16 research outputs found
Mendelian gene identification through mouse embryo viability screening.
- Author
- Braun Robert E
- Bunton-Stasyshyn Rosie
- Cacheiro Pilar
- Cleak James
- Creighton Amie K
- Dickinson Mary E
- Flenniken Ann M
- Genomics England Research Consortium
- Guo Ruolin
- Harrisson Jackie
- Haseli Mashhadi Hamed
- Heaney Jason D
- Hsu Chih-Wei
- International Mouse Phenotyping Consortium
- Lanoue Louise
- Laurin Valerie
- Lloyd K C Kent
- Mager Jesse
- Mallon Ann-Marie
- Mason Jeremy
- McKerlie Colin
- Murray Stephen A
- Muñoz-Fuentes Violeta
- Nutter Lauryl M J
- Parkinson Helen
- Qu Dawei
- Smedley Damian
- Stewart Michelle
- Teboul Lydia
- Van den Veyver Ignatia B
- Wells Sara
- Westerberg Carl Henrik
- White Jacqueline K
- Publication venue
- The Mouseion at the JAXlibrary
- Publication date
- 13/10/2022
- Field of study
BACKGROUND: The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful. A full spectrum of intolerance to loss-of-function variation has been previously described, providing evidence that gene essentiality should not be considered as a simple and fixed binary property.
METHODS: Here we further dissected this spectrum by assessing the embryonic stage at which homozygous loss-of-function results in lethality in mice from the International Mouse Phenotyping Consortium, classifying the set of lethal genes into one of three windows of lethality: early, mid, or late gestation lethal. We studied the correlation between these windows of lethality and various gene features including expression across development, paralogy and constraint metrics together with human disease phenotypes. We explored a gene similarity approach for novel gene discovery and investigated unsolved cases from the 100,000 Genomes Project.
RESULTS: We found that genes in the early gestation lethal category have distinct characteristics and are enriched for genes linked with recessive forms of inherited metabolic disease. We identified several genes sharing multiple features with known biallelic forms of inborn errors of the metabolism and found signs of enrichment of biallelic predicted pathogenic variants among early gestation lethal genes in patients recruited under this disease category. We highlight two novel gene candidates with phenotypic overlap between the patients and the mouse knockouts.
CONCLUSIONS: Information on the developmental period at which embryonic lethality occurs in the knockout mouse may be used for novel disease gene discovery that helps to prioritise variants in unsolved rare disease cases
A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction
- Author
- Adams David J.
- Aguilar-Pimentel Antonio
- Ali-Hadji Dalila
- Allen Sue
- Amarie Oana
- André Philippe
- Ayabe Shinya
- Ayadi Abdel
- Bam'Hamed Chaouki
- Beaudet Arthur L.
- Becker Lore
- Beckers Johannes
- Beig Joachim
- Bekeredjian Raffi
- Berberovic Zorana
- Birling Marie-Christine
- Bour Raphael
- Bower Lynette R.
- Bowl Michael R.
- Bradley Allan
- Braun Robert E.
- Brommage Robert
- Brown Steve D. M.
- Bubshait Mohammed
- Busch Dirk H.
- Bürger Antje
- Cabezas Jorge
- Calzada-Wack Julia
- Carroll Tracy
- Cater Heather
- Chen Chao-Kung
- Chiani Francesco
- Clark Greg
- Clarke Shannon
- Clary Dave A.
- Clementson-Mobbs Sharon
- Codner Gemma
- Conte Nathalie
- Creighton Amie
- Danisment Ozge
- De Angelis Martin Hrabe
- Di Pietro Chiara
- Di Segni Gianfranco
- Dickinson Mary E.
- Eickelberg Oliver
- El Amri Amal
- El Fertak Leila
- Ennah Hamid
- Ermakova Olga
- Eskandarian Mohammad
- Ferrara Filomena
- Feugas Patricia
- Flenniken Ann M.
- Flicek Paul
- Fray Martin
- Fruscoloni Paolo
- Fuchs Helmut
- Furuse Tamio
- Gailus-Durner Valérie
- Gambadoro Aalessia
- Gao Xiang
- Gardiner Wendy
- Garrett Lillian
- Gastaldi Serena
- Gertsenstein Marina
- Giesert Florian
- Golini Elisabetta
- Graw Jochen
- Greenaway Simon
- Guimond Alain
- Guo Ruolin
- Herault Yann
- Hunter Jane
- Hölter Sabine M.
- Ingham Neil J.
- Jacob Elsa
- Jacquot Sylvie
- Joynson Russell
- Justice Monica J.
- Kaneda Hideki
- Karp Natasha
- Kelsey Lois
- Kenyon Janet
- Klingenspor Martin
- Klopstock Thomas
- Kobayashi Kimio
- Kurbatova Natalja
- Kühn Ralf
- Lalanne Valérie
- Lan Qing
- Laurin Valerie
- Law Napoleon
- Le Marchand Elise
- Leblanc Sophie
- Lengger Christoph
- Leuchtenberger Stefanie
- Lloyd K. C. Kent
- Loeffler Jorik
- Lux Aline
- Macmaster Sue
- Maier Holger
- Mallon Ann-Marie
- Mandillo Silvia
- Marazziti Daniela
- Marschall Susan
- Mason Jeremy
- Massimi Marzia
- Masuya Hiroshi
- Matteoni Rafaele
- Matthews Peter
- Mckerlie Colin
- Meehan Terrence F.
- Meziane Hamid
- Miller David
- Minowa Osamu
- Mittelhaeuser Christophe
- Miura Ikuo
- Moore Mark
- Moreth Kristin
- Morikawa Lily
- Moulaert David
- Murray Stephen A.
- Neff Frauke
- Nell Barbara
- Newbigging Susan
- Nutter Lauryl M. J.
- Obata Yuichi
- Ollert Markus
- Oritz Oskar
- Orsini Tiziana
- Owen Celeste
- Parker Andrew
- Parkinson Helen E.
- Pasquini Miriam
- Pavlovic Guillaume
- Pearson Selina
- Penton Patricia
- Pereira Monica
- Putti Sabrina
- Qu Dawei
- Quwailid Deen
- Raspa Marcello
- Rathkolb Birgit
- Rauch Aline
- Reilly Patrick
- Relac Mike
- Riet Fabrice
- Rossi Gianfranco
- Rossi Nicoletta
- Rozman Jan
- Sala Gina La
- Santos Luis
- Scavizzi Ferdinando
- Schick Joel
- Schmidt-Weber Carsten
- Seavitt John
- Seisenberger Claudia
- Selloum Mohammed
- Shang Xueyuan
- Simon Michelle M.
- Skarnes William C.
- Sleep Gillian
- Smedley Damian
- Sohel Khondoker
- Sorg Tania
- Steel Karen P.
- Steinkamp Ralph
- Stewart Michelle
- Stoeger Claudia
- Stoeger Tobias
- Suzuki Tomohiro
- Svenson Karen L.
- Tamura Masaru
- Tanaka Nobuhiko
- Taylor Sarah
- Teboul Lydia M.
