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  1. Research

    Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients

    Understanding longitudinal variability of the microbiome in ill patients is critical to moving microbiome-based measurements and therapeutics into clinical practice. However, the vast majority of data regardin...

    Jessica R. Galloway-Peña, Daniel P. Smith, Pranoti Sahasrabhojane, W. Duncan Wadsworth, Bryan M. Fellman, Nadim J. Ajami, Elizabeth J. Shpall, Naval Daver, Michele Guindani, Joseph F. Petrosino, Dimitrios P. Kontoyiannis and Samuel A. Shelburne

    Genome Medicine 2017 9:21

    Published on: 28 February 2017

  2. Research

    Genomic analysis of 63,220 tumors reveals insights into tumor uniqueness and targeted cancer immunotherapy strategies

    The integration of genomics with immunotherapy has potential value for cancer vaccine development. Given the clinical successes of immune checkpoint modulators, interest in cancer vaccines as therapeutic optio...

    Ryan J. Hartmaier, Jehad Charo, David Fabrizio, Michael E. Goldberg, Lee A. Albacker, William Pao and Juliann Chmielecki

    Genome Medicine 2017 9:16

    Published on: 24 February 2017

  3. Research

    A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus

    Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under i...

    Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H. A. Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun…

    Genome Medicine 2017 9:18

    Published on: 20 February 2017

  4. Research

    Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance

    Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblas...

    David J. Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G. Higgins and Walter Kolch

    Genome Medicine 2017 9:15

    Published on: 10 February 2017

  5. Research

    Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas

    While the role of the gut microbiome in inflammation and colorectal cancers has received much recent attention, there are few data to support an association between the oral microbiome and head and neck squamo...

    Hannah Wang, Pauline Funchain, Gurkan Bebek, Jessica Altemus, Huan Zhang, Farshad Niazi, Charissa Peterson, Walter T. Lee, Brian B. Burkey and Charis Eng

    Genome Medicine 2017 9:14

    Published on: 7 February 2017

  6. Research

    Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation

    The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is ...

    Yuya Kobayashi, Shan Yang, Keith Nykamp, John Garcia, Stephen E. Lincoln and Scott E. Topper

    Genome Medicine 2017 9:13

    Published on: 6 February 2017

  7. Research

    Longitudinal analysis of treatment-induced genomic alterations in gliomas

    Glioblastoma multiforme (GBM) constitutes nearly half of all malignant brain tumors and has a median survival of 15 months. The standard treatment for these lesions includes maximal resection, radiotherapy, an...

    E. Zeynep Erson-Omay, Octavian Henegariu, S. Bülent Omay, Akdes Serin Harmancı, Mark W. Youngblood, Ketu Mishra-Gorur, Jie Li, Koray Özduman, Geneive Carrión-Grant, Victoria E. Clark, Caner Çağlar, Mehmet Bakırcıoğlu, M. Necmettin Pamir, Viviane Tabar, Alexander O. Vortmeyer, Kaya Bilguvar…

    Genome Medicine 2017 9:12

    Published on: 2 February 2017

  8. Research

    High-dimensional assessment of B-cell responses to quadrivalent meningococcal conjugate and plain polysaccharide vaccine

    Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A...

    Daniel O’Connor, Elizabeth A. Clutterbuck, Amber J. Thompson, Matthew D. Snape, Maheshi N. Ramasamy, Dominic F. Kelly and Andrew J. Pollard

    Genome Medicine 2017 9:11

    Published on: 30 January 2017

  9. Research Highlight

    New strategies for cancer immunotherapy: targeting regulatory T cells

    The immunosuppressive action of regulatory T (Treg) cells is one mechanism attributed to the limited success of cancer immunotherapies with checkpoint blockers. Two recent studies report distinct transcriptional ...

    Francesca Finotello and Zlatko Trajanoski

    Genome Medicine 2017 9:10

    Published on: 27 January 2017

  10. Research

    Molecular dissection of germline chromothripsis in a developmental context using patient-derived iPS cells

    Germline chromothripsis causes complex genomic rearrangements that are likely to affect multiple genes and their regulatory contexts. The contribution of individual rearrangements and affected genes to the phe...

    Sjors Middelkamp, Sebastiaan van Heesch, A. Koen Braat, Joep de Ligt, Maarten van Iterson, Marieke Simonis, Markus J. van Roosmalen, Martijn J. E. Kelder, Evelien Kruisselbrink, Ron Hochstenbach, Nienke E. Verbeek, Elly F. Ippel, Youri Adolfs, R. Jeroen Pasterkamp, Wigard P. Kloosterman, Ewart W. Kuijk…

    Genome Medicine 2017 9:9

    Published on: 26 January 2017

  11. Research

    A variant by any name: quantifying annotation discordance across tools and clinical databases

    Clinical genomic testing is dependent on the robust identification and reporting of variant-level information in relation to disease. With the shift to high-throughput sequencing, a major challenge for clinica...

