Zobrazeno 1 - 10
of 18
pro vyhledávání: '"Viraj Deshpande"'
Autor:
Egor Dolzhenko, Ben Weisburd, Kristina Ibañez, Indhu-Shree Rajan-Babu, Christine Anyansi, Mark F. Bennett, Kimberley Billingsley, Ashley Carroll, Samuel Clamons, Matt C. Danzi, Viraj Deshpande, Jinhui Ding, Sarah Fazal, Andreas Halman, Bharati Jadhav, Yunjiang Qiu, Phillip A. Richmond, Christopher T. Saunders, Konrad Scheffler, Joke J. F. A. van Vugt, Ramona R. A. J. Zwamborn, Genomics England Research Consortium, Samuel S. Chong, Jan M. Friedman, Arianna Tucci, Heidi L. Rehm, Michael A. Eberle
Publikováno v:
Genome Medicine, Vol 14, Iss 1, Pp 1-10 (2022)
Abstract Background Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify
Externí odkaz:
https://doaj.org/article/018b5e0870b648eca3506644f3e08453
Autor:
Jens Luebeck, Ceyda Coruh, Siavash R. Dehkordi, Joshua T. Lange, Kristen M. Turner, Viraj Deshpande, Dave A. Pai, Chao Zhang, Utkrisht Rajkumar, Julie A. Law, Paul S. Mischel, Vineet Bafna
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)
Focal copy number amplifications (fCNAs), which drive cancer pathogenicity, arise by a number of mechanisms and can be challenging to call. Here the authors present AmpliconReconstructor for precise and scalable fCNA reconstruction using optical mapp
Externí odkaz:
https://doaj.org/article/f072105319bb4cc08d37a2a5027abc98
Autor:
Utkrisht Rajkumar, Kristen Turner, Jens Luebeck, Viraj Deshpande, Manmohan Chandraker, Paul Mischel, Vineet Bafna
Publikováno v:
iScience, Vol 21, Iss , Pp 428-435 (2019)
Summary: Oncogene amplification is one of the most common drivers of genetic events in cancer, potently promoting tumor development, growth, and progression. The recent discovery that oncogene amplification commonly occurs on extrachromosomal DNA, dr
Externí odkaz:
https://doaj.org/article/26302513220d48faaf6a83ae092393c6
Autor:
Viraj Deshpande, Jens Luebeck, Nam-Phuong D. Nguyen, Mehrdad Bakhtiari, Kristen M. Turner, Richard Schwab, Hannah Carter, Paul S. Mischel, Vineet Bafna
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
Focal amplifications are prevalent in many cancer genomes. Here, the authors present AmpliconArchitect (AA), a computational tool for reconstructing their architecture, and reveal an extrachromosomal origin for focal amplifications, including hybrid
Externí odkaz:
https://doaj.org/article/45e5d01124ae4354be54fd8d47361b1f
Autor:
Kristina Ibañez, James Polke, R Tanner Hagelstrom, Egor Dolzhenko, Dorota Pasko, Ellen Rachel Amy Thomas, Louise C Daugherty, Dalia Kasperaviciute, Katherine R Smith, Zandra C Deans, Sue Hill, Tom Fowler, Richard H Scott, John Hardy, Patrick F Chinnery, Henry Houlden, Augusto Rendon, Mark J Caulfield, Michael A Eberle, Ryan J Taft, Arianna Tucci, Ellen M McDonagh, Antonio Rueda, Dimitris Polychronopoulos, Georgia Chan, Heather Angus-Leppan, Kailash P Bhatia, James E Davison, Richard Festenstein, Pietro Fratta, Paola Giunti, Robin Howard, Laxmi Venkata, Matilde Laurá, Meriel McEntagart, Lara Menzies, Huw Morris, Mary M Reilly, Robert Robinson, Elisabeth Rosser, Francesca Faravelli, Anette Schrag, Jonathan M Schott, Thomas T Warner, Nicholas W Wood, David Bourn, Kelly