- Tocchini-Valentini Giuseppe D.
- Tocchini-Valentini Glauco P.
- Tondat Sandra
- Treise Irina
- Tudose Ilinca
- Vasseur Laurent
- Vukobradovic Igor
- Wakana Shigeharu
- Walling Alison
- Wang Yanchun
- Warren Jonathan
- Wattenhofer-Donze Marie
- Wells Sara
- West David B.
- White Jacqui
- Wolf Eckhard
- Wurst Wolfgang
- Yamada Ikuko
- Yildrim Ali Önder
- Yoshiki Atsushi
- Zaman Rumana
- Zhu Yingchun
- Zimmer Andreas
- Zimprich Annemarie
- Östereicher Manuela A.
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2017
- Field of study
The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function
The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma
- Author
- Ahn Jaeil
- Akbani Rehan
- Aldape Kenneth D.
- Ally Adrian
- Atkins Michael B.
- Auman J. Todd
- Ayala Brenda
- Baboud Julien
- Balasundaram Miruna
- Balu Saianand
- Baylin Stephen B.
- Benz Christopher C.
- Beroukhim Rameen
- Bhanot Gyan
- Biehl Michael
- Birol Inanc
- Black Aaron D.
- Bodenheimer Tom
- Boice Lori
- Bootwalla Moiz S.
- Bowen Jay
- Bristow Christopher A.
- Brooks Denise
- Buda Elizabeth
- Buhay Christian
- Butterfield Yaron S.N.
- Carter Scott L.
- Chao Hsu
- Chen Fengju
- Cherniack Andrew D.
- Cheville John
- Chin Lynda
- Cho Juok
- Choi Yoon La
- Choueiri Toni K.
- Chu Andy
- Chuah Eric
- Chudamani Sudha
- Clarke Amanda
- Coarfa Cristian
- Creighton Chad J.
- Czerniak Bogdan A.
- Dahdouli Mike
- Davidsen Tanja
- Davis Caleb F.
- Demchok John A.
- Dhalla Noreen
- Di-Cara Daniel
- Doddapaneni Harsha
- Donehower Lawrence A.
- Downs Brittany
- Drummond Jennifer
- Eley Greg
- English Adam
- Fahey Catherine C.
- Fan Yu
- Fargo David
- Felau Ina
- Frazer Scott
- Gabriel Stacey B.
- Gastier-Foster Julie M.
- Gehlenborg Nils
- Getz Gad
- Gibbs Richard A.
- Gordenin Dmitry A.
- Guin Ranabir
- Gunaratne Preethi H.
- Guyer Mark S.
- Hacker Kathryn E.
- Hadjipanayis Angela
- Hakimi A. Ari
- Hale Walker
- Hall Tracy M.
- Hanf Benjamin
- Haussler David
- Hawes Alicia
- Hayes D. Neil
- Heiman David I.
- Henske Elizabeth P.
- Hoadley Katherine A.
- Holt Robert A.
- Hoyle Alan P.
- Hsieh James J.
- Huang Mei
- Hutter Carolyn M.
- Jefferys Stuart R.
- Jensen Mark A.
- Jones Corbin D.
- Jones Steven J.M.
- Kaelin William G.
- Kaipparettu Benny A.
- Kakkar Nipun
- Kalra Divya
- Kang Hyojin
- Kasaian Katayoon
- Kim Jaegil
- Kim Sang Cheol
- Klimczak Leszek J.
- Kovar Christie
- Kucherlapati Raju
- Kwiatkowski David J.
- Lai Phillip H.
- Laird Peter W.
- Lang Martin
- Lawrence Michael S.
- Lee Darlene
- Lee Eunjung
- Lee June Koo
- Lee Junehawk
- Lee Semin
- Leraas Kristen M.
- Lewis Lora
- Li Haiyan I.
- Lichtenberg Tara M.
- Lim Emilia
- Lin Pei
- Linehan W. Marston
- Liu Jia
- Liu Yingchun
- Luquette Lovelace J.
- Ma Singer
- Ma Yussanne
- Marra Marco A.
- Mayo Michael
- Meng Qingchang
- Meng Shaowu
- Merino Maria
- Meyerson Matthew
- Mieczkowski Piotr A.
- Moore Richard A.
- Morgan Margaret
- Morton Donna
- Mose Lisle E.
- Mungall Andrew J.
- Murray Bradley A.
- Muzny Donna
- Noble Michael S.
- Ozenberger Bradley A.
- Pantazi Angeliki
- Parfenov Michael
- Park Peter J.
- Park Woong Yang
- Parker Joel S.
- Perou Charles M.
- Peterson James
- Pihl Todd
- Protopopov Alexei
- Radenbaugh Amie
- Ramirez Nilsa C.
- Rathmell W. Kimryn
- Reid Jeffrey G.
- Reuter Victor
- Ricketts Christopher J.
- Roach Jeffrey
- Roberts Steven A.
- Robertson A. Gordon
- Saksena Gordon
- Santoso Netty
- Schein Jacqueline E.
- Schmidt Laura S.
- Schumacher Steven E.
- Seidman Jonathan
- Seiler Michael
- Seth Sahil
- Shaw Kenna R.Mills
- Shen Hui
- Sheth Margi
- Shuch Brian
- Signoretti Sabina
- Simons Janae V.
- Sipahimalani Payal
- Smith Angela B.
- Sofia Heidi J.
- Soloway Mathew G.
- Song Xingzhi
- Sougnez Carrie
- Spellman Paul T.
- Stojanov Petar
- Stuart Josh M.
- Tabak Barbara
- Tam Angela
- Tamboli Pheroze
- Tan Donghui
- Tarnuzzer Roy W.
- Thiessen Nina
- Thompson R. Houston
- Thorne Leigh
- Tickoo Satish K.
- Triche Timothy
- Van Den Berg David J.
- Velaga Sudhakar
- Veluvolu Umadevi
- Vocke Cathy
- Voet Doug
- Walker Kimberly
- Wallen Eric M.
- Walton Jessica
- Wan Yunhu
- Wang Min
- Wang Qiaoyan
- Wang Wenyi
- Wang Zhining
- Waring Scot
- Weinstein John N.
- Weisenberger Daniel J.
- Wheeler David A.
- Wilkerson Matthew D.
- Wise Lisa
- Wong Tina
- Wood Christopher G.
- Worrell Robert
- Wu Junyuan
- Wu Ye
- Xi Liu
- Xu Andrew W.
- Yang Liming
- Yang Lixing
- Zack Travis I.
