
- Adjiratou Aissatou B. A.
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- Adu Bright
- Adu Eric
- Adusei-Poku Mildred
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- Agbodzi B.
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- Ahyong Vida
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- Ajogbasile F.V.
- Ajogbasile Fehintola V.
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- Akhoud Youssef
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- Alemayehu Dawit Hailu
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- Ali Mohamed Ahmed
- Ali Mushal
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- Cortes Carlos
- Cotten Matthew
- Crawford M.
- Crespin Xavier
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- Diab A.
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- Diagne Moussa M.
- Diakite Mandiou
- Diallo Amadou
- Diallo Haby
- Diallo Penda Malhado
- Diallo Sada
- Diarra B.
- Diarra Bassirou
- Diaw Papa Alassane
- Diawara Idrissa
- Dieng Alle Baba
- Dieng Assane
- Diergaardt Azaria
- Diop Mamadou
- Diop Oumy
- Djimde Abdoulaye
- Djingarey Mamoudou Harouna
- Djomsi Dowbiss Meta
- Djontu Jean Claude
- Dobi Paul
- Donati Flora
- Dorkenoo Ameyo
- Doudou Fetouma
- Douffan Messanh
- Doumbia Seydou
- Draper C.
- Dratibi Fred A.
- Drinkovic Dragana
- Drosten Christian
- Duedu Kwabena O.
- Durkin Keith
- Dussart Philippe
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- Dürr Kouriba
- Ebied Fatma
- Ebong Ofonime
- Eckstein Simone
- Edu Emame
- Eggan Stephen M.
- Egli Adrian
- Egoh Ifunanya
- Egyir B.
- Ehlan Amivi
- El Amin Ghizlane
- El ansari Fatima Zahra
- El Atar Jalil
- El Fahime Elmostafa
- El Falaki Fatima
- El Guindy Nancy M.
- El Hady Yassine
- El Jaoudi Rachid
- El Jebari Hanen
- El Mazouri Safae
- El Mrimar Nadia
- El Sayes Mohamed
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- El-Shaqnqery H.
- El-Shesheny Rabeh
- El-Taweel Ahmed
- El-Zayat M.
- Elahmer Omar
- Elalaoui Mly Abdelaziz
- Elannaz Hicham
- Elarab Hoda Ezz
- Elargoubi A.
- Elfihri Mohammed Walid Chemao
- Elgahzaly Hesham
- Elgohary Mohamed Abdel-Salam
- Elguindy Nancy
- Elhadidi Mohamed
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- Elhamoumi Siham
- ElHefnawi Mahmoud
- Elhoseiny Mostfa
- Elhoseny M.M.
- Elhosieny F.W.
- Elisabeth Carniel
- Elkhateeb S.M.
- Elkochri Safae
- Ella Kevine Zang
- Ellis Sean
- ElMoussi Awatef
- Elnakib Mostfa
- Eloualid Mjid
- Elouanass M.
- Elouennass Mostafa
- Elroby Ola
- Elsaid Manal Hamdy
- Elsawy Laila
- Elsayed Ahmed
- Elshora Hagar
- Elsissy M.H.
- Elvy Juliet
- Elzagheid Adam I.
- Embaló Bubacar Delgado Pinto
- Emna Gaies
- Emokpae Uyi
- Enatha Mukantwari
- Endjala Nathalia
- Engelbrecht Susan
- Ennibi H.
- Enouf Vincent
- Erameh Cyril
- Erhart Annette
- Eshun Miriam
- Essabbar Abdelomunim
- Essabbar Mouneem
- Essayagh Touria
- Essomba René G.
- Essone Paulin N.
- Estrella Luis A.
- Everatt Josie
- Exler Jan Felix
- Ezzelarab M.H.
- Fadeyi Abayomi
- Fageer Sameira M.
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- Faggioni G.
- Fahsbender E.
- Fainguem Ndine
- Faisal Muhammad
- Fakayode Oluwatosin
- Fakhfakh Ahmed
- Fall Mbengué
- Faouzi Abdellah
- Faouzia Zemmouri
- Farawyla H.
- Fares Wasfi
- Farghaly Ayman
- Faye Martin
- Faye Ousmane
- Feasey Nicholas
- Fedorov A.V.
