Publications

Authors:

Matthew H, Bailey; William U, Meyerson; Lewis Jonathan, Dursi; Liang-Bo, Wang; Guanlan, Dong; Wen-Wei, Liang; Amila, Weerasinghe; Shantao, Li; Sean, Kelso; Gordon, Saksena; Kyle, Ellrott; Michael C, Wendl; David A, Wheeler; Gad, Getz; Jared T, Simpson; Mark B, Gerstein; Ding, ; Akbani, Lirehan; Anur, Pavana; H Bailey, Matthew; Buchanan, Alex; Chiotti, Kami; Covington, Kyle; Creason, Allison; Ding, Li; Ellrott, Kyle; Fan, Yu; Foltz, Steven; Getz, Gad; Hale, Walker; Haussler, David; M Hess, Julian; M Hutter, Carolyn; Kandoth, Cyriac; Kasaian, Katayoon; Kasapi, Melpomeni; Larson, Dave; Leshchiner, Ignaty; Letaw, John; Ma, Singer; D McLellan, Michael; Men, Yifei; B Mills, Gordon; Niu, Beifang; Peto, Myron; Radenbaugh, Amie; M Reynolds, Sheila; Saksena, Gordon; Sofia, Heidi; Stewart, Chip; J Struck, Adam; M Stuart, Joshua; Wang, Wenyi; N Weinstein, John; A Wheeler, David; K Wong, Christopher; Xi, Liu; Ye, Kai; H Bailey, Matthew; Niu, Beifang; Bieg, Matthias; C Boutros, Paul; Buchhalter, Ivo; P Butler, Adam; Chen, Ken; Chong, Zechen; Ding, Li; Drechsel, Oliver; Jonathan Dursi, Lewis; Eils, Roland; Ellrott, Kyle; G Espiritu, Shadrielle M; Fan, Yu; S Fulton, Robert; Gao, Shengjie; L Gelpi, Josep L; B Gerstein, Mark; Getz, Gad; Gonzalez, Santiago; G Gut, Ivo; Hach, Faraz; C Heinold, Michael; M Hess, Julian; Hinton, Jonathan; Hu, Taobo; Huang, Vincent; Huang, Yi; Hutter, Barbara; R Jones, David; Jung, Jongsun; Jäger, Natalie; Kim, Hyung-Lae; Kleinheinz, Kortine; Kumar, Sushant; Kumar, Yogesh; M Lalansingh, Christopher; Leshchiner, Ignaty; Letunic, Ivica; Livitz, Dimitri; Z Ma, Eric; E Maruvka, Yosef; Jay Mashl, R; D McLellan, Michael; Menzies, Andrew; Milovanovic, Ana; Muhlig Nielsen, Morten; Ossowski, Stephan; Paramasivam, Nagarajan; Skou Pedersen, Jakob; D Perry, Marc; Puiggròs, Montserrat; M Raine, Keiran; Rheinbay, Esther; Royo, Romina; Cenk Sahinalp, S; Saksena, Gordon; Sarrafi, Iman; Schlesner, Matthias; T Simpson, Jared; Stebbings, Lucy; Stewart, Chip; D Stobbe, Miranda; W Teague, Jon; Tiao, Grace; Torrents, David; A Wala, Jeremiah; Wang, Jiayin; Wang, Wenyi; M Waszak, Sebastian; Weischenfeldt, Joachim; C Wendl, Michael; Werner, Johannes; Wu, Zhenggang; Xue, Hong; Yakneen, Sergei; N Yamaguchi, Takafumi; Ye, Kai; D Yellapantula, Venkata; K Yung, Christina; Zhang, Junjun; A Aaltonen, Lauri; Abascal, Federico; Abeshouse, Adam; Aburatani, Hiroyuki; J Adams, David; Agrawal, Nishant; Soo Ahn, Keun; Ahn, Sung-Min; Aikata, Hiroshi; Akbani, Rehan; C Akdemir, Kadir; Al-Ahmadie, Hikmat; T Al-Sedairy, Sultan; Al-Shahrour, Fatima; Alawi, Malik; Albert, Monique; Aldape, Kenneth; B Alexandrov, Ludmil; Ally, Adrian; Alsop, Kathryn; G Alvarez, Eva; Amary, Fernanda; B Amin, Samirkumar; Aminou, Brice; Ammerpohl, Ole; J Anderson, Matthew; Ang, Yeng; Antonello, Davide; Anur, Pavana; Aparicio, Samuel; L Appelbaum, Elizabeth; Arai, Yasuhito; Aretz, Axel; Arihiro, Koji; Ariizumi, Shun-Ichi; Armenia, Joshua; Arnould, Laurent; Asa, Sylvia; Assenov, Yassen; Atwal, Gurnit; Aukema, Sietse; Todd Auman, J; R Aure, Miriam; Awadalla, Philip; Aymerich, Marta; D Bader, Gary; Baez-Ortega, Adrian; H Bailey, Matthew; J Bailey, Peter; Balasundaram, Miruna; Balu, Saianand; Bandopadhayay, Pratiti; E Banks, Rosamonde; Barbi, Stefano; P Barbour, Andrew; Barenboim, Jonathan; Barnholtz-Sloan, Jill; Barr, Hugh; Barrera, Elisabet; Bartlett, John; Bartolome, Javier; Bassi, Claudio; F Bathe, Oliver; Baumhoer, Daniel; Bavi, Prashant; B Baylin, Stephen; Bazant, Wojciech; Beardsmore, Duncan; A Beck, Timothy; Behjati, Sam; Behren, Andreas; Niu, Beifang; Bell, Cindy; Beltran, Sergi; Benz, Christopher; Berchuck, Andrew; K Bergmann, Anke; N Bergstrom, Erik; P Berman, Benjamin; M Berney, Daniel; H Bernhart, Stephan; Beroukhim, Rameen; Berrios, Mario; Bersani, Samantha; Bertl, Johanna; Betancourt, Miguel; Bhandari, Vinayak; G Bhosle, Shriram; V Biankin, Andrew; Bieg, Matthias; Bigner, Darell; Binder, Hans; Birney, Ewan; Birrer, Michael;