- Zenklusen Jean Claude
- Zhang Hailei
- Zhang Jianhua
- Zhang Jiashan
- Zhul Jingchun
- Zmuda Erik
- Zou Lihua
- Publication venue
- Publication date
- 01/01/2014
- Field of study
We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT up-regulation in cancer distinct from previously-observed amplifications and point mutations
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
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
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- Shun-Ichi Ariizumi
- Shuto Hayashi
- Sian Fereday
- Siegfried Haas
- Sietse Aukema
- Siliang Li
- Simon C Heath
- Simon L Parsons
- Simon Mayes
- Simon Tavaré
- Simpson Jared T
- Singer Ma
- Sinisa Ivkovic
- Sissel Juul
- Solomon I Shorser
- Sonia Grimaldi
- Sonia Puig
- Stacey B Gabriel
- Stefan C Dentro
- Stefan G Stark
- Stefan M Pfister
- Stefan Schreiber
- Stefania Tommasi
- Stefano Barbi
- Stefano Serra
- Stephan H Bernhart
- Stephan Ossowski
- Stephan Ossowski
- Stephan Stilgenbauer
- Stephan Wolf
- Stephanie Sungalee
- Stephen B Baylin
- Stephen H Kazakoff
- Stephen J Chanock
- Stephen J Hayes
- Stephen M Cordner
- Stephenie D Prokopec
- Steve Hawkins
- Steve Hoffmann
- Steven A Roberts
- Steven E Schumacher
- Steven Foltz
- Steven G Rozen
- Steven Gallinger
- Steven Hazell
- Steven J M Jones
- Steven J Newhouse
- Steven Van Laere
- Stian Knappskog
- Stuart Edmonds
- Stuart R Jefferys
- Su Pin Choo
- Subhajit Sengupta
- Sue Merson
- Suet-Feung Chin
- Sultan T Al-Sedairy
- Sung-Min Ahn
- Sung-Soo Yoon
- Sunghoon Cho
- Sunil R Lakhani
- Suresh Ramalingam
- Susan Bullman
- Susanna L Cooke
- Sushant Kumar
- Sushant Kumar
- Suyash S Shringarpure
- Syed Haider
- Sylvia Asa
- Søren Brunak
- Takafumi N Yamaguchi
- Takafumi N Yamaguchi
- Takanori Hasegawa
- Takashi Yugawa
- Takashi Yugawa
- Takuji Okusaka
- Tal Shmaya
- Tannistha Nandi
- Taobo Hu
- Taobo Hu
- Tapio Visakorpi
- Tara J Skelly
- Tari A King
- Tatsuhiko Tsunoda
- Tatsuhiro Shibata
- Ted R Hupp
- Tetsuo Ushiku
- Theodorus Van der Kwast
- Thomas E Carey
- Thomas J Hudson
- Thomas J Matthew
- Thomas J Mitchell
- Thorsten Schlomm
- Thorsten Zenz
- Tian Xia
- Tim Dudderidge
- Tim Ley
- Timothy A Beck
- Timothy Defreitas
- Timothy J C Bruxner
- Timothy J Underwood
- Tina Wong
- Tirso Pons
- Tobias Madsen
- Tobias Rausch
- Todd A Johnson
- Todd D Pihl
- Tom Bodenheimer
- Tom Mikkelsen
- Tom Roques
- Tomas J Tanskanen
- Tomas Marques-Bonet
- Tomoko Urushidate
- Torill Sauer
- Toru Nakamura
- Treasa A McPherson
- Troy Shelton
- Tsun-Po Yang
- Ultan McDermott
- Umadevi Veluvolu
- Umut H Toprak
- Valerie Jakrot
- Varsha Tembe
- Vasilisa A Rudneva
- Venkata D Yellapantula
- Venkata D Yellapantula
- Vera B Kaiser
- Veronica Y Sabelnykova
- Victor Reuter
- Vikram Deshpande
- Viktoriya Korchina
- Ville Mustonen
- Vinayak Bhandari
- Vincent Ferretti
- Vincent Huang
- Vincent Huang
- Vincent J Gnanapragasam
- Vincent Khoo
- Vincenzo Corbo
- Vishal S Chandan
- Volker Hovestadt
- W Kimryn Rathmell
- W M Linehan
- Walker Hale
- Wan Choi
- Wanding Zhou
- Wang Liang-Bo
- Weerasinghe Amila
- Wei Jiao
- Wendl Michael C
- Wenyi Wang
- Wenyi Wang
- Wenyi Wang
- Wheeler David A
- William B Isaacs
- William C Faquin
- William Friedman
- William Howat
- William U Meyerson
- Willie Yu
- Winghing Wong
- Wojciech Bazant
- Wolfgang Huber
- Wolfram Klapper
- Xavier Estivill
- Xavier Pivot
- Xiao Xiao
- Xiaobo Li
- Xiaoping Su
- Xiaotong Li
- Xiaotong Yao
- Xing Hua
- Xingmin Liu
- Xinyue Li
- Xiuqing Zhang
- Xiuqing Zheng
- Xose S Puente
- Xuan Le
- Xuanping Zhang
- Xuemei Luo
- Xueqing Zou
- Yan Shi
- Yan Zhang
- Yang Wu
- Yang Yang
- Yann Joly
- Yanxun Xu
- Yao He
- Yasin Senbabaoglu
- Yassen Assenov
- Yasser Riazalhosseini
- Yasuhito Arai
- Yasushi Rino
- Yasushi Totoki
- Yeng Ang
- 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
Electrophysiological Alterations of Pyramidal Cells and Interneurons of the CA1 Region of the Hippocampus in a Novel Mouse Model of Dravet Syndrome
- Author
- Publication venue
- 'Genetics Society of America'
- Publication date
- Field of study
Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy
- Author
- Adissu Hibret
- Aguilar-Pimentel Juan A.
- Ali-Hadji Dalila
- Amarie Oana V.
- Ambrose J. C.
- Andre Philippe
- Arumu gam P.
- Audain Enrique
- Ayadi Abdel
- Beaudet Arthur L.
- Becker Lore
- Berberovic Zorana
- Bevers R.
- Bezginov Alex
- Birling Marie-Christine
- Bleda M.
- Boardman-Pretty F.
- Bohat Ritu
- Bou About Ghina
- Boustred C. R.
- Bower Lynette
- Brandmaier Stefan
- Braun Robert E.
- Brittain H.
- Brown Steve D. M.
- Bunton-Stasyshyn Rosie K. A.
- Bürger Antje
- Calzada-Wack Julia
- Camilleri Susan
- Cater Heather
- Caulder Adam
- Caulfield M. J.
- Champy Marie-France
- Chan G. C.
- Charles Philippe
- Cho Yi-Li
- Christiansen Audrey E.
- Christou Skevoulla
- Clary David
- Cleak James
- Codner Gemma
- Cook Jenn J.
- Creighton Amie
- Cruz Maribelle
- da Silva-Buttkus Patricia
- Dickinson Mary E.
- Duffin Kyle
- D’Souza Abigail
- Ermakova Olga
- Eskandarian Mohammed
- Ferrara Anna
- Flenniken Ann M.
- Fobo Gisela
- Fowler T.
- Frishman Goar
- Fruscoloni Paolo
- Fuchs Helmut
- Gailus-Durner Valerie
- Gallegos Juan J.
- Galter Isabella Rikarda
- Ganguly Milan
- Gao Xiang
- Gardiner Wendy
- Garrett Lillian
- Garza Arturo
- Gaspero Angelina
- Gerlini Raffaele
- Gertsenstein Marina
- Giesert Florian
- Giess A.