- Fekkak Jamal
- Femi Ayoade
- Femi Oladiji
- Femi Saibu
- Fenollar Florence
- Ferjani Asma
- Ferjani Sana
- Fidelia Hinson
- Fikry A.E.
- Fillo S.
- Fki-berrajah L.
- Fki-Berrajah Lamia
- Foda Iman
- Fokam Joseph
- Folarino O.
- Folorunsho Francine
- Foster-Nyarko Ebenezer
- Foudi Martin Maidadi
- Foulkes Benjamin H.
- Fournier Pierre-Edouard
- Fowora Muinah Adenike
- Fowotade Adeola
- Francisco Ngiambudulu M.
- Frans Ndahafa
- Fred Tei-Maya
- Freed Nikki
- Freeman Josh
- Freitas R. H.
- Frempong Hilda Opoku
- Fuh-Neba T.
- Fwoloshi Somda Soro Georgina
- Gaaloul I.
- Gad Ahmed F.
- Gadzama Galadima
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- Galal
- Galiwango Ronald M.
- Galvao Bruna
- Garcia Guillermo
- Gardoul Mouhcine
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- Gargouri Saba
- Garry R.
- Garus-Oas Nathalia
- Gaseitsiwe Simani
- Gatare Swaibu
- Gaye-Gaye Astou
- Gdoura Mariem
- Gedeon Jude
- Gelanew Tesfaye
- George Uwem E.
- Gerard Izuwayo
- GeurtsvanKessel Corine H.
- Gevao Sahr
- Gharmaz Hamza
- Ghassan Adib
- Ghedira Kais
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- Giandhari Jennifer
- Gideon Nsubuga
- Giordani F.
- Girgis Samia Abdou
- Gismondo Maria Rita
- Githii Rachid
- Githinji George
- Gnimadi Thibaut Armel Cherif
- Goba Augustine
- Godwe Celestin
- Goedhals Dominique
- Goldstone R.
- Gomaa C.
- Gomaa Mokhtar
- Goodfellow Ian
- Goredema Alexander
- Gorman Richmond
- Gorova Vivianne
- Gosnell B. I.
- Gottberg A.
- Gouider Riadh
- Grace Chukwa
- Grad Alia
- Grant Donald S.
- Grantz Kyra
- Grayo Solène
- Greninger Alexander
- Guedouar Houssem
- Gueye Abdou Salam
- Gueye Khadim
- Gueye Ousseynou
- Guindo Ibrahima
- Gumbo Hlanai
- Gumede Nicksy
- Guseva N. P.
- Gutema Gadissa
- Gutierrez Ana V.
- Gwayi S.
- Gyamfi Jones
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- Hadad A.
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- Hafez Hala
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- Hailu Getnet
- Halafawy A.
- Halatoko Jacqueline Wemboo Afiwa
- Halilou Ibrahima
- Hamdani T.N.
- Hamdy M.S.
- Hammad M.
- Hammami A.
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- Hamza Ghamaz
- Hamzaoui Zaineb
- Handrick Susann
- Happi Anise N.
- Happi Christian
- Harding Doris
- Harvey R.
- Hassan Iman Abdillahi
- Hassan R.
- Hassan W.
- Hassany Mohamed
- Hawi Adede
- Hayette Marie-Pierre
- Heikel Jaafar
- Hellemans Jorn
- Helmy Sherine
- Hemlali Mouhssine
- Henson Sondes
- Heraud Jean-Michel
- Herring Belinda L.
- Hicham Charoute
- Hicham Elannaz
- Hihi Nardjes
- Hilali Abderraouf
- Hilali Farida
- Holland LaRinda A.
- Hoornaert Laurien
- Hope Virginia
- Hosch Salome
- Houda Harmak
- Houechenou Rotimi Myrabelle Avome
- Houhamdi Linda
- Hounkanrin Gildas
- Hounkpatin Benjamin
- Howard Julia
- Hsiao Marvin
- Hsiao Nei-yuan
- Hsu Sharon
- Huang Meei-Li
- Huddleston John
- Hultquist Judd F.
- Hussein Salah Eldin
- Ian Lipkin W.
- Ibrahim Muntaser elTayeb
- Ibrahim Samira F.