Title:

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Year:

2020

Type of item:

Articolo in Rivista

Tipologia ANVUR:

Articolo su rivista

Language:

Inglese

Format:

Elettronico

Referee:

No

Name of journal:

NATURE COMMUNICATIONS

ISSN of journal:

2041-1723

N° Volume:

11

Number or Folder:

1

Page numbers:

1-25

Keyword:

Base Composition; DNA, Intergenic; Databases, Genetic; Exome; Exons; Genome, Human; Humans; Neoplasms; Retrospective Studies; Whole Exome Sequencing; Whole Genome Sequencing; Mutation

Short description of contents:

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.

Product ID:

117576

Handle IRIS:

11562/1029820

Last Modified:

March 6, 2024

Bibliographic citation:

Matthew H, Bailey; William U, Meyerson; Lewis Jonathan, Dursi; Liang-Bo, Wang; Guanlan, Dong; Wen-Wei, Liang; Amila, Weerasinghe; Shantao, Li; Sean, Kelso; Gordon, Saksena; Kyle, Ellrott; Michael C, Wendl; David A, Wheeler; Gad, Getz; Jared T, Simpson; Mark B, Gerstein; Ding, ; Akbani, Lirehan; Anur, Pavana; H Bailey, Matthew; Buchanan, Alex; Chiotti, Kami; Covington, Kyle; Creason, Allison; Ding, Li; Ellrott, Kyle; Fan, Yu; Foltz, Steven; Getz, Gad; Hale, Walker; Haussler, David; M Hess, Julian; M Hutter, Carolyn; Kandoth, Cyriac; Kasaian, Katayoon; Kasapi, Melpomeni; Larson, Dave; Leshchiner, Ignaty; Letaw, John; Ma, Singer; D McLellan, Michael; Men, Yifei; B Mills, Gordon; Niu, Beifang; Peto, Myron; Radenbaugh, Amie; M Reynolds, Sheila; Saksena, Gordon; Sofia, Heidi; Stewart, Chip; J Struck, Adam; M Stuart, Joshua; Wang, Wenyi; N Weinstein, John; A Wheeler, David; K Wong, Christopher; Xi, Liu; Ye, Kai; H Bailey, Matthew; Niu, Beifang; Bieg, Matthias; C Boutros, Paul; Buchhalter, Ivo; P Butler, Adam; Chen, Ken; Chong, Zechen; Ding, Li; Drechsel, Oliver; Jonathan Dursi, Lewis; Eils, Roland; Ellrott, Kyle; G Espiritu, Shadrielle M; Fan, Yu; S Fulton, Robert; Gao, Shengjie; L Gelpi, Josep L; B Gerstein, Mark; Getz, Gad; Gonzalez, Santiago; G Gut, Ivo; Hach, Faraz; C Heinold, Michael; M Hess, Julian; Hinton, Jonathan; Hu, Taobo; Huang, Vincent; Huang, Yi; Hutter, Barbara; R Jones, David; Jung, Jongsun; Jäger, Natalie; Kim, Hyung-Lae; Kleinheinz, Kortine; Kumar, Sushant; Kumar, Yogesh; M Lalansingh, Christopher; Leshchiner, Ignaty; Letunic, Ivica; Livitz, Dimitri; Z Ma, Eric; E Maruvka, Yosef; Jay Mashl, R; D McLellan, Michael; Menzies, Andrew; Milovanovic, Ana; Muhlig