- Gilly Arthur
- Goodwin Leslie O.
- Grallert Harald
- Green Jennie R.
- Guo Ruolin
- Görlach Agnes
- Hamblin A.
- Hancock Rhys
- Haseli Mashhadi Hamed
- Heaney Jason D.
- Henderson S.
- Herault Yann
- Hitz Marc-Phillip
- Hrabe de Angelis Martin
- Hsu Chih-Wei
- Huang Ziyue
- Hubbard T. J. P.
- Hy Wang
- Hölter Sabine M.
- Jackson R.
- Jacobs Hugues
- Jacquot Sylvie
- Johnson Jennifer
- Johnson Sara
- Jones L. J.
- Kalaga Sowmya
- Kane Coleen
- Kasperaviciute D.
- Kayikci M.
- Kašpárek Petr
- Kelsey Lois
- Kenyon Janet
- King Ruairidh
- Klein-Rodewald Tanja
- Kousathanas A.
- Lahnstein L.
- Lan Qing
- Lanza Denise G.
- Laurin Valerie
- Leblanc Sophie
- Leigh S. E. A.
- Lengger Christoph
- Leong I. U. S.
- Leuchtenberger Stefanie
- Lintott Lauri
- Liu Zhiwei
- Lloyd K. C. Kent
- Lopez F. J.
- Lorenzo Isabel
- Lowy Jacob P.
- Mackenzie Matthew
- Maleady-Crowe F.
- Mallon Ann-Marie
- Mammano Fabio
- Marschall Susan
- Mason Jeremy
- Mayer-Kuckuk Philipp
- Mayr Daniela
- McElwee Melissa L.
- McEntagart M.
- McFarland Michael
- Mckay Matthew
- McKerlie Colin
- Meehan Terrence F.
- Meziane Hamid
- Miller David
- Miller Gregor
- Minneci F.
- Montrone Corinna
- Moore Michayla A.
- Moutsianas L.
- Mueller M.
- Munoz Fuentes Violeta
- Munson Rebecca
- Murray Steven A.
- Murugaesu N.
- Need A. C.
- Norris Claire
- Nutter Lauryl M. J.
- Odhams C. A.
- Oprea Tudor I.
- O‘Donovan P.
- Parkinson Helen
- Patch C.
- Patel Amit
- Pavlovic Guillaume
- Pereira M. B.
- Pereira Monica
- Perez-Gil D.
- Peterson Kevin A.
- Petrezsélyová Silvia
- Phelps Hayley
- Prochazka Jan
- Pullinger J.
- Qu Dawei
- Rahim T.
- Rasmussen Tara L.
- Rathkolb Birgit
- Rayner Nigel W.
- Rendon A.
- Reynolds Corey L.
- Riet Fabrice
- Roberton Kyle
- Rogers T.
- Roper Willson B.
- Rozman Jan
- Ruepp Andreas
- Salazar Jason
- Samaco Rodney C.
- Sanz-Moreno Adrián
- Savage K.
- Sawant K.
- Schuchbauer Michael
- Scott R. H.
- Seavitt John
- Sedlacek Radislav
- Seisenberger Claudia
- Selloum Mohammed
- Seluke Audrie M.
- Seong Je Kyung
- Shang Xueyuan
- Sharma Sapna
- Shiroishi Toshihiko
- Siddiq A.
- Sieghart A.
- Sleep Gillian
- Smedley Damian
- Smith S. C.
- Sorg Tania
- Sosinsky A.
- Spielmann Nadine
- Stewart Michelle
- Stoeger Claudia
- Stuckey A.
- Svenson Karen L.
- Szkoe-Kovacs Zsombor
- Tamura Masaru
- Tanaka Nobuhiko
- Tanguy M.
- Taylor-Tavares A. L.
- Teboul Lydia
- Teperino Raffaele
- Thomas E. R. A.
- Thompson S. R.
- Tocchini-Valentini Glauco P.
- Tolentino Heather
- Tolentino Todd
- Tondat Sandra
- Tucci A.
- Urban Rachel
- Veeraragaven Surabi
- Vukobradovic Igor
- Wagner Matias
- Ward Christopher S.
- Welland M. J.
- Wells Sara E.
- Wendling Olivia
- Westerberg Henrik
- Westphal Dominik S.
- White Jaqueline K.
- Willett Amelia M.
- Williams E.
- Willis Brandon J.
- Witkowska K.
- Wolf Cordula
- Wolf Eckhard
- Wong Leeyean
- Wood Joshua A.
- Wood S. M.
- Wotton Janine M.
- Wurst Wolfgang
- Xu Catherine
- Xu Ying
- Yoshiki Atsushi
- Zapf Lilly
- Zeggini Eleftheria
- Östereicher Manuela A.
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2022
- Field of study
Clinical presentation of congenital heart disease is heterogeneous, making identification of the disease-causing genes and their genetic pathways and mechanisms of action challenging. By using in vivo electrocardiography, transthoracic echocardiography and microcomputed tomography imaging to screen 3,894 single-gene-null mouse lines for structural and functional cardiac abnormalities, here we identify 705 lines with cardiac arrhythmia, myocardial hypertrophy and/or ventricular dilation. Among these 705 genes, 486 have not been previously associated with cardiac dysfunction in humans, and some of them represent variants of unknown relevance (VUR). Mice with mutations in Casz1, Dnajc18, Pde4dip, Rnf38 or Tmem161b genes show developmental cardiac structural abnormalities, with their human orthologs being categorized as VUR. Using UK Biobank data, we validate the importance of the DNAJC18 gene for cardiac homeostasis by showing that its loss of function is associated with altered left ventricular systolic function. Our results identify hundreds of previously unappreciated genes with potential function in congenital heart disease and suggest causal function of five VUR in congenital heart disease
Recommended from our members
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- Author
- Aaltonen Lauri A.
- 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
- Alvarez Eva G.
- Amary Fernanda
- Amin Samirkumar B.
- Aminou Brice
- Ammerpohl Ole
- Anderson Matthew J.
- Ang Yeng
- Antonello Davide
- Anur Pavana
- Aparicio Samuel
- Appelbaum Elizabeth L.
- Arai Yasuhito
- Aretz Axel
- Arihiro Koji
- Ariizumi Shun-ichi
- Armenia Joshua
- Arnau Gisela Mir
- Arnould Laurent
- Asa Sylvia
- Assenov Yassen
- Atwal Gurnit
- Aukema Sietse
- Auman J. Todd
- Aure Miriam R.
- Awadalla Philip
- Aymerich Marta
- Bader Gary D.
- Baez-Ortega Adrian
- Bailey Matthew H.
- Bailey Peter J.
- Balasundaram Miruna
- Balu Saianand
- Bandopadhayay Pratiti
- Banks Rosamonde E.
- Barbi Stefano
- Barbour Andrew P.
- Barenboim Jonathan
- Barnholtz-Sloan Jill
- Barr Hugh
- Barrera Elisabet
- Bartlett John
- Bartolome Javier
- Bassi Claudio
- Bathe Oliver F.