- Ibrahim Tomade A.M.
- Ige F.A.
- Iguosadolo Nosamiefan
- Ihazmad Hassan
- Ihekweazu Chikwe
- Iknane A.A.
- Imam Zeinab S.
- Inglês L.
- Inndi Rui
- Intyre Leigh-Anne MC
- Iranzadeh Arash
- Ismael Nalia
- Ismail A.
- Ismail Arshad
- Isong Josiah Ayoola
- Issa Zoukaneirii
- Iwalokun Bamidele
- Iyanu Fred-Akintunwa
- Jain Komal
- Jalal D.
- Jalal Nourlil
- Jalloh Simbirie
- Jamal Fekkak
- Jambo Kondwani
- James Ayorinde Babatunde
- Jannoo N.
- Jefferies Sarah
- Jegede-Williams Anu
- Jelly Lauren
- Jerome Keith R
- Jimoh Yusuf
- Jiménez-Serrano Santiago
- Jo Wendy Karen
- JOEL Ireoluwa Yinka
- Johane Shirley
- Johnson Adeniji A.
- Johnson Bankole
- Joloba Moses
- Joseph Rageema
- Jouali Farah
- Jumaa A.B.
- Juru Agnes
- Kabamba Gabriel
- Kabanda Alice
- Kabatesi Francisca
- Kabbaj Hakima
- Kaboré Firmin
- Kacem Imen
- Kadjo Herve Albéric Adje
- Kagnissode Sidonie A.M.
- Kagoné Thérèse
- Kakai Clement G.
- Kalantar K.
- Kaleebu Pontiano
- Kamal Mohamed
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- Kamga Rodrigue
- Kamoun S.
- Kamulegeya Rogers
- Kandaswamy Krishna Kumar
- Kandeil Ahmed
- Kandeil Ahmed
- Kane Mouhamed
- Kane Ndéye Coumba Touré
- Kanjau Lilian
- Kanjerwa Oscar
- Kanteh Abdoulie
- Kanyerezi Stephen
- Kapata Nathan
- Kapata P.C.
- Kapaya F.
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- Karidioula Safiatou
- Karim Wasim Abdul
- Karray Hakim H.
- Karray Hela
- Kartti Souad
- Kasambara W.
- Kasmy Zohour
- Kassab Reham
- Kassim Samar Kamal
- Katabazi Ashaba Fred
- Katagirya Eric
- Kateete David Patrick
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- Kayali Ghazi
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- Khamadi Samoel Ashimosi
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- Khardine Fayez
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- Kibet Gilbert
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- Kidane Eleni
- Kiemdé Franklin
- Kifude Carol
- Kigozi Edgar
- Kiiza Ronald
- Kim L.
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- Kirimunda Samuel
- Kiritu Edward
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- Konstantinus Iyaloo S.
- Koné Amariane
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- Kooepile Legodile
- Koopmans Marion
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- Kossi Komlan
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- Kouriba Bourema
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- Krasnov Y.M.
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- Kritsky A.A.
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- Kumordjie Selassie
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- Kwasah Lorreta
- Kwenda S.
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- Laamrti Rokaia
- Laatiris Abdelkader
- Ladhari Hafsia
- Lagare Adamou
- Laguda-Akingba Oluwakemi
- Lahlou Amine Idriss
- Lahlou Idriss-Amine
- Lahlou Kitane Driss
- Lako Richard Lino Loro
- Lalemi Mary
- Lambisia Arnold W.
- Lamboni Lallepak
- Lamiae Belayachi
- Langat Sombo
- Laraqui Abdelilah
- Laryea Dennis
- Latif Elwaleed M. Elamin Sara A.I
- Latifa Anga
- Layibo Yasser
- Le Viet Thanh
- Le-Viet Thanh
- Lee Justin
- Lee Kwok
- Leendertz Fabian
- Lefrançois Louise
- Lekana-Douki Bernard
- Lekana-Douki Sonia
- Lell Bertrand
- Lelo Eric A.
- Lemoine Frederick
- Lemtudo Alan
- Lesego Kuate-lere
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- Lessells Richard
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- Leta D.
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- Letaief A.