Eggleton, Robyn Labrum, Philip Twiss, Stephen Abbs, Liana Santos, Ghareesa Almheiri, Isabella Sheikh, Jana Vandrovcova, Christine Patch, Ana Lisa Taylor Tavares, Zerin Hyder, Anna Need, Helen Brittain, Emma Baple, Loukas Moutsianas, Viraj Deshpande, Denise L Perry, Subramanian S. Ajay, Aditi Chawla, Vani Rajan, Kathryn Oprych, Angela Douglas, Gill Wilson, Sian Ellard, I Karen Temple, Andrew Mumford, Dom McMullan, Kikkeri Naresh, Frances A Flinter, Jenny C Taylor, Lynn Greenhalgh, William Newman, Paul Brennan, John A Sayer, F Lucy Raymond, Lyn S Chitty, John C. Ambrose, Prabhu Arumugam, Marta Bleda, Freya Boardman-Pretty, Jeanne M. Boissiere, Christopher R. Boustred, Clare E.H. Craig, Anna de Burca, Andrew Devereau, Greg Elgar, Rebecca E. Foulger, Pedro Furió-Tarí, Joanne Hackett, Dina Halai, Angela Hamblin, Shirley Henderson, James Holman, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Melis Kayikci, Lea Lahnstein, Kay Lawson, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Joanne Mason, Michael Mueller, Nirupa Murugaesu, Chris A. Odhams, Daniel Perez-Gil, John Pullinger, Tahrima Rahim, Pablo Riesgo-Ferreiro, Tim Rogers, Mina Ryten, Kevin Savage, Kushmita Sawant, Afshan Siddiq, Alexander Sieghart, Damian Smedley, Alona Sosinsky, William Spooner, Helen E. Stevens, Alexander Stuckey, Razvan Sultana, Simon R. Thompson, Carolyn Tregidgo, Emma Walsh, Sarah A. Watters, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, Suzanne M. Wood, Magdalena Zarowiecki
Publikováno v:
WGS for Neurological Diseases Group 2022, ' Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK : a retrospective diagnostic accuracy and prospective clinical validation study ', The Lancet. Neurology, vol. 21, no. 3, pp. 234-245 . https://doi.org/10.1016/S1474-4422(21)00462-2
BACKGROUND: Repeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who h
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8164460c3f9da55229a5e7da7b58924d
https://eprints.soton.ac.uk/455528/
https://eprints.soton.ac.uk/455528/
Autor:
Jens Luebeck, Sandeep Namburi, Paul S. Mischel, Roel G.W. Verhaak, Howard Y. Chang, Hoon Kim, Kristen M. Turner, Samirkumar B. Amin, Vineet Bafna, Eun Hee Yi, Sihan Wu, Johannes H. Schulte, Nam-Phuong Nguyen, Utkrisht Rajkumar, Francesca Menghi, Anton G. Henssen, Viraj Deshpande, Christine R. Beck, Amit D. Gujar, Jihe Liu
Publikováno v:
Nature genetics
Kim, H, Nguyen, N-P, Turner, K, Wu, S, Gujar, A D, Luebeck, J, Liu, J, Deshpande, V, Rajkumar, U, Namburi, S, Amin, S B, Yi, E, Menghi, F, Schulte, J H, Henssen, A G, Chang, H Y, Beck, C R, Mischel, P S, Bafna, V & Verhaak, R G W 2020, ' Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers ', Nature Genetics, vol. 52, no. 9, pp. 891-897 . https://doi.org/10.1038/s41588-020-0678-2
Nature Genetics, 52(9), 891-897. Nature Publishing Group
Kim, H, Nguyen, N-P, Turner, K, Wu, S, Gujar, A D, Luebeck, J, Liu, J, Deshpande, V, Rajkumar, U, Namburi, S, Amin, S B, Yi, E, Menghi, F, Schulte, J H, Henssen, A G, Chang, H Y, Beck, C R, Mischel, P S, Bafna, V & Verhaak, R G W 2020, ' Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers ', Nature Genetics, vol. 52, no. 9, pp. 891-897 . https://doi.org/10.1038/s41588-020-0678-2
Nature Genetics, 52(9), 891-897. Nature Publishing Group
Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution1–3, but its frequency and clinical impact are unclear. Here we show, using computational analysis of whole-genome sequencing data
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dbba3c526ec72965936a1e0f21b09a82
http://europepmc.org/articles/PMC7484012
http://europepmc.org/articles/PMC7484012
Autor:
Yunjiang Qiu, Arianna Tucci, Sarah Fazal, Kimberley Billingsley, Samuel S. Chong, Joke J.F.A. van Vugt, Viraj Deshpande, Egor Dolzhenko, Jan M. Friedman, Ashley Carroll, Matt C. Danzi, Phillip A. Richmond, Kristina Ibanez Garikano, Ramona A. J. Zwamborn, Michael A. Eberle, Ben Weisburd, Konrad Scheffler, Jinhui Ding, Andreas Halman, Bharati Jadhav, Indhu Shree Rajan Babu, Mark F. Bennett, Heidi L. Rehm
BackgroundExpansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat ex
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::af07b6578d36ff39814bf479f876e746
https://doi.org/10.1101/2021.10.20.465046
https://doi.org/10.1101/2021.10.20.465046
Autor:
Egor, Dolzhenko, Ben, Weisburd, Kristina, Ibañez, Indhu-Shree, Rajan-Babu, Christine, Anyansi, Mark F, Bennett, Kimberley, Billingsley, Ashley, Carroll, Samuel, Clamons, Matt C, Danzi, Viraj, Deshpande, Jinhui, Ding, Sarah, Fazal, Andreas, Halman, Bharati, Jadhav, Yunjiang, Qiu, Phillip A, Richmond, Christopher T, Saunders, Konrad, Scheffler, Joke J F A, van Vugt, Ramona R A J, Zwamborn, Samuel S, Chong, Jan M, Friedman, Arianna, Tucci, Heidi L, Rehm, Michael A, Eberle
Publikováno v:
Genome medicine. 14(1)
Background Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat e
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::078f7a028bea55569630165c5d260af9
https://pubmed.ncbi.nlm.nih.gov/35948990
https://pubmed.ncbi.nlm.nih.gov/35948990
Autor:
Kristen M. Turner, Utkrisht Rajkumar, Jens Luebeck, Paul S. Mischel, Siavash R. Dehkordi, Dave A. Pai, Julie A. Law, Joshua T. Lange, Ceyda Coruh, Vineet Bafna, Chao Zhang, Viraj Deshpande
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)
Nature Communications
Nature Communications
Oncogene amplification, a major driver of cancer pathogenicity, is often mediated through focal amplification of genomic segments. Recent results implicate extrachromosomal DNA (ecDNA) as the primary driver of focal copy number amplification (fCNA) -
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b9a3efd7c08ed96a7b6476db653b665b
https://doi.org/10.1038/s41467-020-18099-z
https://doi.org/10.1038/s41467-020-18099-z
Autor:
Kristen M. Turner, Viraj Deshpande, Siavash R. Dehkordi, Dave A. Pai, Jens Luebeck, Paul S. Mischel, Chao Zhang, Joshua T. Lange, Ceyda Coruh, Utkrisht Rajkumar, Julie A. Law, Vineet Bafna
Oncogene amplification, a major driver of cancer pathogenicity, is often mediated through focal amplification of genomic segments. Recent results implicate extrachromosomal DNA (ecDNA) as the primary mechanism driving focal copy number amplification
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f679cddd1d48cd1ed16e4cb7e547195
https://doi.org/10.1101/2020.01.22.916031
https://doi.org/10.1101/2020.01.22.916031