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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. Research

    Alternate-locus aware variant calling in whole genome sequencing

    The last two human genome assemblies have extended the previous linear golden-path paradigm of the human genome to a graph-like model to better represent regions with a high degree of structural variability. T...

    Marten Jäger, Max Schubach, Tomasz Zemojtel, Knut Reinert, Deanna M. Church and Peter N. Robinson

    Genome Medicine 2016 8:130

    Published on: 13 December 2016

  15. Research

    Non-coding single nucleotide variants affecting estrogen receptor binding and activity

    Estrogen receptor (ER) activity is critical for the development and progression of the majority of breast cancers. It is known that ER is differentially bound to DNA leading to transcriptomic and phenotypic ch...

    Amir Bahreini, Kevin Levine, Lucas Santana-Santos, Panayiotis V. Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich and Adrian V. Lee

    Genome Medicine 2016 8:128

    Published on: 13 December 2016

  16. Research

    Truncating de novo mutations in the Krüppel-type zinc-finger gene ZNF148 in patients with corpus callosum defects, developmental delay, short stature, and dysmorphisms

    Krüppel-type zinc finger genes (ZNF) constitute a large yet relatively poorly characterized gene family. ZNF genes encode proteins that recognize specific DNA motifs in gene promotors. They act as transcriptio...

    Servi J. C. Stevens, Anthonie J. van Essen, Conny M. A. van Ravenswaaij, Abdallah F. Elias, Jaclyn A. Haven, Stefan H. Lelieveld, Rolph Pfundt, Willy M. Nillesen, Helger G. Yntema, Kees van Roozendaal, Alexander P. Stegmann, Christian Gilissen and Han G. Brunner

    Genome Medicine 2016 8:131

    Published on: 13 December 2016

  17. Research

    Allele-specific expression in the human heart and its application to postoperative atrial fibrillation and myocardial ischemia

    Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from t...

    Martin I. Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S. Couper, Stanton K. Shernan, Jon G. Seidman, Simon C. Body and Jochen D. Muehlschlegel

    Genome Medicine 2016 8:127

    Published on: 6 December 2016

  18. Research

    Potential contribution of the uterine microbiome in the development of endometrial cancer

    Endometrial cancer studies have led to a number of well-defined but mechanistically unconnected genetic and environmental risk factors. One of the emerging modulators between environmental triggers and genetic...

    Marina R. S. Walther-António, Jun Chen, Francesco Multinu, Alexis Hokenstad, Tammy J. Distad, E. Heidi Cheek, Gary L. Keeney, Douglas J. Creedon, Heidi Nelson, Andrea Mariani and Nicholas Chia

    Genome Medicine 2016 8:122

    Published on: 25 November 2016

  19. Opinion

    Looking beyond the cancer cell for effective drug combinations

    Combinations of therapies are being actively pursued to expand therapeutic options and deal with cancer’s pervasive resistance to treatment. Research efforts to discover effective combination treatments have f...

    Jonathan R. Dry, Mi Yang and Julio Saez-Rodriguez

    Genome Medicine 2016 8:125

    Published on: 25 November 2016

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