- Baumhoer Daniel
- Bavi Prashant
- Baylin Stephen B.
- Bazant Wojciech
- Beardsmore Duncan
- Beck Timothy A.
- Behjati Sam
- Behren Andreas
- Bell Cindy
- Beltran Sergi
- Benz Christopher
- Berchuck Andrew
- Bergmann Anke K.
- Bergstrom Erik N.
- Berman Benjamin P.
- Berney Daniel M.
- Bernhart Stephan H.
- Beroukhim Rameen
- Berrios Mario
- Bersani Samantha
- Bertl Johanna
- Betancourt Miguel
- Bhandari Vinayak
- Bhosle Shriram G.
- Biankin Andrew V.
- Bieg Matthias
- Bigner Darell
- Bin Zhu
- Binder Hans
- Birney Ewan
- Birrer Michael
- Biswas Nidhan K.
- Bjerkehagen Bodil
- Bodenheimer Tom
- Boice Lori
- Bonizzato Giada
- Boot Arnoud
- Bootwalla Moiz S.
- Borg Ake
- Borkhardt Arndt
- Boroevich Keith A.
- Borozan Ivan
- Borst Christoph
- Bosenberg Marcus
- Bosio Mattia
- Boultwood Jacqueline
- Bourque Guillaume
- Boutros Paul C.
- Bova G. Steven
- Bowen David T.
- Bowlby Reanne
- Bowtell David D. L.
- Boyault Sandrine
- Boyce Rich
- Boyd Jeffrey
- Brazma Alvis
- Brennan Paul
- Brewer Daniel S.
- Brinkman Arie B.
- Bristow Robert G.
- Broaddus Russell R.
- Brock Jane E.
- Brock Malcolm
- Broeks Annegien
- Brooks Angela N.
- Brooks Denise
- Brors Benedikt
- Brunak Søren
- Bruxner Timothy J. C.
- Bruzos Alicia L.
- Buchanan Alex
- Buchhalter Ivo
- Buchholz Christiane
- Bullman Susan
- Burke Hazel
- Burkhardt Birgit
- Burns Kathleen H.
- Busanovich John
- Bustamante Carlos D.
- Butler Adam P.
- Butte Atul J.
- Byrne Niall J.
- Børresen-Dale Anne-Lise
- Caesar-Johnson Samantha J.
- Cafferkey Andy
- Cahill Declan
- Calabrese Claudia
- Caldas Carlos
- Calvo Fabien
- Camacho Niedzica
- Campbell Peter J.
- Campo Elias
- Cantù Cinzia
- Cao Shaolong
- Carey Thomas E.
- Carlevaro-Fita Joana
- Carlsen Rebecca
- Cataldo Ivana
- Cazzola Mario
- Cebon Jonathan
- Cerfolio Robert
- Chadwick Dianne E.
- Chakravarty Dimple
- Chalmers Don
- Chan Calvin Wing Yiu
- Chan Kin
- Chan-Seng-Yue Michelle
- Chandan Vishal S.
- Chang David K.
- Chanock Stephen J.
- Chantrill Lorraine A.
- Chateigner Aurélien
- Chatterjee Nilanjan
- Chayama Kazuaki
- Chen Hsiao-Wei
- Chen Jieming
- Chen Ken
- Chen Yiwen
- Chen Zhaohong
- Cherniack Andrew D.
- Chien Jeremy
- Chiew Yoke-Eng
- Chin Suet-Feung
- Chiotti Kami
- Cho Juok
- Cho Sunghoon
- Choi Jung Kyoon
- Choi Wan
- Chomienne Christine
- Chong Zechen
- Choo Su Pin
- Chou Angela
- Christ Angelika N.
- Christie Elizabeth L.
- Chuah Eric
- Cibulskis Carrie
- Cibulskis Kristian
- Cingarlini Sara
- Clapham Peter
- Claviez Alexander
- Cleary Sean
- Cloonan Nicole
- Cmero Marek
- Collins Colin C.
- Connor Ashton A.
- Cooke Susanna L.
- Cooper Colin S.
- Cope Leslie
- Corbo Vincenzo
- Cordes Matthew G.
- Cordner Stephen M.
- Cortés-Ciriano Isidro
- Covington Kyle
- Cowin Prue A.
- Craft Brian
- Craft David
- Creason Allison
- Creighton Chad J.
- Cun Yupeng
- Curley Erin
- Cutcutache Ioana
- Czajka Karolina
- Czerniak Bogdan
- Dagg Rebecca A.
- Danilova Ludmila
- Davi Maria Vittoria
- Davidson Natalie R.
- Davies Helen
- Davis Ian J.
- Davis-Dusenbery Brandi N.
- Dawson Kevin J.
- De Bono Johann S.
- De La Vega Francisco M.
- De Paoli-Iseppi Ricardo
- deFazio Anna
- Defreitas Timothy
- Dei Tos Angelo P.
- Delaneau Olivier
- Demchok John A.
- Demeulemeester Jonas
- Demidov German M.
- Demircioğlu Deniz
- Dennis Nening M.
- Denroche Robert E.
- Dentro Stefan C.
- Desai Nikita
- Deshpande Vikram
- Deshwar Amit G.
- Desmedt Christine
- Deu-Pons Jordi
- Dhalla Noreen
- Dhani Neesha C.
- Dhingra Priyanka
- Dhir Rajiv
- Diamanti Klev
- DiBiase Anthony
- Ding Li
- Ding Shuai
- Dinh Huy Q.
- Dirix Luc
- Doddapaneni HarshaVardhan
- Dong Guanlan
- Donmez Nilgun
- Dow Michelle T.
- Drapkin Ronny
- Drechsel Oliver
- Drews Ruben M.
- Dudderidge Tim
- Dueso-Barroso Ana
- Dunford Andrew J.
- Dunn Michael
- Dursi Lewis Jonathan
- Duthie Fraser R.
- Dutton-Regester Ken
- Eagles Jenna
- Easton Douglas F.
- Edmonds Stuart
- Edwards Paul A.
- Edwards Sandra E.
- Eeles Rosalind A.
- Ehinger Anna
- Eils Juergen
- Eils Roland
- El-Naggar Adel
- Eldridge Matthew
- Ellrott Kyle
- Erkek Serap
- Escaramis Georgia
- Espiritu Shadrielle M. G.
- Estivill Xavier
- Etemadmoghadam Dariush
- Eyfjord Jorunn E.
- Faltas Bishoy M.
- Fan Daiming
- Fan Yu
- Faquin William C.
- Farcas Claudiu
- Fassan Matteo
- Fatima Aquila
- Favero Francesco
- Fayzullaev Nodirjon
- Felau Ina
- Fereday Sian
- Ferguson Martin L.
- Ferretti Vincent
- Feuerbach Lars
- Field Matthew A.
- Fink J. Lynn
- Finocchiaro Gaetano
- Fisher Cyril
- Fittall Matthew W.
- Fitzgerald Anna
- Fitzgerald Rebecca C.
