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  1. Content type: Research

    Studies have shown that complex structural variants (cxSVs) contribute to human genomic variation and can cause Mendelian disease. We aimed to identify cxSVs relevant to Mendelian disease using short-read whol...

    Authors: Alba Sanchis-Juan, Jonathan Stephens, Courtney E. French, Nicholas Gleadall, Karyn Mégy, Christopher Penkett, Olga Shamardina, Kathleen Stirrups, Isabelle Delon, Eleanor Dewhurst, Helen Dolling, Marie Erwood, Detelina Grozeva, Luca Stefanucci, Gavin Arno, Andrew R. Webster…

    Citation: Genome Medicine 2018 10:95

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  2. Content type: Research

    Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical significance. However, it remains a challenge to define disease biology solely based on gene expression because tumor bi...

    Authors: Wei Tang, Ming Zhou, Tiffany H. Dorsey, DaRue A. Prieto, Xin W. Wang, Eytan Ruppin, Timothy D. Veenstra and Stefan Ambs

    Citation: Genome Medicine 2018 10:94

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  3. Content type: Research

    Based on promising phase II data, the histone deacetylase inhibitor entinostat is in phase III trials for patients with metastatic estrogen receptor-positive breast cancer. Predictors of sensitivity and resist...

    Authors: Maki Tanioka, Kevin R. Mott, Daniel P. Hollern, Cheng Fan, David B. Darr and Charles M. Perou

    Citation: Genome Medicine 2018 10:86

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  4. Content type: Review

    Immune checkpoint blockade (ICB) therapies, which potentiate the body’s natural immune response against tumor cells, have shown immense promise in the treatment of various cancers. Currently, tumor mutational ...

    Authors: Jake R. Conway, Eric Kofman, Shirley S. Mo, Haitham Elmarakeby and Eliezer Van Allen

    Citation: Genome Medicine 2018 10:93

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  5. Content type: Research

    Chemotherapeutic agents such as anthracyclines and taxanes are commonly used in the neoadjuvant setting. Bevacizumab is an antibody which binds to vascular endothelial growth factor A (VEGFA) and inhibits its ...

    Authors: Elen Kristine Höglander, Silje Nord, David C. Wedge, Ole Christian Lingjærde, Laxmi Silwal-Pandit, Hedda vdL Gythfeldt, Hans Kristian Moen Vollan, Thomas Fleischer, Marit Krohn, Ellen Schlitchting, Elin Borgen, Øystein Garred, Marit M. Holmen, Erik Wist, Bjørn Naume, Peter Van Loo…

    Citation: Genome Medicine 2018 10:92

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  6. Content type: Research

    Mutations in KRAS are frequent in human cancer, yet effective targeted therapeutics for these cancers are still lacking. Attempts to drug the MEK kinases downstream of KRAS have had limited success in clinical tr...

    Authors: Tonći Šuštić, Sake van Wageningen, Evert Bosdriesz, Robert J. D. Reid, John Dittmar, Cor Lieftink, Roderick L. Beijersbergen, Lodewyk F. A. Wessels, Rodney Rothstein and René Bernards

    Citation: Genome Medicine 2018 10:90

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  7. Content type: Comment

    Telomere crisis is linked with many of the genomic alterations found in cancer genomes. A new understanding of how these alterations arise points towards an active role for innate immune sensors during crisis ...

    Authors: Patrick von Morgen and John Maciejowski

    Citation: Genome Medicine 2018 10:89

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  8. Content type: Comment

    Immunotherapy has revolutionized the management of numerous cancers; however, a substantial proportion that initially respond subsequently acquire means of immune escape and relapse. Analysis of recent clinica...

    Authors: J. Bryan Iorgulescu, David Braun, Giacomo Oliveira, Derin B. Keskin and Catherine J. Wu

    Citation: Genome Medicine 2018 10:87

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  9. Content type: Research

    There are multiple existing and emerging therapeutic avenues for metastatic prostate cancer, with a common denominator, which is the need for predictive biomarkers. Circulating tumor DNA (ctDNA) has the potent...

