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  1. Content type: Research

    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...

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

    Citation: Genome Medicine 2017 9:14

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  2. Content type: Research

    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 ...

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

    Citation: Genome Medicine 2017 9:13

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  3. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2017 9:12

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  4. Content type: Research

    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...

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

    Citation: Genome Medicine 2017 9:11

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  5. Content type: Research

    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...

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

    Citation: Genome Medicine 2017 9:8

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  6. Content type: Research

    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...

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

    Citation: Genome Medicine 2017 9:7

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  7. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2017 9:9

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  8. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2017 9:5

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  9. Content type: Research

    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...

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

    Citation: Genome Medicine 2017 9:6

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  10. Content type: Method

    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...

    Authors: 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

    Citation: Genome Medicine 2017 9:4

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  11. Content type: Software

    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...

    Authors: 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…

    Citation: Genome Medicine 2017 9:3

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  12. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2016 8:133

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  13. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2016 8:132

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  14. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2016 8:136

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  15. Content type: Method

    Cancer results from the acquisition of somatic driver mutations. Several computational tools can predict driver genes from population-scale genomic data, but tools for analyzing personal cancer genomes are und...

    Authors: Chengliang Dong, Yunfei Guo, Hui Yang, Zeyu He, Xiaoming Liu and Kai Wang

    Citation: Genome Medicine 2016 8:135

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  16. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2016 8:131

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  17. Content type: Research

    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...

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

    Citation: Genome Medicine 2016 8:128

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  18. Content type: Software

    Biological interpretation of genomic summary data such as those resulting from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies is one of the major bottlenecks in me...

    Authors: Hai Fang, Bogdan Knezevic, Katie L. Burnham and Julian C. Knight

    Citation: Genome Medicine 2016 8:129

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  19. Content type: Research

    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...

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

    Citation: Genome Medicine 2016 8:130

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  20. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2016 8:127

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  21. Content type: Opinion

    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...

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

    Citation: Genome Medicine 2016 8:125

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  22. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2016 8:122

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  23. Content type: Research

    Twin studies are powerful models to elucidate epigenetic modifications resulting from gene–environment interactions. Yet, commonly a limited number of clinical twin samples are available, leading to an underpo...

    Authors: David Gomez-Cabrero, Malin Almgren, Louise K. Sjöholm, Aase H. Hensvold, Mikael V. Ringh, Rakel Tryggvadottir, Juha Kere, Annika Scheynius, Nathalie Acevedo, Lovisa Reinius, Margaret A. Taub, Carolina Montano, Martin J. Aryee, Jason I. Feinberg, Andrew P. Feinberg, Jesper Tegnér…

    Citation: Genome Medicine 2016 8:124

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  24. Content type: Erratum

    Authors: Thuy Doan, Michael R. Wilson, Emily D. Crawford, Eric D. Chow, Lillian M. Khan, Kristeene A. Knopp, Brian D. O’Donovan, Dongxiang Xia, Jill K. Hacker, Jay M. Stewart, John A. Gonzales, Nisha R. Acharya and Joseph L. DeRisi

    Citation: Genome Medicine 2016 8:123

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    The original article was published in Genome Medicine 2016 8:90

  25. Content type: Method

    Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describ...

    Authors: Tanjina Kader, David L. Goode, Stephen Q. Wong, Jacquie Connaughton, Simone M. Rowley, Lisa Devereux, David Byrne, Stephen B. Fox, Gisela Mir Arnau, Richard W. Tothill, Ian G. Campbell and Kylie L. Gorringe

    Citation: Genome Medicine 2016 8:121

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  26. Content type: Research

    Efflux transporters like MDR1 and MRP2 may modulate the pharmacokinetics of about 50 % of all drugs. It is currently unknown how much of the variation in the activities of important drug membrane transporters ...

    Authors: Johannes Matthaei, Mladen V. Tzvetkov, Valerie Gal, Cordula Sachse-Seeboth, Daniel Sehrt, Jakob B. Hjelmborg, Ute Hofmann, Matthias Schwab, Reinhold Kerb and Jürgen Brockmöller

    Citation: Genome Medicine 2016 8:119

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  27. Content type: Erratum

    Authors: Charles Auffray, Rudi Balling, Inês Barroso, László Bencze, Mikael Benson, Jay Bergeron, Enrique Bernal-Delgado, Niklas Blomberg, Christoph Bock, Ana Conesa, Susanna Del Signore, Christophe Delogne, Peter Devilee, Alberto Di Meglio, Marinus Eijkemans, Paul Flicek…

    Citation: Genome Medicine 2016 8:118

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    The original article was published in Genome Medicine 2016 8:71

  28. Content type: Research

    To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (C...

    Authors: Deborah I. Ritter, Sameek Roychowdhury, Angshumoy Roy, Shruti Rao, Melissa J. Landrum, Dmitriy Sonkin, Mamatha Shekar, Caleb F. Davis, Reece K. Hart, Christine Micheel, Meredith Weaver, Eliezer M. Van Allen, Donald W. Parsons, Howard L. McLeod, Michael S. Watson, Sharon E. Plon…

    Citation: Genome Medicine 2016 8:117

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  29. Content type: Research

    Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep ...

    Authors: Maria Nicla Loviglio, Christine R. Beck, Janson J. White, Marion Leleu, Tamar Harel, Nicolas Guex, Anne Niknejad, Weimin Bi, Edward S. Chen, Isaac Crespo, Jiong Yan, Wu-Lin Charng, Shen Gu, Ping Fang, Zeynep Coban-Akdemir, Chad A. Shaw…

    Citation: Genome Medicine 2016 8:105

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  30. Content type: Research

    Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial...

