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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. Content type: Research

    Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD invo...

    Authors: Eilis Hannon, Diana Schendel, Christine Ladd-Acosta, Jakob Grove, Christine Søholm Hansen, Shan V. Andrews, David Michael Hougaard, Michaeline Bresnahan, Ole Mors, Mads Vilhelm Hollegaard, Marie Bækvad-Hansen, Mady Hornig, Preben Bo Mortensen, Anders D. Børglum, Thomas Werge, Marianne Giørtz Pedersen…

    Citation: Genome Medicine 2018 10:19

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  15. 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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  16. Content type: Method

    B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstr...

    Authors: Amit A. Upadhyay, Robert C. Kauffman, Amber N. Wolabaugh, Alice Cho, Nirav B. Patel, Samantha M. Reiss, Colin Havenar-Daughton, Reem A. Dawoud, Gregory K. Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F. Eun-Hyung Lee, Jens Wrammert and Steven E. Bosinger

    Citation: Genome Medicine 2018 10:20

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  17. Content type: Research

    A comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs of next-generation sequencing (NGS). However, the complexity of interpreting genomic data is hind...

    Authors: Júlia Perera-Bel, Barbara Hutter, Christoph Heining, Annalen Bleckmann, Martina Fröhlich, Stefan Fröhling, Hanno Glimm, Benedikt Brors and Tim Beißbarth

    Citation: Genome Medicine 2018 10:18

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  18. Content type: Research

    There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous ...

    Authors: Timothy D. O’Brien, Peilin Jia, Neil E. Caporaso, Maria Teresa Landi and Zhongming Zhao

    Citation: Genome Medicine 2018 10:16

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  19. Content type: Research

    Use of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to protect against tetraploidy, aneuploidy, and chromosomal alterations in the metaplastic condition Barrett’s esophagus (...

    Authors: Patricia C. Galipeau, Kenji M. Oman, Thomas G. Paulson, Carissa A. Sanchez, Qing Zhang, Jerry A. Marty, Jeffrey J. Delrow, Mary K. Kuhner, Thomas L. Vaughan, Brian J. Reid and Xiaohong Li

    Citation: Genome Medicine 2018 10:17

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  20. Content type: Research

    One of the major challenges in current psychiatric epigenetic studies is the tissue specificity of epigenetic changes since access to brain samples is limited. Peripheral tissues have been studied as surrogate...

    Authors: Dongdong Lin, Jiayu Chen, Nora Perrone-Bizzozero, Juan R. Bustillo, Yuhui Du, Vince D. Calhoun and Jingyu Liu

    Citation: Genome Medicine 2018 10:13

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  21. Content type: Research

    Genome-wide association studies of Alzheimer’s disease (AD) have identified a number of significant risk loci, the majority of which lie in non-coding regions of the genome. The lack of causal alleles and cons...

    Authors: Katherine E. Tansey, Darren Cameron and Matthew J. Hill

    Citation: Genome Medicine 2018 10:14

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  22. Content type: Research

    Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymor...

    Authors: A. R. Last, H. Pickering, C. h. Roberts, F. Coll, J. Phelan, S. E. Burr, E. Cassama, M. Nabicassa, H. M. B. Seth-Smith, J. Hadfield, L. T. Cutcliffe, I. N. Clarke, D. C. W. Mabey, R. L. Bailey, T. G. Clark, N. R. Thomson…

    Citation: Genome Medicine 2018 10:15

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  23. Content type: Comment

    Novel associations between the human microbiome and health and disease are routinely emerging, and important host–microbiome interactions are targets for new diagnostics and therapeutics. Understanding how bro...

    Authors: Joseph F. Petrosino

    Citation: Genome Medicine 2018 10:12

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  24. Content type: Comment

    Specific prophylactic migraine treatments are urgently needed because of the unmet needs of many migraine patients. Antibodies targeting calcitonin gene-related peptide (CGRP) or its receptor have recently sho...

    Authors: Antoinette MaassenVanDenBrink, Gisela M. Terwindt and Arn M. J. M. van den Maagdenberg

    Citation: Genome Medicine 2018 10:10

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  25. Content type: Research

    Genome–phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regu...

    Authors: Junfei Zhao, Feixiong Cheng, Peilin Jia, Nancy Cox, Joshua C. Denny and Zhongming Zhao

    Citation: Genome Medicine 2018 10:7

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  26. Content type: Research

    Severe infections with highly virulent community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are a global problem. However, the molecular events defining the evolution of CA-MRSA are still po...

    Authors: Lei He, Hong-Xiang Zheng, Yanan Wang, Katherine Y. Le, Qian Liu, Jun Shang, Yingxin Dai, Hongwei Meng, Xing Wang, Tianming Li, Qianqian Gao, Juanxiu Qin, Huiying Lu, Michael Otto and Min Li

    Citation: Genome Medicine 2018 10:5

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  27. Content type: Research

    Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the comp...