- Flanagan Adrienne M.
- Fleshner Neil E.
- Flicek Paul
- Foekens John A.
- Foltz Steven
- Fong Kwun M.
- Fonseca Nuno A.
- Foster Christopher S.
- Fox Natalie S.
- Fraser Michael
- Frazer Scott
- Frenkel-Morgenstern Milana
- Friedman William
- Frigola Joan
- Fronick Catrina C.
- Fujimoto Akihiro
- Fujita Masashi
- Fukayama Masashi
- Fulton Lucinda A.
- Fulton Robert S.
- Furuta Mayuko
- Futreal P. Andrew
- Füllgrabe Anja
- Gabriel Stacey B.
- Gallinger Steven
- Gambacorti-Passerini Carlo
- Gao Jianjiong
- Gao Shengjie
- Garraway Levi
- Garred Øystein
- Garrison Erik
- Garsed Dale W.
- Gehlenborg Nils
- Gelpi Josep L. l.
- George Joshy
- Gerhard Daniela S.
- Gerhauser Clarissa
- Gershenwald Jeffrey E.
- Gerstein Mark B.
- Gerstung Moritz
- Getz Gad
- Ghori Mohammed
- Ghossein Ronald
- Giama Nasra H.
- Gibbs Richard A.
- Gill Anthony J.
- Gill Pelvender
- Giri Dilip D.
- Glodzik Dominik
- Gnanapragasam Vincent J.
- Goebler Maria Elisabeth
- Goldman Mary J.
- Gomez Carmen
- Gonzalez Santiago
- Gonzalez-Perez Abel
- Gordenin Dmitry A.
- Gossage James
- Gotoh Kunihito
- Govindan Ramaswamy
- Grabau Dorthe
- Graham Janet S.
- Grant Robert C.
- Green Anthony R.
- Green Eric
- Greger Liliana
- Grehan Nicola
- Grimaldi Sonia
- Grimmond Sean M.
- Grossman Robert L.
- Grundhoff Adam
- Gundem Gunes
- Guo Qianyun
- Gupta Manaswi
- Gupta Shailja
- Gut Ivo G.
- Gut Marta
- Göke Jonathan
- Ha Gavin
- Haake Andrea
- Haan David
- Haas Siegfried
- Haase Kerstin
- Haber James E.
- Habermann Nina
- Hach Faraz
- Haider Syed
- Hale Walker
- Hama Natsuko
- Hamdy Freddie C.
- Hamilton Anne
- Hamilton Mark P.
- Han Leng
- Hanna George B.
- Hansmann Martin
- Haradhvala Nicholas J.
- Harismendy Olivier
- Harliwong Ivon
- Harmanci Arif O.
- Harrington Eoghan
- Hasegawa Takanori
- Haussler David
- Hawkins Steve
- Hayami Shinya
- Hayashi Shuto
- Hayes D. Neil
- Hayes Stephen J.
- Hayward Nicholas K.
- Hazell Steven
- He Yao
- Heath Allison P.
- Heath Simon C.
- Hedley David
- Hegde Apurva M.
- Heiman David I.
- Heinold Michael C.
- Heins Zachary
- Heisler Lawrence E.
- Hellstrom-Lindberg Eva
- Helmy Mohamed
- Heo Seong Gu
- Hepperla Austin J.
- Heredia-Genestar José María
- Herrmann Carl
- Hersey Peter
- Hess Julian M.
- Hilmarsdottir Holmfridur
- Hinton Jonathan
- Hirano Satoshi
- Hiraoka Nobuyoshi
- Hoadley Katherine A.
- Hobolth Asger
- Hodzic Ermin
- Hoell Jessica I.
- Hoffmann Steve
- Hofmann Oliver
- Holbrook Andrea
- Holik Aliaksei Z.
- Hollingsworth Michael A.
- Holmes Oliver
- Holt Robert A.
- Hong Chen
- Hong Eun Pyo
- Hong Jongwhi H.
- Hooijer Gerrit K.
- Hornshøj Henrik
- Hosoda Fumie
- Hou Yong
- Hovestadt Volker
- Howat William
- Hoyle Alan P.
- Hruban Ralph H.
- Hu Jianhong
- Hu Taobo
- Hua Xing
- Huang Kuan-lin
- Huang Mei
- Huang Mi Ni
- Huang Vincent
- Huang Yi
- Huber Wolfgang
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- Xi Liu
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- Xiao Xiao
- Xing Rui
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- Xue Hong
- Yachida Shinichi
- Yakneen Sergei
- Yamaguchi Rui
- Yamaguchi Takafumi N.
- Yamamoto Masakazu
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- Yang Fan
- Yang Huanming
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- Yang Yang
- Yao Xiaotong
- Yaspo Marie-Laure
- Yates Lucy
- Yau Christina
- Ye Chen
- Ye Kai
- Yellapantula Venkata D.
- Yoon Christopher J.
- Yoon Sung-Soo
- Yousif Fouad
- Yu Jun
- Yu Kaixian
- Yu Willie
- Yu Yingyan
- Yuan Ke
- Yuan Yuan
- Yuen Denis
- Yugawa Takashi
- Yung Christina K.
- Zaikova Olga
- Zamora Jorge
- Zapatka Marc
- Zenklusen Jean C.