Nielsen, Morten; Ossowski, Stephan; Paramasivam, Nagarajan; Skou Pedersen, Jakob; D Perry, Marc; Puiggròs, Montserrat; M Raine, Keiran; Rheinbay, Esther; Royo, Romina; Cenk Sahinalp, S; Saksena, Gordon; Sarrafi, Iman; Schlesner, Matthias; T Simpson, Jared; Stebbings, Lucy; Stewart, Chip; D Stobbe, Miranda; W Teague, Jon; Tiao, Grace; Torrents, David; A Wala, Jeremiah; Wang, Jiayin; Wang, Wenyi; M Waszak, Sebastian; Weischenfeldt, Joachim; C Wendl, Michael; Werner, Johannes; Wu, Zhenggang; Xue, Hong; Yakneen, Sergei; N Yamaguchi, Takafumi; Ye, Kai; D Yellapantula, Venkata; K Yung, Christina; Zhang, Junjun; A Aaltonen, Lauri; Abascal, Federico; Abeshouse, Adam; Aburatani, Hiroyuki; J Adams, David; Agrawal, Nishant; Soo Ahn, Keun; Ahn, Sung-Min; Aikata, Hiroshi; Akbani, Rehan; C Akdemir, Kadir; Al-Ahmadie, Hikmat; T Al-Sedairy, Sultan; Al-Shahrour, Fatima; Alawi, Malik; Albert, Monique; Aldape, Kenneth; B Alexandrov, Ludmil; Ally, Adrian; Alsop, Kathryn; G Alvarez, Eva; Amary, Fernanda; B Amin, Samirkumar; Aminou, Brice; Ammerpohl, Ole; J Anderson, Matthew; Ang, Yeng; Antonello, Davide; Anur, Pavana; Aparicio, Samuel; L Appelbaum, Elizabeth; Arai, Yasuhito; Aretz, Axel; Arihiro, Koji; Ariizumi, Shun-Ichi; Armenia, Joshua; Arnould, Laurent; Asa, Sylvia; Assenov, Yassen; Atwal, Gurnit; Aukema, Sietse; Todd Auman, J; R Aure, Miriam; Awadalla, Philip; Aymerich, Marta; D Bader, Gary; Baez-Ortega, Adrian; H Bailey, Matthew; J Bailey, Peter; Balasundaram, Miruna; Balu, Saianand; Bandopadhayay, Pratiti; E Banks, Rosamonde; Barbi, Stefano; P Barbour, Andrew; Barenboim, Jonathan; Barnholtz-Sloan, Jill; Barr, Hugh; Barrera, Elisabet; Bartlett, John; Bartolome, Javier; Bassi, Claudio; F Bathe, Oliver; Baumhoer, Daniel; Bavi, Prashant; B Baylin, Stephen; Bazant, Wojciech; Beardsmore, Duncan; A Beck, Timothy; Behjati, Sam; Behren, Andreas; Niu, Beifang; Bell, Cindy; Beltran, Sergi; Benz, Christopher; Berchuck, Andrew; K Bergmann, Anke; N Bergstrom, Erik; P Berman, Benjamin; M Berney, Daniel; H Bernhart, Stephan; Beroukhim, Rameen; Berrios, Mario; Bersani, Samantha; Bertl, Johanna; Betancourt, Miguel; Bhandari, Vinayak; G Bhosle, Shriram; V Biankin, Andrew; Bieg, Matthias; Bigner, Darell; Binder, Hans; Birney, Ewan; Birrer, Michael;, Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples «NATURE COMMUNICATIONS» , vol. 11 , n. 1 , 2020 , pp. 1-25

Consulta la scheda completa presente nel repository istituzionale della Ricerca di Ateneo