    Authors: Markus Mayrhofer, Bram De Laere, Tom Whitington, Peter Van Oyen, Christophe Ghysel, Jozef Ampe, Piet Ost, Wim Demey, Lucien Hoekx, Dirk Schrijvers, Barbara Brouwers, Willem Lybaert, Els Everaert, Daan De Maeseneer, Michiel Strijbos, Alain Bols…

    Citation: Genome Medicine 2018 10:85

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  10. Content type: Research

    Major histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide to MHC-II binding are trained on binding affinity data, ...

    Authors: Carolina Barra, Bruno Alvarez, Sinu Paul, Alessandro Sette, Bjoern Peters, Massimo Andreatta, Søren Buus and Morten Nielsen

    Citation: Genome Medicine 2018 10:84

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  11. Content type: Research

    Comprehensive mutational profiling data now available on all major cancers have led to proposals of novel molecular tumor classifications that modify or replace the established organ- and tissue-based tumor ty...

    Authors: Daniel Heim, Grégoire Montavon, Peter Hufnagl, Klaus-Robert Müller and Frederick Klauschen

    Citation: Genome Medicine 2018 10:83

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  12. Content type: Research

    Staphylococcus aureus is an opportunistic pathogen and a leading cause of nosocomial infections. It can acquire resistance to all the antibiotics that entered the clinics to date, and the World Health Organizatio...

    Authors: Serena Manara, Edoardo Pasolli, Daniela Dolce, Novella Ravenni, Silvia Campana, Federica Armanini, Francesco Asnicar, Alessio Mengoni, Luisa Galli, Carlotta Montagnani, Elisabetta Venturini, Omar Rota-Stabelli, Guido Grandi, Giovanni Taccetti and Nicola Segata

    Citation: Genome Medicine 2018 10:82

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  13. Content type: Research

    Links between colorectal cancer (CRC) and the gut microbiome have been established, but the specific microbial species and their role in carcinogenesis remain an active area of inquiry. Our understanding would...

    Authors: Vanessa L. Hale, Patricio Jeraldo, Jun Chen, Michael Mundy, Janet Yao, Sambhawa Priya, Gary Keeney, Kelly Lyke, Jason Ridlon, Bryan A. White, Amy J. French, Stephen N. Thibodeau, Christian Diener, Osbaldo Resendis-Antonio, Jaime Gransee, Tumpa Dutta…

    Citation: Genome Medicine 2018 10:78

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  14. Content type: Research

    Patients diagnosed with high-grade serous ovarian cancer (HGSOC) who received initial debulking surgery followed by platinum-based chemotherapy can experience highly variable clinical responses. A small percen...

    Authors: S. Y. Cindy Yang, Stephanie Lheureux, Katherine Karakasis, Julia V. Burnier, Jeffery P. Bruce, Derek L. Clouthier, Arnavaz Danesh, Rene Quevedo, Mark Dowar, Youstina Hanna, Tiantian Li, Lin Lu, Wei Xu, Blaise A. Clarke, Pamela S. Ohashi, Patricia A. Shaw…

    Citation: Genome Medicine 2018 10:81

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  15. Content type: Research

    Klebsiella pneumoniae is a recognised agent of multidrug-resistant (MDR) healthcare-associated infections; however, individual strains vary in their virulence potential due to the presence of mobile accessory gen...

    Authors: Margaret M. C. Lam, Kelly L. Wyres, Louise M. Judd, Ryan R. Wick, Adam Jenney, Sylvain Brisse and Kathryn E. Holt

    Citation: Genome Medicine 2018 10:77

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  16. Content type: Research

    The IRE1a-XBP1 pathway is a conserved adaptive mediator of the unfolded protein response. The pathway is indispensable for the development of secretory cells by facilitating protein folding and enhancing secre...

    Authors: Jhuma Pramanik, Xi Chen, Gozde Kar, Johan Henriksson, Tomás Gomes, Jong-Eun Park, Kedar Natarajan, Kerstin B. Meyer, Zhichao Miao, Andrew N. J. McKenzie, Bidesh Mahata and Sarah A. Teichmann

    Citation: Genome Medicine 2018 10:76

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  17. Content type: Research

    Mutation of the IL2RG gene results in a form of severe combined immune deficiency (SCID-X1), which has been treated successfully with hematopoietic stem cell gene therapy. SCID-X1 gene therapy results in reconsti...