- Zenz Thorsten
- Zeps Nikolajs
- Zhang Cheng-Zhong
- Zhang Fan
- Zhang Hailei
- Zhang Hongwei
- Zhang Hongxin
- Zhang Jiashan
- Zhang Jing
- Zhang Junjun
- Zhang Xiuqing
- Zhang Xuanping
- Zhang Yan
- Zhang Zemin
- Zhao Zhongming
- Zheng Liangtao
- Zheng Xiuqing
- Zhou Wanding
- Zhou Yong
- Zhu Hongtu
- Zhu Jingchun
- Zhu Shida
- Zou Lihua
- Zou Xueqing
- Publication venue
- Nature Communications
- Publication date
- 21/09/2020
- 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
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
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- Shumpei Ishikawa
- Shun-Ichi Ariizumi
- Shuto Hayashi
- Sian Fereday
- Siegfried Haas
- Sietse Aukema
- Siliang Li
- Simon C Heath
- Simon L Parsons
- Simon Mayes
- Simon Tavaré
- Simpson Jared T
- Singer Ma
- Sinisa Ivkovic
- Sissel Juul
- Solomon I Shorser
- Sonia Grimaldi
- Sonia Puig
- Stacey B Gabriel
- Stefan C Dentro
- Stefan G Stark
- Stefan M Pfister
- Stefan Schreiber
- Stefania Tommasi
- Stefano Barbi
- Stefano Serra
- Stephan H Bernhart
- Stephan Ossowski
- Stephan Ossowski
- Stephan Stilgenbauer
- Stephan Wolf
- Stephanie Sungalee
- Stephen B Baylin
- Stephen H Kazakoff
- Stephen J Chanock
- Stephen J Hayes
- Stephen M Cordner
- Stephenie D Prokopec
- Steve Hawkins
- Steve Hoffmann
- Steven A Roberts
- Steven E Schumacher
- Steven Foltz
- Steven G Rozen
- Steven Gallinger
- Steven Hazell
- Steven J M Jones
- Steven J Newhouse
- Steven Van Laere
- Stian Knappskog
- Stuart Edmonds
- Stuart R Jefferys
- Su Pin Choo
- Subhajit Sengupta
- Sue Merson
- Suet-Feung Chin
- Sultan T Al-Sedairy
- Sung-Min Ahn
- Sung-Soo Yoon
- Sunghoon Cho
- Sunil R Lakhani
- Suresh Ramalingam
- Susan Bullman
- Susanna L Cooke
- Sushant Kumar
- Sushant Kumar
- Suyash S Shringarpure
- Syed Haider
- Sylvia Asa
- Søren Brunak
- Takafumi N Yamaguchi
- Takafumi N Yamaguchi
- Takanori Hasegawa
- Takashi Yugawa
- Takashi Yugawa
- Takuji Okusaka
- Tal Shmaya
- Tannistha Nandi
- Taobo Hu
- Taobo Hu
- Tapio Visakorpi
- Tara J Skelly
- Tari A King
- Tatsuhiko Tsunoda
- Tatsuhiro Shibata
- Ted R Hupp
- Tetsuo Ushiku
- Theodorus Van der Kwast
- Thomas E Carey
- Thomas J Hudson
- Thomas J Matthew
- Thomas J Mitchell
- Thorsten Schlomm
- Thorsten Zenz
- Tian Xia
- Tim Dudderidge
- Tim Ley
- Timothy A Beck
- Timothy Defreitas
- Timothy J C Bruxner
- Timothy J Underwood
- Tina Wong
- Tirso Pons
- Tobias Madsen
- Tobias Rausch
- Todd A Johnson
- Todd D Pihl
- Tom Bodenheimer
- Tom Mikkelsen
- Tom Roques
- Tomas J Tanskanen
- Tomas Marques-Bonet
- Tomoko Urushidate
- Torill Sauer
- Toru Nakamura
- Treasa A McPherson
- Troy Shelton
- Tsun-Po Yang
- Ultan McDermott
- Umadevi Veluvolu
- Umut H Toprak
- Valerie Jakrot
- Varsha Tembe
- Vasilisa A Rudneva
- Venkata D Yellapantula
- Venkata D Yellapantula
- Vera B Kaiser
- Veronica Y Sabelnykova
- Victor Reuter
- Vikram Deshpande
- Viktoriya Korchina
- Ville Mustonen
- Vinayak Bhandari
- Vincent Ferretti
- Vincent Huang
- Vincent Huang
- Vincent J Gnanapragasam
- Vincent Khoo
- Vincenzo Corbo
- Vishal S Chandan
- Volker Hovestadt
- W Kimryn Rathmell
- W M Linehan
- Walker Hale
- Wan Choi
- Wanding Zhou
- Wang Liang-Bo
- Weerasinghe Amila
- Wei Jiao
- Wendl Michael C
- Wenyi Wang
- Wenyi Wang
- Wenyi Wang
- Wheeler David A
- William B Isaacs
- William C Faquin
- William Friedman
- William Howat
- William U Meyerson
- Willie Yu
- Winghing Wong
- Wojciech Bazant
- Wolfgang Huber
- Wolfram Klapper
- Xavier Estivill
- Xavier Pivot
- Xiao Xiao
- Xiaobo Li
- Xiaoping Su
- Xiaotong Li
- Xiaotong Yao
- Xing Hua
- Xingmin Liu
- Xinyue Li
- Xiuqing Zhang
- Xiuqing Zheng
- Xose S Puente
- Xuan Le
- Xuanping Zhang
- Xuemei Luo
- Xueqing Zou
- Yan Shi
- Yan Zhang
- Yang Wu
- Yang Yang
- Yann Joly
- Yanxun Xu
- Yao He
- Yasin Senbabaoglu
- Yassen Assenov
- Yasser Riazalhosseini
- Yasuhito Arai
- Yasushi Rino
- Yasushi Totoki
- Yeng Ang
- 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
- 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
Comprehensive molecular profiling of lung adenocarcinoma
- Author
- Akbani Rehan
- Aksoy B. Arman
- Albert Monique
- Amos Christopher I.
- Asiedu Michael K.
- Auman J. Todd
- Baboud Julien
- Balasundaram Miruna
- Balu Saianand
- Bartlett John M. S.
- Bauer Thomas
- Baylin Stephen B.
- Baylin Stephen B.
- Beer David G.
- Behera Madhusmita
- Benz Christopher C.
- Berger Alice H.
- Beroukhim Rameen
- Bodenheimer Tom
- Boice Lori
- Bonomi Philip
- Bootwalla Moiz S.
- Borgia Jeffrey A.
- Bowman Rayleen V.
- Boyd Jeff
- Brock Malcolm V.
- Brooks Angela N.
- Brooks Angela N.
- Broom Bradley M.
- Brown Jennifer
- Bryant Ayesha
- Buda Elizabeth
- Burks Eric
- Butterfield Yaron S. N.
- Byers Lauren Averett
- Byers Lauren Averett
- Cabanski Christopher
- Campbell Joshua D.
- Campbell Joshua D.
- Carlsen Rebecca
- Carter Scott L.
- Cerfolio Robert
- Chen Peng-Chieh
- Cheney Richard
- Cheney Richard
- Cherniack Andrew D.
- Cherniack Andrew D.
- Chin Lynda
- Chin Lynda
- Chmielecki Juliann
- Chmielecki Juliann
- Cho Juok
- Chu Andy
- Chu Andy
- Chuah Eric
- Cibulskis Kristian
- Ciriello Giovanni
- Clarke Belinda
- Clarke Belinda
- Collisson Eric A.
- Cope Leslie
- Cope Leslie
- Creighton Chad J.
- Creighton Chad J.
- Curley Erin
- Czerwinski Christine
- Dacic Sanja
- Dacic Sanja
- Dang Huy Quoc Thinh
- Danilova Ludmila
- Danilova Ludmila
- Davidsen Tanja
- Demchok John A.
- Dhalla Noreen
- Dhir Rajiv
- Diao Lixia
- DiCara Daniel
- Dienemann Hendrik
- Ding Li
- Ding Li
- Dolzhanskiy Oleg
- Dresdner Gideon
- Duhig Edwina
- Duhig Edwina
- Eckman John
- Egea Sophie
- Farver Carol
- Farver Carol
- Fedosenko Konstantin V.
- Flieder Douglas
- Fong Kwun M.
- Fronick Catrina C.
- Fulton Lucinda L.
- Fulton Robert
- Funkhouser William K.
- Funkhouser William K.
- Gabriel Stacey B.
- Gabriel Stacey B.
