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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. Content type: Research

    Alzheimer’s disease (AD) is characterized by neuronal loss and astrocytosis in the cerebral cortex. However, the specific effects that pathological mutations and coding variants associated with AD have on the ...

    Authors: Zeran Li, Jorge L. Del-Aguila, Umber Dube, John Budde, Rita Martinez, Kathleen Black, Qingli Xiao, Nigel J. Cairns, Joseph D. Dougherty, Jin-Moo Lee, John C. Morris, Randall J. Bateman, Celeste M. Karch, Carlos Cruchaga and Oscar Harari

    Citation: Genome Medicine 2018 10:43

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  26. Content type: Method

    Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of m...

    Authors: Mamoru Kato, Hiromi Nakamura, Momoko Nagai, Takashi Kubo, Asmaa Elzawahry, Yasushi Totoki, Yuko Tanabe, Eisaku Furukawa, Joe Miyamoto, Hiromi Sakamoto, Shingo Matsumoto, Kuniko Sunami, Yasuhito Arai, Yutaka Suzuki, Teruhiko Yoshida, Katsuya Tsuchihara…

    Citation: Genome Medicine 2018 10:44

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  27. Content type: Software

    Large-sequencing cancer genome projects have shown that tumors have thousands of molecular alterations and their frequency is highly heterogeneous. In such scenarios, physicians and oncologists routinely face ...

    Authors: Elena Piñeiro-Yáñez, Miguel Reboiro-Jato, Gonzalo Gómez-López, Javier Perales-Patón, Kevin Troulé, José Manuel Rodríguez, Héctor Tejero, Takeshi Shimamura, Pedro Pablo López-Casas, Julián Carretero, Alfonso Valencia, Manuel Hidalgo, Daniel Glez-Peña and Fátima Al-Shahrour

    Citation: Genome Medicine 2018 10:41

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  28. Content type: Research

    Heterotaxy (Htx) syndrome comprises a class of congenital disorders resulting from malformations in left-right body patterning. Approximately 90% of patients with heterotaxy have serious congenital heart disea...

    Authors: Chunjie Liu, Ruixue Cao, Yuejuan Xu, Tingting Li, Fen Li, Sun Chen, Rang Xu and Kun Sun

    Citation: Genome Medicine 2018 10:40

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  29. Content type: Research

    Hepatocellular carcinoma (HCC) is the one of the most common cancers and lethal diseases in the world. DNA methylation alteration is frequently observed in HCC and may play important roles in carcinogenesis an...

    Authors: Jinming Cheng, Dongkai Wei, Yuan Ji, Lingli Chen, Liguang Yang, Guang Li, Leilei Wu, Ting Hou, Lu Xie, Guohui Ding, Hong Li and Yixue Li

    Citation: Genome Medicine 2018 10:42

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  30. Content type: Research

    Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely...

    Authors: Genevieve Stein-O’Brien, Luciane T. Kagohara, Sijia Li, Manjusha Thakar, Ruchira Ranaweera, Hiroyuki Ozawa, Haixia Cheng, Michael Considine, Sandra Schmitz, Alexander V. Favorov, Ludmila V. Danilova, Joseph A. Califano, Evgeny Izumchenko, Daria A. Gaykalova, Christine H. Chung and Elana J. Fertig

    Citation: Genome Medicine 2018 10:37

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  31. Content type: Method

    Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple a...

    Authors: Praneeth Reddy Devulapally, Jörg Bürger, Thorsten Mielke, Zoltán Konthur, Hans Lehrach, Marie-Laure Yaspo, Jörn Glökler and Hans-Jörg Warnatz

    Citation: Genome Medicine 2018 10:34

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  32. Content type: Comment

    CRISPR–Cas systems have provided revolutionary tools for genome editing. The discovery of Cas proteins with alternative activities has now enabled sensitive and robust tools for detecting nucleic acids. Recent...

    Authors: Dipali G. Sashital

    Citation: Genome Medicine 2018 10:32

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  33. Content type: Method

    We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DN...

    Authors: Yingleong Chan, Ying Kai Chan, Daniel B. Goodman, Xiaoge Guo, Alejandro Chavez, Elaine T. Lim and George M. Church

    Citation: Genome Medicine 2018 10:31

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  34. Content type: Research

    Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chroma...

    Authors: Tianbao Li, Qi Liu, Nick Garza, Steven Kornblau and Victor X. Jin

    Citation: Genome Medicine 2018 10:30

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  35. Content type: Research

    The interplay of epigenetic processes and the intestinal microbiota may play an important role in intestinal development and homeostasis. Previous studies have established that the microbiota regulates a large...

    Authors: Wei-Hung Pan, Felix Sommer, Maren Falk-Paulsen, Thomas Ulas, Philipp Best, Antonella Fazio, Priyadarshini Kachroo, Anne Luzius, Marlene Jentzsch, Ateequr Rehman, Fabian Müller, Thomas Lengauer, Jörn Walter, Sven Künzel, John F. Baines, Stefan Schreiber…

    Citation: Genome Medicine 2018 10:27

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  36. Content type: Comment

    New computational and database-driven tools are emerging to aid in the interpretation of cancer genomic data as its use becomes more common in clinical evidence-based cancer medicine. Two such open source tool...

    Authors: Elaine R. Mardis

    Citation: Genome Medicine 2018 10:28

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  37. Content type: Research

    Cerebral amyloidosis, neuroinflammation, and tauopathy are key features of Alzheimer’s disease (AD), but interactions among these features remain poorly understood. Our previous multiscale molecular network mo...

    Authors: Michiko Sekiya, Minghui Wang, Naoki Fujisaki, Yasufumi Sakakibara, Xiuming Quan, Michelle E. Ehrlich, Philip L. De Jager, David A. Bennett, Eric E. Schadt, Sam Gandy, Kanae Ando, Bin Zhang and Koichi M. Iijima

    Citation: Genome Medicine 2018 10:26

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  38. Content type: Database

    While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of tumor somatic variants remains an important bottleneck. Here we present the Cancer Genome Inte...

    Authors: David Tamborero, Carlota Rubio-Perez, Jordi Deu-Pons, Michael P. Schroeder, Ana Vivancos, Ana Rovira, Ignasi Tusquets, Joan Albanell, Jordi Rodon, Josep Tabernero, Carmen de Torres, Rodrigo Dienstmann, Abel Gonzalez-Perez and Nuria Lopez-Bigas

    Citation: Genome Medicine 2018 10:25

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