    Authors: Erik L. Clarke, A. Jesse Connell, Emmanuelle Six, Nadia A. Kadry, Arwa A. Abbas, Young Hwang, John K. Everett, Casey E. Hofstaedter, Rebecca Marsh, Myriam Armant, Judith Kelsen, Luigi D. Notarangelo, Ronald G. Collman, Salima Hacein-Bey-Abina, Donald B. Kohn, Marina Cavazzana…

    Citation: Genome Medicine 2018 10:70

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  18. Content type: Research

    Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of infor...

    Authors: Elizabeth A. Normand, Alicia Braxton, Salma Nassef, Patricia A. Ward, Francesco Vetrini, Weimin He, Vipulkumar Patel, Chunjing Qu, Lauren E. Westerfield, Samantha Stover, Avinash V. Dharmadhikari, Donna M. Muzny, Richard A. Gibbs, Hongzheng Dai, Linyan Meng, Xia Wang…

    Citation: Genome Medicine 2018 10:74

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  19. Content type: Research

    We have previously reported an antigen-specific protocol to induce transplant tolerance and linked suppression to human embryonic stem cell (hESC)-derived tissues in immunocompetent mice through coreceptor and...

    Authors: Cherry S. Leung, Kevin Y. Yang, Xisheng Li, Vicken W. Chan, Manching Ku, Herman Waldmann, Shohei Hori, Jason C. H. Tsang, Yuk Ming Dennis Lo and Kathy O. Lui

    Citation: Genome Medicine 2018 10:71

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  20. Content type: Research

    Cancer susceptibility germline variants generally require somatic alteration of the remaining allele to drive oncogenesis and, in some cases, tumor mutational profiles. Whether combined germline and somatic bi...

    Authors: Alexandra R. Buckley, Trey Ideker, Hannah Carter, Olivier Harismendy and Nicholas J. Schork

    Citation: Genome Medicine 2018 10:69

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  21. Content type: Research

    Rheumatoid arthritis is a common autoimmune disorder influenced by both genetic and environmental factors. Epigenome-wide association studies can identify environmentally mediated epigenetic changes such as al...

    Authors: Amy P. Webster, Darren Plant, Simone Ecker, Flore Zufferey, Jordana T. Bell, Andrew Feber, Dirk S. Paul, Stephan Beck, Anne Barton, Frances M. K. Williams and Jane Worthington

    Citation: Genome Medicine 2018 10:64

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  22. Content type: Method

    Mutation acquisition is a major mechanism of bacterial antibiotic resistance that remains insufficiently characterised. Here we present RM-seq, a new amplicon-based deep sequencing workflow based on a molecula...

    Authors: Romain Guérillot, Lucy Li, Sarah Baines, Brian Howden, Mark B. Schultz, Torsten Seemann, Ian Monk, Sacha J. Pidot, Wei Gao, Stefano Giulieri, Anders Gonçalves da Silva, Anthony D’Agata, Takehiro Tomita, Anton Y. Peleg, Timothy P. Stinear and Benjamin P. Howden

    Citation: Genome Medicine 2018 10:63

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  23. Content type: Research

    Adaptive immune responses to newly encountered pathogens depend on the mobilization of antigen-specific clonotypes from a vastly diverse pool of naive T cells. Using recent advances in immune repertoire sequen...

    Authors: Mikhail V. Pogorelyy, Alla D. Fedorova, James E. McLaren, Kristin Ladell, Dmitri V. Bagaev, Alexey V. Eliseev, Artem I. Mikelov, Anna E. Koneva, Ivan V. Zvyagin, David A. Price, Dmitry M. Chudakov and Mikhail Shugay

    Citation: Genome Medicine 2018 10:68

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  24. Content type: Research

    Large-scale genomic studies of within-host diversity in Staphylococcus aureus bacteraemia (SAB) are needed to understanding bacterial adaptation underlying persistence and thus refining the role of genomics in ma...