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- Leye Nafisatou
- Li Zhenghui
- Liberator Paul
- Liboro G.
- Licastro Danilo
- Lieu Vivi Hue-Trang
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- Lima Mendonça Maria da Luz
- Limbaso Samson Konongoi
- Lin L.
- Lin Michelle
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- Lipsi Maria Rosaria
- Lissauer Sam
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- Lista F.
- Livo Esemu
- Liwewe M.M.
- Liyai Rehema
- Lo Gora
- Lo Mamadou Beye Cheikh Ibrahima
- Lockman Shahin
- Lodiongo Dennis Kenyi
- Lojuan Abe
- Lokilo Emmanuel
- Long Kyle A.
- Lontchi Roméo Aimé Laclong
- Lorenzo-Redondo Ramy
- Loucoubar Cheikh
- Lule Daniel B.
- Lumembe Raphael
- Luo Hu
- Luquette Andrea E.
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- Lutalo Tom
- Lutucuta Silvia
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- Luutu Moses
- M'cormack Violette V.
- Maaroufi Anderrahmane
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- Mabunda Nedio
- Mabunda Nédio
- MaCauley Jane
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- Mad W.
- Madeira Carla
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- Maeka Kenneth K.
- Maes Piet
- Magalhães Erica Luis Maria
- Magdeldin S.
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- Maharaj Arisha
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- Mahlangu B.
- Mahmoud Galal
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- Maida A.
- Maidane Yakob Gebregziabher
- Maiga Almoustapha I.
- Maiga Mamoudou
- Maiga Zimmerman
- Majanja Janet
- Makamure Beuty
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- Makhema Joseph
- Makiala-Mandanda Sheila
- Makki Yousif Rabih
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- Malabat Christophe
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- Malolo I.
- Maloum Moustapha Nzamba
- Maluzi Kwitaka
- Maman Issaka
- Manangazira Portia
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- Mandomando Inacio
- Manene Bulelani
- Manga Pasacaline
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- Manneh Jarra
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- Marais Gert
- Marcello Alessandro
- Mareka Mathabo
- Margaglione Maurizio
- Mari Alfredo
- Maria da Costa Edmira
- Marie Claire Okomo Assoumou
- Marion Amujal
- Maritz Jean
- Marks Michael
- Marondera Blessing T.
- Marti-Carerras Joan
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- Maruapula Dorcas
- Marx Jacques
- Marycelin Baba
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- Massinga Arsenia
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- Mathur H.
- Matobo Mooko Marethabile
- Matshaba Mogomotsi
- Matsheka Maitshwarelo I.
- Maufrais Corinne
- Mavingui Patrick
- Mayaphi Sim
- Mayor Alfredo
- Maïté Soundélé
- Mba Nwando
- Mbala Placide K.
- Mbanne Maimouna
- Mbaye Aminata
- Mbegnan Coulibaly
- Mbembo Guy Paterne Malonga
- Mbhele Nokuzola
- Mbondoukwe Noé Patrick
- Mbongo-Nkama Elvyre
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- Mboup Aminata
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- Melingui Sylvie
- Melloul Marouane
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- Mewono Ludovic
- Meyer Philippe Lavrard
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- Micelli Loris
- Micheli Valeria
- Michuki George
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- Mine Madisa
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- Mohammed Hajjaji
- Mohammed K.S.
- Mohammed Khadija Said
- Mohammed Oumaima Ait Si
- Mohammed Youbi
- Mohktar Quaneeta
- Mohr Vanessa
- Moir Monika
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- Mouallif Mustapha
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- Mouhssine Hemlali
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- Ndaruhutse Jerome
- Ndeboko Bénédicte
- NDiaye Anna Julienne Selbe
- Ndiaye Birahim Piere
- Ndiaye Halimatou Diop
- Ndiaye Ndack
- Ndiaye Yacine DIA Seni
- Ndiour Samba
- Ndjolo Alexis
- Ndodo Nnaemeka
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- Nkurunziza Jerome
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- Nkwembe Edith
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- Oteng F.
- Otieno Edward
- Otuonye Ngozi Mirabel
- Ouadghiri Ouna
- Ouangole Garba
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- von Gottberg Anne
- Waberi Zeinab Ali
- Wadi Amira Suliaman
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- Wadula J.