    Authors: Mohammad K. Eldomery, Zeynep C. Akdemir, F.-Nora Vögtle, Wu-Lin Charng, Patrycja Mulica, Jill A. Rosenfeld, Tomasz Gambin, Shen Gu, Lindsay C. Burrage, Aisha Al Shamsi, Samantha Penney, Shalini N. Jhangiani, Holly H. Zimmerman, Donna M. Muzny, Xia Wang, Jia Tang…

    Citation: Genome Medicine 2016 8:106

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  31. Content type: Research

    Alzheimer’s disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. However, despite extensive clinical and genomic studies, the molecular bas...

    Authors: Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen J. Brennand, Gabriele C. De Luca, John F. Crary, Patrizia Casaccia, Joseph D. Buxbaum, Michelle Ehrlich, Sam Gandy, Alison Goate, Pavel Katsel, Eric Schadt, Vahram Haroutunian…

    Citation: Genome Medicine 2016 8:104

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  32. Content type: Research

    Precision medicine approaches are ideally suited for rare tumors where comprehensive characterization may have diagnostic, prognostic, and therapeutic value. We describe the clinical case and molecular charact...

    Authors: Filemon S. Dela Cruz, Daniel Diolaiti, Andrew T. Turk, Allison R. Rainey, Alberto Ambesi-Impiombato, Stuart J. Andrews, Mahesh M. Mansukhani, Peter L. Nagy, Mariano J. Alvarez, Andrea Califano, Farhad Forouhar, Beata Modzelewski, Chelsey M. Mitchell, Darrell J. Yamashiro, Lianna J. Marks, Julia L. Glade Bender…

    Citation: Genome Medicine 2016 8:116

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  33. Content type: Method

    Homologous recombination (HR) is the primary pathway for repairing double-strand DNA breaks implicating in the development of cancer. RNAi-based knockdowns of BRCA1 and RAD51 in this pathway have been performed t...

    Authors: Yue Wang, Kenneth M. K. Mark, Matthew H. Ung, Arminja Kettenbach, Todd Miller, Wei Xu, Wenqing Cheng, Tian Xia and Chao Cheng

    Citation: Genome Medicine 2016 8:114

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  34. Content type: Review

    The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10–15 years. At the same time, new technologies and the electronic health record (EHR) in pa...

    Authors: Jeremy L. Warner, Sandeep K. Jain and Mia A. Levy

    Citation: Genome Medicine 2016 8:113

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  35. Content type: Research

    The clinical utility of molecular profiling of tumor tissue to guide treatment of patients with advanced solid tumors is unknown. Our objectives were to evaluate the frequency of genomic alterations, clinical ...

    Authors: Tracy L. Stockley, Amit M. Oza, Hal K. Berman, Natasha B. Leighl, Jennifer J. Knox, Frances A. Shepherd, Eric X. Chen, Monika K. Krzyzanowska, Neesha Dhani, Anthony M. Joshua, Ming-Sound Tsao, Stefano Serra, Blaise Clarke, Michael H. Roehrl, Tong Zhang, Mahadeo A. Sukhai…

    Citation: Genome Medicine 2016 8:109

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  36. Content type: Opinion

    Precision medicine (PM) can be defined as a predictive, preventive, personalized, and participatory healthcare service delivery model. Recent developments in molecular biology and information technology make P...

    Authors: Gabrielle Bertier, Jian Carrot-Zhang, Vassilis Ragoussis and Yann Joly

    Citation: Genome Medicine 2016 8:108

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  37. Content type: Research

    In high-grade serous ovarian cancer (HGSOC), intrinsic and/or acquired resistance against platinum-containing chemotherapy is a major obstacle for successful treatment. A low frequency of somatic mutations but...

    Authors: Tushar Tomar, Steven de Jong, Nicolette G. Alkema, Rieks L. Hoekman, Gert Jan Meersma, Harry G. Klip, Ate GJ van der Zee and G. Bea A. Wisman

    Citation: Genome Medicine 2016 8:107

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  38. Content type: Comment

    Advances in genetic analysis have revealed new complexities in the interpretation of genetic variants. Correct assessment of a genetic variant relies on the clinical context and knowledge of the underlying bio...

    Authors: Eric Q. Konnick and Colin C. Pritchard

    Citation: Genome Medicine 2016 8:100

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  39. Content type: Software

    Profiling the somatic mutations of genes which may inform about tumor evolution, prognostics and treatment is becoming a standard tool in clinical oncology. Commercially available cancer gene panels rely on ma...

    Authors: Carlota Rubio-Perez, Jordi Deu-Pons, David Tamborero, Nuria Lopez-Bigas and Abel Gonzalez-Perez

    Citation: Genome Medicine 2016 8:98

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  40. Content type: Research

    Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant Staphylococcus aureus (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Wh...

    Authors: Ewan M. Harrison, Catherine Ludden, Hayley J. Brodrick, Beth Blane, Gráinne Brennan, Dearbháile Morris, Francesc Coll, Sandra Reuter, Nicholas M. Brown, Mark A. Holmes, Brian O’Connell, Julian Parkhill, M. Estee Török, Martin Cormican and Sharon J. Peacock

    Citation: Genome Medicine 2016 8:102

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