    Authors: Stefano G. Giulieri, Sarah L. Baines, Romain Guerillot, Torsten Seemann, Anders Gonçalves da Silva, Mark Schultz, Ruth C. Massey, Natasha E. Holmes, Timothy P. Stinear and Benjamin P. Howden

    Citation: Genome Medicine 2018 10:65

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  25. Content type: Research

    The immune system plays a fundamental role in development during pregnancy and early life. Alterations in circulating maternal and neonatal immune mediators have been associated with pregnancy complications as...

    Authors: Michela Traglia, Lisa A. Croen, Karen L. Jones, Luke S. Heuer, Robert Yolken, Martin Kharrazi, Gerald N. DeLorenze, Paul Ashwood, Judy Van de Water and Lauren A. Weiss

    Citation: Genome Medicine 2018 10:67

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  26. Content type: Comment

    Recent work has reported that the activation of the p53 pathway in primary cells hampers the efficiency of genome editing by CRISPR/Cas9 via induction of apoptosis or cell cycle arrest. These findings highligh...

    Authors: Anastasia Conti and Raffaella Di Micco

    Citation: Genome Medicine 2018 10:66

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  27. Content type: Research

    The 2014–2016 Ebola virus (EBOV) outbreak in West Africa highlighted the need for improved therapeutic options against this virus. Approaches targeting host factors/pathways essential for the virus are advanta...

    Authors: Scott Martin, Abhilash I. Chiramel, Marie Luisa Schmidt, Yu-Chi Chen, Nadia Whitt, Ari Watt, Eric C. Dunham, Kyle Shifflett, Shelby Traeger, Anne Leske, Eugen Buehler, Cynthia Martellaro, Janine Brandt, Lisa Wendt, Andreas Müller, Stephanie Peitsch…

    Citation: Genome Medicine 2018 10:58

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  28. Content type: Software

    The widespread incorporation of next-generation sequencing into clinical oncology has yielded an unprecedented amount of molecular data from thousands of patients. A main current challenge is to find out relia...

    Authors: Lidia Mateo, Oriol Guitart-Pla, Miquel Duran-Frigola and Patrick Aloy

    Citation: Genome Medicine 2018 10:61

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  29. Content type: Research

    Humoral immune responses to infectious agents or vaccination vary substantially among individuals, and many of the factors responsible for this variability remain to be defined. Current evidence suggests that ...

    Authors: Petar Scepanovic, Cécile Alanio, Christian Hammer, Flavia Hodel, Jacob Bergstedt, Etienne Patin, Christian W. Thorball, Nimisha Chaturvedi, Bruno Charbit, Laurent Abel, Lluis Quintana-Murci, Darragh Duffy, Matthew L. Albert and Jacques Fellay

    Citation: Genome Medicine 2018 10:59

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  30. Content type: Research

    Although large-scale, next-generation sequencing (NGS) studies of cancers hold promise for enabling precision oncology, challenges remain in integrating NGS with clinically validated biomarkers.

    Authors: Sohini Sengupta, Sam Q. Sun, Kuan-lin Huang, Clara Oh, Matthew H. Bailey, Rajees Varghese, Matthew A. Wyczalkowski, Jie Ning, Piyush Tripathi, Joshua F. McMichael, Kimberly J. Johnson, Cyriac Kandoth, John Welch, Cynthia Ma, Michael C. Wendl, Samuel H. Payne…

    Citation: Genome Medicine 2018 10:60

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  31. Content type: Research

    Despite extensive molecular characterization, we lack a comprehensive understanding of lineage identity, differentiation, and proliferation in high-grade gliomas (HGGs).

    Authors: Jinzhou Yuan, Hanna Mendes Levitin, Veronique Frattini, Erin C. Bush, Deborah M. Boyett, Jorge Samanamud, Michele Ceccarelli, Athanassios Dovas, George Zanazzi, Peter Canoll, Jeffrey N. Bruce, Anna Lasorella, Antonio Iavarone and Peter A. Sims

    Citation: Genome Medicine 2018 10:57

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  32. Content type: Research

    Pulmonary arterial hypertension (PAH) is a rare disease characterized by distinctive changes in pulmonary arterioles that lead to progressive pulmonary arterial pressures, right-sided heart failure, and a high...

    Authors: Na Zhu, Carrie L. Welch, Jiayao Wang, Philip M. Allen, Claudia Gonzaga-Jauregui, Lijiang Ma, Alejandra K. King, Usha Krishnan, Erika B. Rosenzweig, D. Dunbar Ivy, Eric D. Austin, Rizwan Hamid, Michael W. Pauciulo, Katie A. Lutz, William C. Nichols, Jeffrey G. Reid…

    Citation: Genome Medicine 2018 10:56

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  33. Content type: Research

    Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy characterized by tumor heterogeneity, locoregional metastases, and resistance to existing treatments. Although a number of genomic and ...

    Authors: Vinay K. Kartha, Khalid A. Alamoud, Khikmet Sadykov, Bach-Cuc Nguyen, Fabrice Laroche, Hui Feng, Jina Lee, Sara I. Pai, Xaralabos Varelas, Ann Marie Egloff, Jennifer E. Snyder-Cappione, Anna C. Belkina, Manish V. Bais, Stefano Monti and Maria A. Kukuruzinska

    Citation: Genome Medicine 2018 10:54

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  34. Content type: Research

    Non-small cell lung cancer (NSCLC) is the most common cause of cancer-related deaths worldwide and is primarily treated with radiation, surgery, and platinum-based drugs like cisplatin and carboplatin. The maj...

    Authors: Sabrina Grasse, Matthias Lienhard, Steffen Frese, Martin Kerick, Anne Steinbach, Christina Grimm, Michelle Hussong, Jana Rolff, Michael Becker, Felix Dreher, Uwe Schirmer, Stefan Boerno, Anna Ramisch, Gunda Leschber, Bernd Timmermann, Christian Grohé…

    Citation: Genome Medicine 2018 10:55

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  35. Content type: Research

    Plasmodium vivax poses a significant challenge to malaria elimination due to its ability to cause relapsed infections from reactivation of dormant liver parasites called hypnozoites. We analyzed 69 P. vivax whole...

    Authors: Annie N. Cowell, Hugo O. Valdivia, Danett K. Bishop and Elizabeth A. Winzeler

    Citation: Genome Medicine 2018 10:52

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  36. Content type: Software

    A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and in...

    Authors: Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar and João Paulo Gomes

    Citation: Genome Medicine 2018 10:46

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  37. Content type: Research

    Studies have shown that low haemoglobin and anaemia are associated with poor cognition, and anaemia is known to be associated with Alzheimer’s disease (AD), but the mechanism of this risk is unknown. Here, we ...

    Authors: Laura M. Winchester, John Powell, Simon Lovestone and Alejo J. Nevado-Holgado

    Citation: Genome Medicine 2018 10:51

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  38. Content type: Research

    The genetic and immunological factors that contribute to differences in susceptibility and progression between sub-types of inflammatory and autoimmune diseases continue to be elucidated. Inflammatory bowel di...

    Authors: Angela Mo, Urko M. Marigorta, Dalia Arafat, Lai Hin Kimi Chan, Lori Ponder, Se Ryeong Jang, Jarod Prince, Subra Kugathasan, Sampath Prahalad and Greg Gibson

    Citation: Genome Medicine 2018 10:48

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  39. Content type: Research

    Abnormal pre-mRNA splicing regulation is common in cancer, but the effects of chemotherapy on this process remain unclear.

    Authors: Ksenia S. Anufrieva, Victoria О. Shender, Georgij P. Arapidi, Marat S. Pavlyukov, Michail I. Shakhparonov, Polina V. Shnaider, Ivan O. Butenko, Maria A. Lagarkova and Vadim M. Govorun

    Citation: Genome Medicine 2018 10:49

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  40. Content type: Comment

    There is an urgent need to develop vaccines against emerging diseases, including those caused by pathogens that are currently unknown to cause human disease, termed ‘disease X’. Here, Zika virus infection is c...

    Authors: Alan D. T. Barrett

    Citation: Genome Medicine 2018 10:47

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