    Jennifer L. Yen, Sarah Garcia, Aldrin Montana, Jason Harris, Stephen Chervitz, Massimo Morra, John West, Richard Chen and Deanna M. Church

    Genome Medicine 2017 9:7

    Published on: 26 January 2017

  12. Research

    De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease

    Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disease of the gastrointestinal tract which includes ulcerative colitis and Crohn's disease. Genetic risk factors for IBD are not well unde...

    Shinichi Takahashi, Gaia Andreoletti, Rui Chen, Yoichi Munehira, Akshay Batra, Nadeem A. Afzal, R. Mark Beattie, Jonathan A. Bernstein, Sarah Ennis and Michael Snyder

    Genome Medicine 2017 9:8

    Published on: 26 January 2017

  13. Research

    Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae

    Klebsiella pneumoniae is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recentl...

    Chakkaphan Runcharoen, Danesh Moradigaravand, Beth Blane, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Julian Parkhill, Narisara Chantratita and Sharon J. Peacock

    Genome Medicine 2017 9:6

    Published on: 24 January 2017

  14. Research

    Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal

    As public health interventions drive parasite populations to elimination, genetic epidemiology models that incorporate population genomics can be powerful tools for evaluating the effectiveness of continued in...

    Wesley Wong, Allison D. Griggs, Rachel F. Daniels, Stephen F. Schaffner, Daouda Ndiaye, Amy K. Bei, Awa B. Deme, Bronwyn MacInnis, Sarah K. Volkman, Daniel L. Hartl, Daniel E. Neafsey and Dyann F. Wirth

    Genome Medicine 2017 9:5

    Published on: 24 January 2017

  15. Method

    3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets

    Many mutations in cancer are of unknown functional significance. Standard methods use statistically significant recurrence of mutations in tumor samples as an indicator of functional impact. We extend such ana...

    Jianjiong Gao, Matthew T. Chang, Hannah C. Johnsen, Sizhi Paul Gao, Brooke E. Sylvester, Selcuk Onur Sumer, Hongxin Zhang, David B. Solit, Barry S. Taylor, Nikolaus Schultz and Chris Sander

    Genome Medicine 2017 9:4

    Published on: 23 January 2017

  16. Software

    ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants

    The success of the clinical use of sequencing based tests (from single gene to genomes) depends on the accuracy and consistency of variant interpretation. Aiming to improve the interpretation process through p...

    Ronak Y. Patel, Neethu Shah, Andrew R. Jackson, Rajarshi Ghosh, Piotr Pawliczek, Sameer Paithankar, Aaron Baker, Kevin Riehle, Hailin Chen, Sofia Milosavljevic, Chris Bizon, Shawn Rynearson, Tristan Nelson, Gail P. Jarvik, Heidi L. Rehm, Steven M. Harrison…

    Genome Medicine 2017 9:3

    Published on: 12 January 2017

  17. Research

    Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations

    Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has b...

    Jennifer A. Oberg, Julia L. Glade Bender, Maria Luisa Sulis, Danielle Pendrick, Anthony N. Sireci, Susan J. Hsiao, Andrew T. Turk, Filemon S. Dela Cruz, Hanina Hibshoosh, Helen Remotti, Rebecca J. Zylber, Jiuhong Pang, Daniel Diolaiti, Carrie Koval, Stuart J. Andrews, James H. Garvin…

    Genome Medicine 2016 8:133

    Published on: 23 December 2016

  18. Research

    Genomic landscape of colorectal cancer in Japan: clinical implications of comprehensive genomic sequencing for precision medicine

    Comprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been li...

    Masayuki Nagahashi, Toshifumi Wakai, Yoshifumi Shimada, Hiroshi Ichikawa, Hitoshi Kameyama, Takashi Kobayashi, Jun Sakata, Ryoma Yagi, Nobuaki Sato, Yuko Kitagawa, Hiroyuki Uetake, Kazuhiro Yoshida, Eiji Oki, Shin-ei Kudo, Hiroshi Izutsu, Keisuke Kodama…

    Genome Medicine 2016 8:136

    Published on: 22 December 2016

  19. Research

    The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

    The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resis...

    Jody Phelan, Denise M. O’Sullivan, Diana Machado, Jorge Ramos, Alexandra S. Whale, Justin O’Grady, Keertan Dheda, Susana Campino, Ruth McNerney, Miguel Viveiros, Jim F. Huggett and Taane G. Clark

    Genome Medicine 2016 8:132

    Published on: 22 December 2016

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