- Gabrielson Edward
- Gal Anthony
- Gao Jianjiong
- Gardner Johanna
- Garraway Levi
- Gaudioso Carmelo
- Gehlenborg Nils
- Getz
- Getz Gad
- Getz Gad
- Getz Gad
- Gomez-Fernandez Carmen
- Goparaju Chandra
- Govindan Ramaswamy
- Govindan Ramaswamy
- Gross Benjamin
- Guin Ranabir
- Hadjipanayis Angela
- Hadjipanayis Angela
- Hajek Richard
- Hammerman Peter S.
- Haussler David
- Hayes D. Neil
- Hayes D. Neil
- Hayes D. Neil
- Heiman David
- Helman Elena
- Herbert Lynn
- Herman James G.
- Hernandez Bryan
- Hernandez Bryan
- Heymach John V.
- Heymach John V.
- Hirst Carrie
- Hoadley Katherine A.
- Hoadley Katherine A.
- Hodis Eran
- Holt Robert A.
- Holway Antonia
- Hoyle Alan P.
- Huang Mei
- Huelsenbeck-Dill Lori
- Hunter Lindy
- Iacocca Mary
- Illei Peter
- Illei Peter
- Imielinski Marcin
- Jefferys Stuart R.
- Jensen Mark A.
- Jones Corbin D.
- Jones Steven J. M.
- Juhl Hartmut
- Jurisica Igor
- Kahn Ari B.
- Kandoth Cyriac
- Khan Khurram Z.
- Kim Jaegil
- Kimes Patrick K.
- Kodeeswaran Sugy
- Kohl Bernard
- Kosari Farhad
- Kucherlapati Raju
- Kucherlapati Raju
- Kwiatkowski David
- Ladanyi Marc
- Ladanyi Marc
- Lai Philip H.
- Laird Peter W.
- Laird Peter W.
- Lander Eric S.
- Lau Kevin
- Lawrence Michael S.
- Lawrence Michael S.
- Lee Beverly
- Lee Darlene
- Lee Semin
- Lee William
- Lee William
- Letovanec Igor
- Li Haiyan I.
- Lichtenstein Lee
- Lin Pei
- Liptay Michael J.
- Liu Jinze
- Liu Wenbin
- Lu Yiling
- Ma Singer
- Ma Singer
- Maglinte Dennis T.
- Mahadeshwar Harshad S.
- Maher Christopher A.
- Mallard William
- Mallery David
- Mardis Elaine
- Marra Marco A.
- Marron J. S.
- Mayo Michael
- McDonald Sandra
- McLellan Michael D.
- Meister Michael
- Meng Shaowu
- Mesirov Jill
- Mesirov Jill
- Meyers Bryan
- Meyerson Matthew
- Meyerson Matthew
- Mieczkowski Piotr A.
- Miller Christopher A.
- Mills Gordon B.
- Moiseenko Fedor
- Moore Richard A.
- Morris Scott
- Morrison Carl
- Muley Thomas R.
- Mungall Andrew J.
- Myers Jerome B.
- Nazaire Marc-Danie
- Nemirovich-Danchenko Elena
- Noble Michael S.
- Onofrio Robert C.
- Owusu-Sarpong Yvonne
- Ozenberger Bradley A.
- Pantazi Angeliki
- Parfenov Michael
- Parfitt Jeremy
- Park Peter J.
- Parker Joel S.
- Parker Joel S.
- Pass Harvey
- Patrick Kwok Shing Ng
- Paulauskis Joseph
- Pedamallu Chandra Sekhar
- Peifer Martin
- Pennell Nathan A.
- Penny Robert
- Perou Charles M.
- Perou Charles M.
- Peters Solange
- Petrelli Nicholas
- Pool Mark
- Pot David A.
- Potapova Olga
- Prins Jan F.
- Protopopov Alexei
- Rabeno Brenda
- Radenbaugh Amie
- Radenbaugh Amie
- Ramalingam Suresh S.
- Rathmell W. Kimryn
- Raymond Daniel P.
- Rekhtman Natasha
- Rekhtman Natasha
- Ren Xiaojia
- Reva Boris
- Richards William G.
- Rieger-Christ Kimberly
- Roach Jeffrey
- Robertson A. Gordon
- Robertson Gordon
- Robinson Jim
- Rogers Kristen
- Rosenberg Mara
- Rosenberg Mara
- Rosenberg Mara
- Rotin Daniil
- Rusch Valerie W.
- Saksena Gordon
- Saksena Gordon
- Salazar Ashley Hill
- Saller Charles
- Sam Ng
- Sander Chris
- Sandusky George
- Santoso Netty
- Schein Jacqueline E.
- Schnabel Philipp A.
- Schneider Frank
- Schultz Nikolaus
- Schultz Nikolaus
- Schumacher Steven E.
- Sekhon Harmanjatinder
- Seshan Venkatraman E.
- Seth Sahil
- Shaw Kenna R. Mills
- Shelton Troy
- Shen Ronglai
- Shen Ronglai
- Sheth Margi
- Shi Yan
- Shin James
- Sica Gabriel
- Sica Gabriel
- Siegfried Jill M.
- Simons Janae V.
- Singh Darshan
- Sinha Rileen
- Sinha Rileen
- Sipahimalani Payal
- Snyder Eric E.
- Sofia Heidi J.
- Soloway Matthew G.
- Song Xingzhi
- Sougnez Carrie
- Sougnez Carrie
- Sougnez Carrie
- Spellman Paul T.
- Srinivasan Deepak
- Stewart Chip
- Stuart Joshua M.
- Stuart Joshua M.
- Suh James
- Suh James
- Sullivan Travis
- Sumer S. Onur
- Tam Angela
- Tan Donghui
- Tang Jiabin
- Tarnuzzer Roy
- Tarvin Katherine
- Taylor Barry S.
- Thiessen Nina
- Thorne Leigh B.
- Thorvaldsdottir Helga
- Travis William D.
- Travis William D.
- Travis William D.
- Triche Timothy, Jr.
- Trusty Dante
- Tsao Ming-Sound
- Tsao Ming-Sound
- Van Den Berg David J.
- Varhol Richard
- Veluvolu Umadevi
- Voet Douglas
- Voronina Olga
- Wang Jing
- Wang Zhining
- Waring Scot
- Watson Mark A.
- Weaver JoEllen
- Weinhold Nils
- Weinstein John N.
- Weinstein John N.
- Weisenberger Daniel J.
- Weisenberger Daniel J.
- Wendl Michael C.
- Wheeler David
- Wigle Dennis A.
- Wigle Dennis A.
- Wilkerson Matthew D.
- Wilkerson Matthew D.
- Williamson Christina
- Wilson Richard K.
- Windsor Morgan
- Wu Junyuan
- Wye Natasja
- Xu Andrew Wei
- Yang Ian A.
- Yang Liming
- Yang Lixing
- Yau Christina
- Ye Kai
- Yousem Samuel A.
- Zack Travis
- Zakowski Maureen
- Zaytseva Irina
- Zenklusen Jean Claude
- Zhang Hailei
- Zhang Jianhua
- Zhang Jianhua
- Zhu Jingchun
- Zippile Paul
- Zou Lihua
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/06/2013
- Field of study
Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen(mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesisclose24