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4 results on '"Arnold Liao"'

1. The DNA methylation landscape of advanced prostate cancer

Author

Karen E. Knudsen, Nupam P. Mahajan, Housheng Hansen He, Martin Sjöström, Kathleen E. Houlahan, Jianhua Luo, S. Laura Chang, Meng Zhang, Kim N. Chi, Paul C. Boutros, Joseph F. Costello, Adam Foye, Denise Playdle, Lawrence Fong, M. Yvonne Kim, Serafim Batzoglou, Martin E. Gleave, Rahul Aggarwal, Li Zhang, Eric D. Chow, Scott A. Tomlins, Felix Y. Feng, Jiaoti Huang, Franklin W. Huang, Hui Li, Haolong Li, George Thomas, Junjie Tony Hua, Irfan A. Asangani, Marc D. Perry, Ha X. Dang, Todd M. Morgan, Robert E. Reiter, Alexander W. Wyatt, Shahneen Sandhu, Amina Zoubeidi, Christopher G. Maher, Daniel E. Spratt, Tanushree R. Shenoy, Luke A. Gilbert, Arul M. Chinnaiyan, Joshi J. Alumkal, Scott M. Dehm, Phillip G. Febbo, Primo N. Lara, Tomasz M. Beer, Adina M. Bailey, Rajdeep Das, Owen N. Witte, Alan Ashworth, Lisa N. Chesner, Joshua M. Lang, Mohammed Alshalalfa, Eric J. Small, Rohit Bose, Wilbert Zwart, David A. Quigley, Christopher P. Evans, Arnold Liao, Shuang G. Zhao, Yu Jia Shiah, Kyle Kai-How Farh, Hani Goodarzi, Travis J. Barnard, William S. Chen, Rendong Yang, Jonathan Chou, Ruhollah Moussavi-Baygi, and Matthew Rettig

Subjects
Epigenomics, Male, Carcinogenesis, Bisulfite sequencing, medicine.disease_cause, Somatic evolution in cancer, Medical and Health Sciences, Whole Exome Sequencing, 0302 clinical medicine, 80 and over, 2.1 Biological and endogenous factors, Prospective Studies, Aetiology, Exome sequencing, Cancer, Regulation of gene expression, Aged, 80 and over, 0303 health sciences, Genome, Prostate Cancer, Methylation, Biological Sciences, Middle Aged, Gene Expression Regulation, Neoplastic, DNA methylation, Sequence Analysis, Biotechnology, Urologic Diseases, Biology, Article, 03 medical and health sciences, Exome Sequencing, medicine, Genetics, Humans, 030304 developmental biology, Aged, Neoplastic, Whole Genome Sequencing, Human Genome, Prostatic Neoplasms, DNA, Sequence Analysis, DNA, DNA Methylation, Gene Expression Regulation, Mutation, Cancer research, 030217 neurology & neurosurgery, Developmental Biology
Abstract

Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes that were detectable only with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and somatic mutations in TET2, DNMT3B, IDH1 and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer that provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.

Published
2020

2. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

Author

Eric J. Small, Lawrence Fong, Karen E. Knudsen, Brad Sickler, Robert E. Reiter, Charles J. Ryan, Theodore C. Goldstein, Tomasz M. Beer, Martin E. Gleave, Rahul Aggarwal, Julian S. Gehring, Rajdeep Das, John Shon, Scott M. Dehm, Alan Ashworth, David A. Quigley, Ha X. Dang, Terence W. Friedlander, R. Keira Cheetham, Denise Playdle, Paul Lloyd, Serafim Batzoglou, Jack F. Youngren, Jin Zhang, Nathan A. Lack, Adam Foye, Felix Y. Feng, Jörg Hakenberg, Adina M. Bailey, Owen N. Witte, Abhijit Parolia, Scott A. Tomlins, Travis J. Barnard, Donavan T. Cheng, Jiaoti Huang, Li Zhang, P. G. Febbo, Alexander W. Wyatt, Kim N. Chi, Matthew Rettig, Vishal Kothari, Daniel E. Spratt, Housheng Hansen He, Haolong Li, George Thomas, Arnold Liao, Shuang G. Zhao, Hui Li, Joshua M. Stuart, Won Kim, Primo N. Lara, Christopher G. Maher, Jonathan Chou, Joshi J. Alumkal, Amina Zoubeidi, Marc D. Perry, Ruhollah Moussavi-Baygi, Luke A. Gilbert, Arul M. Chinnaiyan, Christopher P. Evans, Hani Goodarzi, Marcin Cieslik, and Kyle Kai-How Farh