- Wagner Philipp
- Wahab Kolawole Wasiu
- Waitumbi John
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- Wamala Joseph F.
- Wandera Dennis N.
- Wang Jing
- Wang Xiuhua
- Wani Gregory
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- Waruhiu Cecilia
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- Wawina-Bokalanga Tony
- Wayengera Misaki
- Wayoro Oby
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- Webby Richard
- Weldemariam A.G.
- Weldemariam Atsbeha G.
- Werno Anja
- Wiley Michael R.
- Wilkinson David
- Wilkinson Eduan
- Williamson Carolyn
- Wilson Shannon
- Woelfel R.
- Wohl Shirlee
- Wolh S.
- Wolter Nicole
- Wuduri Zara
- Wulf Ben
- Wurie I.
- Wurie Isatta
- Xavier Joicymara S.
- Xiang Zuzheng
- Xie Hong
- Yadouleton Anges
- Yadouleton Yahya
- Yakout Mostfa
- Yandoko Rivalyn Nakoune
- Yang Qi
- Yao Kouadio T.
- Yassine Kasmi
- Yassine Zouheir
- Yasuda Jiro
- Yatassaye Bouna
- Yeboah C.
- Yeboah Richmond
- Yeboah-Manu Dorothy
- Yemi Bright K.
- Yiaba Cyrus
- Yiaba Warren Cyrus
- Yu Popova A.
- Yusuf Nyam Itse
- Yusuf Yacob Mohamed
- Zablon J. Matoke D.
- Zablon J.O.
- Zaher Tarek Refaat Elnagdy Raafat
- Zahra El Ansari Fatima
- Zahran Manal Hamdy
- Zekri Abdel-Rahman N.
- Zhang J.
- Zhou Pei
- Zinyowera Sekesai
- Zong Minko O.
- Zongo Arsène
- Zorgani A.
- Zouaki Amal
- Zulu P.
- Zumla Ali
- Zumla Alimuddin
- Zuze Boitumelo
- Publication venue
- 'American Association for the Advancement of Science (AAAS)'
- Publication date
- 07/10/2022
- Field of study
INTRODUCTION
Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic.
RATIONALE
We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs).
RESULTS
Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants.
CONCLUSION
Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- Author
- A Gordon Robertson
- Abdullah Kahraman
- Abel Gonzalez-Perez
- Adam A Margolin
- Adam Abeshouse
- Adam Grundhoff
- Adam J Struck
- Adam J Struck
- Adam J Wright
- Adam Lambert
- Adam P Butler
- Adam P Butler
- Adel El-Naggar
- Adnan M Nagrial
- Adrian Ally
- Adrian Baez-Ortega
- Adrian Thorogood
- Adriana Salcedo
- Adrienne M Flanagan
- Ake Borg
- Akihiro Fujimoto
- Akihiro Suzuki
- Akinyemi I Ojesina
- Alain Viari
- Alan J Robertson
- Alan P Hoyle
- Alan Thompson
- Alasdair Stenhouse
- Alastair M Thompson
- Aldo Scarpa
- Alessandro Pastore
- Alex Buchanan
- Alex Buchanan
- Alexander Claviez
- Alexander J Lazar
- Alexander Martinez-Fundichely
- Alfonso Muñoz
- Alfonso Valencia
- Aliaksei Z Holik
- Alice Meng
- Alicia L Bruzos
- Allison Creason
- Allison P Heath
- Alvin Wei Tian Ng
- Alvis Brazma
- Amaro Taylor-Weiner
- Amber L Johns
- Amie Radenbaugh
- Amit G Deshwar
- Ana Dueso-Barroso
- Ana Mijalkovic Mijalkovic-Lazic
- Ana Milovanovic
- Ana Milovanovic
- Andre Kahles
- Andrea Haake
- Andrea Holbrook
- Andrea L Richardson
- Andrea Mafficini
- Andrea Ruzzenente
- Andreas Behren
- Andreas Rosenwald
- Andreia V Pinho
- Andrew Berchuck
- Andrew D Cherniack
- Andrew J Dunford
- Andrew J Mungall
- Andrew J Spillane
- Andrew Menzies
- Andrew Menzies
- Andrew P Barbour
- Andrew Tutt
- Andrew V Biankin
- Andrey Korshunov
- Andrés Lanzós
- Andy Cafferkey
- Andy G Lynch
- Angela Chou
- Angela N Brooks
- Angela Tam
- Angelica Ochoa
- Angelika N Christ
- Angelo P Dei Tos
- Anieta M Sieuwerts
- Anil K Sood
- Anita Langerød
- Anja Füllgrabe
- Anke K Bergmann
- Ann-Marie Patch
- Anna deFazio
- Anna Ehinger
- Anna Fitzgerald
- Anne Hamilton
- Anne Vincent-Salomon
- Anne Y Warren
- Anne-Lise Børresen-Dale
- Annegien Broeks
- Anthony DiBiase
- Anthony J Gill
- Anthony Ng
- Anthony R Green
- Antonia L Pritchard
- Antonio Pea
- Antonios Koures
- Aparna Prasad
- Apurva M Hegde
- Aquila Fatima
- Arcadi Navarro
- Arie B Brinkman
- Arif O Harmanci
- Arindam Maitra
- Armando Lopez-Guillermo
- Arndt Borkhardt
- Arnoud Boot
- Asger Hobolth
- Ashley Williams
- Ashton A Connor
- Atul J Butte
- Aurélien Chateigner
- Austin J Hepperla
- Axel Aretz
- Aya Sasaki-Oku
- Ayellet V Segre
- B F Francis Ouellette
- Bailey Matthew H
- Barbara Hutter
- Barbara Hutter
- Barbara Kremeyer
- Bartha M Knoppers
- Beifang Niu
- Beifang Niu
- Beifang Niu
- Benedikt Brors
- Benita Kiat Tee Tan
- Benjamin J Raphael
- Benjamin P Berman
- Benjamin Raeder
- Bernardo Rodriguez-Martin
- Bernhard Radlwimmer
- Bernice H Wong
- Beth Karlan
- Bin Tean Teh
- Bin Zhu
- Birgit Burkhardt
- Bishoy M Faltas
- Bodil Bjerkehagen
- Bogdan Czerniak
- Boris Winterhoff
- Borislav C Rusev
- Bradly G Wouters
- Brandi N Davis-Dusenbery
- Brian Craft
- Brian D O'Connor
- Brian Patrick O'Neill
- Brice Aminou
- Calvin Wing Yiu Chan
- Cameron M Soulette
- Carl Herrmann
- Carl Morrison
- Carlo Gambacorti-Passerini
- Carlos Caldas
- Carlos D Bustamante
- Carlos López-OtÃn
- Carlota Rubio-Perez
- Carmen Gomez
- Carolien H M van Deurzen
- Carolyn M Hutter
- Carolyn M Hutter
- Carrie Cibulskis
- Caterina Vicentini
- Catherine A Shang
- Catherine D Moser
- Catherine J Kennedy
- Catrina C Fronick
- Chad J Creighton
- Chandra Sekhar Pedamallu
- Chang Li
- Charles David Imbusch
- Charles M Perou
- Charles Saller
- Charles Short
- Charlie E Massie
- Chawalit Pairojkul
- Chen Hong
- Chen Ye
- Cheng-Zhong Zhang
- Chin-Lee Wu
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- Chip Stewart
- Chip Stewart
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- Chris Mitchell
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- Christian von Mering
- Christiane Buchholz
- Christina K Yung
- Christina K Yung
- Christina Yau
- Christine A Iacobuzio-Donahue
- Christine Chomienne
- Christine Desmedt
- Christine P'ng
- Christof von Kalle
- Christoph Borst
- Christoph Plass
- Christopher A Miller
- Christopher Benz
- Christopher J Scarlett
- Christopher J Yoon
- Christopher K Wong
- Christopher M Lalansingh
- Christopher M Lalansingh
- Christopher Ogden
- Christopher S Foster
- Christopher Umbricht
- Christopher W Toon
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- Cindy Bell
- Cinzia Cantù
- Ciyue Shen
- Claes Wadelius
- Clare Verrill
- Clarissa Gerhauser
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- Claudio Bassi
- Claudio Luchini
- Claudiu Farcas
- Clemency Jolly