    Authors: Raivo Kolde, Eric A. Franzosa, Gholamali Rahnavard, Andrew Brantley Hall, Hera Vlamakis, Christine Stevens, Mark J. Daly, Ramnik J. Xavier and Curtis Huttenhower

    Citation: Genome Medicine 2018 10:6

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  28. Content type: Correction

    The original version of this article [1] unfortunately contained a typographical error. The ‘Alzheimer’s Disease Neuroimaging Initiative’ was erroneously included as ‘Alzheimer’s Disease Neuroimaging Initative...

    Authors: Perry G. Ridge, Celeste M. Karch, Simon Hsu, Ivan Arano, Craig C. Teerlink, Mark T. W. Ebbert, Josue D. Gonzalez Murcia, James M. Farnham, Anna R. Damato, Mariet Allen, Xue Wang, Oscar Harari, Victoria M. Fernandez, Rita Guerreiro, Jose Bras, John Hardy…

    Citation: Genome Medicine 2018 10:4

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    The original article was published in Genome Medicine 2017 9:100

  29. Content type: Research

    Glycosylphosphatidylinositol biosynthesis defects (GPIBDs) cause a group of phenotypically overlapping recessive syndromes with intellectual disability, for which pathogenic mutations have been described in 16...

    Authors: Alexej Knaus, Jean Tori Pantel, Manuela Pendziwiat, Nurulhuda Hajjir, Max Zhao, Tzung-Chien Hsieh, Max Schubach, Yaron Gurovich, Nicole Fleischer, Marten Jäger, Sebastian Köhler, Hiltrud Muhle, Christian Korff, Rikke S. Møller, Allan Bayat, Patrick Calvas…

    Citation: Genome Medicine 2018 10:3

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  30. Content type: Research

    The Ras pathway genes KRAS, BRAF, or ERBBs have somatic mutations in ~ 60% of human colorectal carcinomas. At present, it is unknown whether the remaining cases lack mutations activating the Ras pathway or whethe...

    Authors: Snehangshu Kundu, Muhammad Akhtar Ali, Niklas Handin, Narendra Padhan, Jimmy Larsson, Maria Karoutsou, Kenneth Ban, Jacek R. Wiśniewski, Per Artursson, Liqun He, Mats Hellström and Tobias Sjöblom

    Citation: Genome Medicine 2018 10:2

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  31. Content type: Research

    Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host e...

    Authors: Danesh Moradigaravand, Theodore Gouliouris, Beth Blane, Plamena Naydenova, Catherine Ludden, Charles Crawley, Nicholas M. Brown, M. Estée Török, Julian Parkhill and Sharon J. Peacock

    Citation: Genome Medicine 2017 9:119

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  32. Content type: Research

    Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in...

    Authors: Martin Widschwendter, Michal Zikan, Benjamin Wahl, Harri Lempiäinen, Tobias Paprotka, Iona Evans, Allison Jones, Shohreh Ghazali, Daniel Reisel, Johannes Eichner, Tamas Rujan, Zhen Yang, Andrew E. Teschendorff, Andy Ryan, David Cibula, Usha Menon…

    Citation: Genome Medicine 2017 9:116

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  33. Content type: Research

    The phenotypic severity of congenital muscular dystrophy-dystroglycanopathy (MDDG) syndromes associated with aberrant glycosylation of α-dystroglycan ranges from the severe Walker-Warburg syndrome or muscle-ey...

    Authors: Reza Maroofian, Moniek Riemersma, Lucas T. Jae, Narges Zhianabed, Marjolein H. Willemsen, Willemijn M. Wissink-Lindhout, Michèl A. Willemsen, Arjan P. M. de Brouwer, Mohammad Yahya Vahidi Mehrjardi, Mahmoud Reza Ashrafi, Benno Kusters, Tjitske Kleefstra, Yalda Jamshidi, Mojila Nasseri, Rolph Pfundt, Thijn R. Brummelkamp…

    Citation: Genome Medicine 2017 9:118

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  34. Content type: Research

    Variability in drug efficacy and adverse effects are observed in clinical practice. While the extent of genetic variability in classic pharmacokinetic genes is rather well understood, the role of genetic varia...

    Authors: Charlotta Pauline Irmgard Schärfe, Roman Tremmel, Matthias Schwab, Oliver Kohlbacher and Debora Susan Marks

    Citation: Genome Medicine 2017 9:117

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  35. Content type: Research

    Monitoring treatment and early detection of fatal breast cancer (BC) remains a major unmet need. Aberrant circulating DNA methylation (DNAme) patterns are likely to provide a highly specific cancer signal. We ...

    Authors: Martin Widschwendter, Iona Evans, Allison Jones, Shohreh Ghazali, Daniel Reisel, Andy Ryan, Aleksandra Gentry-Maharaj, Michal Zikan, David Cibula, Johannes Eichner, Marianna Alunni-Fabbroni, Julian Koch, Wolfgang J. Janni, Tobias Paprotka, Timo Wittenberger, Usha Menon…

    Citation: Genome Medicine 2017 9:115

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