Subjects
0301 basic medicine, Male, castration resistant prostate cancer, Cell, medicine.disease_cause, Medical and Health Sciences, Androgen, Transcriptome, Prostate cancer, androgen receptor, Receptors, 80 and over, 2.1 Biological and endogenous factors, Exome, Neoplasm Metastasis, Aetiology, Cancer, Aged, 80 and over, Mutation, Chromothripsis, Prostate Cancer, Genomics, Middle Aged, Biological Sciences, Cyclin-Dependent Kinases, medicine.anatomical_structure, Receptors, Androgen, Tandem Repeat Sequences, whole-genome sequencing, Tandem exon duplication, Urologic Diseases, DNA Copy Number Variations, Prostate cancer cell, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Structural variation, Proto-Oncogene Proteins c-myc, 03 medical and health sciences, medicine, genomics, Genetics, Humans, metastases, Aged, BRCA2 Protein, Whole Genome Sequencing, Gene Expression Profiling, Human Genome, structural variation, Prostatic Neoplasms, gene fusion, medicine.disease, BRCA2, 030104 developmental biology, Genomic Structural Variation, Cancer research, tandem duplication, chromothripsis, Tumor Suppressor Protein p53, Carcinogenesis, Developmental Biology
Abstract

© 2018 Elsevier Inc. While mutations affecting protein-coding regions have been examined across many cancers, structural variants at the genome-wide level are still poorly defined. Through integrative deep whole-genome and -transcriptome analysis of 101 castration-resistant prostate cancer metastases (109X tumor/38X normal coverage), we identified structural variants altering critical regulators of tumorigenesis and progression not detectable by exome approaches. Notably, we observed amplification of an intergenic enhancer region 624 kb upstream of the androgen receptor (AR) in 81% of patients, correlating with increased AR expression. Tandem duplication hotspots also occur near MYC, in lncRNAs associated with post-translational MYC regulation. Classes of structural variations were linked to distinct DNA repair deficiencies, suggesting their etiology, including associations of CDK12 mutation with tandem duplications, TP53 inactivation with inverted rearrangements and chromothripsis, and BRCA2 inactivation with deletions. Together, these observations provide a comprehensive view of how structural variations affect critical regulators in metastatic prostate cancer. Integrative whole-genome and -transcriptome sequencing provides a comprehensive view of structural variations that affect major regulators in prostate cancer and would escape detection by exome-based approaches.

Published
2018
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3. Whole Genome Sequencing in the Clinical Laboratory

Author

Suneer Jain, Brad Sickler, Tina Hambuch, Arnold Liao, and Philip Cotter

Subjects
Whole genome sequencing, Sanger sequencing, Massive parallel sequencing, Genomics, Computational biology, Biology, Bioinformatics, DNA sequencing, symbols.namesake, Proteome, symbols, Human genome, Gene, health care economics and organizations
Abstract

With the advent of massively parallel sequencing (MPS) technologies, it is now possible to sequence an entire human genome for about the price it would cost to sequence four or five genes at comparable accuracy using Sanger sequencing methods. In this chapter, we discuss the opportunities and challenges of developing a MPS protocol for whole genome sequencing within a clinical laboratory as well as its potential applications for clinical use.

Published
2012
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4. Accurate whole human genome sequencing using reversible terminator chemistry