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- Colin A Semple
- Colin C Collins
- Colin S Cooper
- Conrad R Leonard
- Constance H Li
- Corbin D Jones
- Craig Shriver
- Cristina López
- Cyriac Kandoth
- Cyril Fisher
- D Neil Hayes
- Dai-Ying Wu
- Daiming Fan
- Daisuke Komura
- Dale W Garsed
- Daniel A Leongamornlert
- Daniel Baumhoer
- Daniel Hübschmann
- Daniel J Turner
- Daniel J Weisenberger
- Daniel M Berney
- Daniel Rosebrock
- Daniel S Brewer
- Daniela S Gerhard
- Danielle Pasternack
- Darell Bigner
- Dariush Etemadmoghadam
- Darlene Lee
- Darrin F Taylor
- Dave Larson
- David A Wheeler
- David A Wheeler
- David C Wedge
- David Craft
- David D L Bowtell
- David E Neal
- David Haan
- David Haussler
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- David Hedley
- David Huntsman
- David I Heiman
- David J Adams
- David J Van Den Berg
- David K Chang
- David K Miller
- David Khoo
- David Mutch
- David N Louis
- David Nicol
- David Ocana
- David R Jones
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- David Scott
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- Davide Antonello
- Declan Cahill
- Denis Larsimont
- Denis Yuen
- Denise Brooks
- Deniz DemircioÄŸlu
- Dennis C Sgroi
- Dennis Karsch
- Dennis T Maglinte
- Dennis Wigle
- Derek W Wright
- Dianne E Chadwick
- Dido Lenze
- Dieter Kube
- Dieter Weichenhan
- Dilip D Giri
- Dimitri Livitz
- Dimitri Livitz
- Dimple Chakravarty
- Ding
- Dirk Schadendorf
- Dmitry A Gordenin
- Dominik Glodzik
- Don Chalmers
- Dong Guanlan
- Dongbing Liu
- Donghoon Lee
- Donghui Tan
- Donna M Muzny
- Dorthe Grabau
- Douglas A Levine
- Douglas F Easton
- Douglas Voet
- Duncan Beardsmore
- Dursi Lewis Jonathan
- Edward W Rowe
- Eigo Shimizu
- Ekta Khurana
- Elaine R Mardis
- Electron Kebebew
- Elena Piñeiro-Yáñez
- Elena Provenzano
- Elias Campo
- Elisabet Barrera
- Elisabetta Sereni
- Elizabeth A Musgrove
- Elizabeth L Appelbaum
- Elizabeth L Christie
- Elli Papaemmanuil
- Ellrott Kyle
- Emilie Lalonde
- Eoghan Harrington
- Eric Chuah
- Eric Green
- Eric Lander
- Eric Minwei Liu
- Eric Z Ma
- Eric Z Ma
- Erik Garrison
- Erik Larsson
- Erik Mayer
- Erik N Bergstrom
- Erin Curley
- Ermin Hodzic
- Erwin G Van Meir
- Esa Pitkänen
- Esther Rheinbay
- Esther Rheinbay
- Eun Pyo Hong
- Eunjung Alice Lee
- Eva G Alvarez
- Eva Hellstrom-Lindberg
- Ewan Birney
- F Germán RodrÃguez-González
- Fabien C Lamaze
- Fabien Calvo
- Fabio C P Navarro
- Faiyaz Notta
- Fan Yang
- Fan Zhang
- Faraz Hach
- Faraz Hach
- Faridah Mbabaali
- Fatima Al-Shahrour
- Federico Abascal
- Fei-Fei Liu
- Felicity Newell
- Fenglin Liu
- Fernanda Amary
- Ferran Muiños
- Florian Markowetz
- Fouad Yousif
- Francesc Muyas
- Francesco Favero
- Francisco M De La Vega
- Francisco Sanchez-Vega
- Fraser R Duthie
- Fred Sweep
- Freddie C Hamdy
- Fruzsina Molnár-Gábor
- Fumie Hosoda
- G Petur Nielsen
- G Steven Bova
- Gad Getz
- Gad Getz
- Gad Getz
- Gaetan MacGrogan
- Gaetano Finocchiaro
- Gary D Bader
- Gavin Ha
- Gavin W Wilson
- Genta Nagae
- Geoff Macintyre
- George B Hanna
- George L Mihaiescu
- Georgia Escaramis
- Georgina V Long
- Gerd Nettekoven
- German M Demidov
- German Ott
- Gerrit K Hooijer
- Gerstein Mark B
- Gert G Van den Eynden
- Getz Gad
- Ghislaine Scelo
- Giada Bonizzato
- Giampaolo Tortora
- Gilles Romieu
- Gilles Thomas
- Giovanni Marchegiani
- Gisela Mir Arnau
- Giuseppe Malleo
- Gloria M Petersen
- Gordon B Mills
- Gordon B Mills
- Gordon Saksena
- Gordon Saksena
- Gordon Saksena
- Grace Tiao
- Grace Tiao
- Graham J Mann
- Grant Sanders
- Gu Kong
- Guanming Wu
- Guido Reifenberger
- Guido Sauter
- Guillaume Bourque
- Gulietta M Pupo
- Gun Ho Jang
- Gunes Gundem
- Gunnar Rätsch
- Gurnit Atwal
- Hailei Zhang
- Haiyan Irene Li
- Han Liang
- Hana Susak
- Hans Binder
- Hans Lehrach
- Hans-Jörg Warnatz
- Hardeep K Nahal-Bose
- Hark Kyun Kim
- HarshaVardhan Doddapaneni
- Hartmut Juhl
- Harvey Pass
- Hayley C Whitaker
- Hayley J Luxton
- Hazel Burke
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- Yifei Men
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- Yingyan Yu
- Yiwen Chen
- Yogesh Kumar
- Yogesh Kumar
- Yoke-Eng Chiew
- Yong Hou
- Yong Zhou
- Yong-Jie Lu
- Yongzhan Nie
- Yosef E Maruvka
- Yosef E Maruvka
- Yoshiiku Kawakami
- Young Seok Ju
- Youngchoon Woo
- Youngil Koh
- Youngwook Kim
- Youyong Lu
- Yu Fan
- Yu Fan
- Yu Fan
- Yu-Jia Shiah
- Yuan Ji
- Yuan Yuan
- Yuichi Shiraishi
- Yulia Newton
- Yulia Rubanova
- Yumeng Wang
- Yupeng Cun
- Yussanne Ma
- Zachary Heins
- Zechen Chong
- Zechen Chong
- Zemin Zhang
- Zhaohong Chen
- Zhenggang Wu
- Zhenggang Wu
- Zhining Wang
- Zhongming Zhao
- Ziao Lin
- Zsofia Kote-Jarai
- Ólafur Andri Stefánsson
- Øystein Garred
- Publication venue
- Publication date
- 01/01/2020
- Field of study
The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe
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- Abascal Federico
- Abeshouse Adam
- Aburatani Hiroyuki
- Adams David J.
- Agrawal Nishant
- Ahn Keun Soo
- Ahn Sung-Min
- Aikata Hiroshi
- Akbani Rehan
- Akdemir Kadir C.
- Al-Ahmadie Hikmat
- Al-Sedairy Sultan T.
- Al-Shahrour Fatima
- Alawi Malik
- Albert Monique
- Aldape Kenneth
- Alexandrov Ludmil B.
- Ally Adrian
- Alsop Kathryn
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- Yang Yang
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- Yau Christina
- Ye Chen
- Ye Kai
- Yellapantula Venkata D.
- Yoon Christopher J.
- Yoon Sung-Soo
- Yousif Fouad
- Yu Jun
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- Yu Yingyan
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- Yuan Yuan
- Yuen Denis
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- Zaikova Olga
- Zamora Jorge
- Zapatka Marc
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- Zhang Hongwei
- Zhang Hongxin
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- Zhang Xiuqing
- Zhang Xuanping
- Zhang Yan
- Zhang Zemin
- Zhao Zhongming
- Zheng Liangtao
- Zheng Xiuqing
- Zhou Wanding
- Zhou Yong
- Zhu Bin
- Zhu Hongtu
- Zhu Jingchun
- Zhu Shida
- Zou Lihua
- Zou Xueqing
- Publication venue
- Nature Communications
- Publication date
- 28/08/2020
- Field of study
Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research