Author

Zoya Kingsbury, Marc Laurent, Jason Bryant, Konstantinos D. Diakoumakos, Klaus Maisinger, Louise Fraser, Jean Ernest Sohna Sohna, Adrian Horgan, Patrick Mccauley, Jane Rogers, David W. Elmore, Mark A. Osborne, Juying Yan, Mark Smith, Milan Fedurco, Gary P. Schroth, Belen Dominguez-Fernandez, Heng Li, Andrea Sabot, Suzanne Wakelin, Cindy Lawley, Carole Anastasi, David Klenerman, David George, Daniel P. Pliskin, Mohammed D. Alam, Svilen S. Tzonev, Mark T. Reed, Xiaohai Liu, Asha Boodhun, Lu Zhang, Aylwyn Scally, T. A. Huw Jones, Ugonna C. Egbujor, Tzvetana H. Kerelska, George Stefan Golda, Shankar Balasubramanian, Lukasz Szajkowski, Mitch Lok, Mitch K. Shiver, Paul McNitt, Simon Chang, Maria Q. Johnson, Gyoung-Dong Kang, Victor J. Quijano, Sarah E. Lee, Mike Zuerlein, Maria Candelaria Rogert Bacigalupo, Alan D. Kersey, Selena G. Barbour, Dirk J. Evers, Andrew C. Pike, Stephen Rawlings, Karin Fuentes Fajardo, Mirian S. Karbelashvili, Matthew E. Hurles, Sonia M. Novo, Xavier Lee, James C. Burrows, John Stephen West, Jingwen Wang, Ify C. Aniebo, Natasha R. Crake, Christian D. Haudenschild, Richard Shaw, Come Raczy, W. Scott Furey, Wu Xiaolin, Lambros L. Paraschos, Josefina M. Seoane, John W. Martin, Katya Hoschler, Raquel Maria Sanches-Kuiper, Nick J. McCooke, Colin Barnes, Johannes P. Sluis, Abass A. Bundu, John Milton, R. Keira Cheetham, Nancy F. Hansen, Clive Gavin Brown, Nigel P. Carter, Richard J. Carter, Chiara Rodighiero, Kim B. Stevens, Shujun Luo, Radhika M. Mammen, Phyllida M. Roe, Melanie Anne Smith, Bojan Obradovic, Johnny T. Ho, Jennifer A. Loch, Terena James, Harold Swerdlow, Dale Buermann, David E. Green, Steve Hurwitz, Joe W. Mullens, Ning Sizto, Frank L. Oaks, Eli Rusman, Natalie J. Rourke, Nikolai Romanov, Anthony J. Smith, Claire Bevis, Selene M. Virk, Ling Yau, Yuli Verhovsky, D. Chris Pinkard, Stephanie Vandevondele, Vincent Peter Smith, Rob C. Brown, Eric J. Spence, Joe Podhasky, Ana Chiva Rodriguez, Michael Lawrence Parkinson, Anthony Romieu, Joe S. Brennan, Rithy K. Roth, David Mark Dunstan Bailey, Roberto Rigatti, Anil Kumar, Phillip J. Black, Primo Baybayan, Saibal Banerjee, Matthew M. Hims, Arnold Liao, R. Neil Cooley, Omead Ostadan, Vincent A. Benoit, Andrew A. Brown, Silke Ruediger, Leslie J. Irving, Parul Mehta, James C. Mullikin, Klaudia Walter, John Rogers, Jonathan Mark Boutell, Alex P. Kindwall, Paula Kokko-Gonzales, Alger C. Pike, Michael J. O'Neill, Eric Vermaas, Subramanian V. Sankar, Sean Humphray, Steven W. Short, Gerardo Turcatti, Helen Bignell, Kimberley J. Gietzen, Peta E. Torrance, Narinder I. Heyer, David James Earnshaw, Kevin Hall, Martin R. Schenker, Richard Durbin, Philip A. Granieri, Tobias William Barr Ost, Iain R. Bancarz, Lea Pickering, David L. Gustafson, Peter Lundberg, Niall Anthony Gormley, John Bridgham, Andrew Osnowski, Scott M. Kirk, Mark R. Ewan, Keith W. Moon, Bee Ling Ng, Graham John Worsley, Anthony J. Cox, Olubunmi O. Dada, Gregory C. Walcott, Sergey Etchin, Irina Khrebtukova, Kevin Benson, Vicki H. Rae, Zemin Ning, Carolyn Tregidgo, Nestor Castillo, Colin P. Goddard, Taksina Newington, Denis V. Ivanov, Anastassia Spiridou, Maria Chiara E. Catenazzi, Neil Sutton, Kevin Harnish, Darren James Ellis, Lisa Murray, Geoffrey Paul Smith, Mark T. Ross, David R. Bentley, M. R. Pratt, Isabelle Rasolonjatovo, and Michael R. Flatbush

Subjects
Male, Genotype, 2 base encoding, Nigeria, Sequence assembly, Hybrid genome assembly, Genomics, Computational biology, Biology, Polymorphism, Single Nucleotide, Sensitivity and Specificity, Deep sequencing, Article, 03 medical and health sciences, 0302 clinical medicine, Consensus Sequence, Humans, Paired-end tag, 030304 developmental biology, Genetics, Whole genome sequencing, Chromosomes, Human, X, 0303 health sciences, Multidisciplinary, Genome, Human, DNA sequencing theory, Sequence Analysis, DNA, 030220 oncology & carcinogenesis
Abstract

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

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