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  1. Shigella is a major diarrheal pathogen for which there is presently no vaccine. Whole genome sequencing provides the ability to predict and derive novel antigens for use as vaccines. Here, we aimed to identify no...

    Authors: Ruklanthi de Alwis, Li Liang, Omid Taghavian, Emma Werner, Hao Chung The, Trang Nguyen Hoang Thu, Vu Thuy Duong, D. Huw Davies, Philip L. Felgner and Stephen Baker

    Citation: Genome Medicine 2021 13:8

    Content type: Research

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  2. The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases wit...

    Authors: Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger…

    Citation: Genome Medicine 2021 13:7

    Content type: Research

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  3. Clinical laboratory (lab) tests are used in clinical practice to diagnose, treat, and monitor disease conditions. Test results are stored in electronic health records (EHRs), and a growing number of EHRs are l...

    Authors: Jessica K. Dennis, Julia M. Sealock, Peter Straub, Younga H. Lee, Donald Hucks, Ky’Era Actkins, Annika Faucon, Yen-Chen Anne Feng, Tian Ge, Slavina B. Goleva, Maria Niarchou, Kritika Singh, Theodore Morley, Jordan W. Smoller, Douglas M. Ruderfer, Jonathan D. Mosley…

    Citation: Genome Medicine 2021 13:6

    Content type: Research

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  4. Ebola virus disease (EVD) is an often-fatal infection where the effectiveness of medical countermeasures is uncertain. During the West African outbreak (2013–2016), several patients were treated with different...

    Authors: Andrew Bosworth, Natasha Y. Rickett, Xiaofeng Dong, Lisa F. P. Ng, Isabel García-Dorival, David A. Matthews, Tom Fletcher, Michael Jacobs, Emma C. Thomson, Miles W. Carroll and Julian A. Hiscox

    Citation: Genome Medicine 2021 13:5

    Content type: Research

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  5. During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online “immuno-analytics” resource that...

    Authors: Daniel Ward, Matthew Higgins, Jody E. Phelan, Martin L. Hibberd, Susana Campino and Taane G. Clark

    Citation: Genome Medicine 2021 13:4

    Content type: Database

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  6. Family history has traditionally been an essential part of clinical care to assess health risks. However, declining sequencing costs have precipitated a shift towards genomics-first approaches in population sc...

    Authors: Yasmin Bylstra, Weng Khong Lim, Sylvia Kam, Koei Wan Tham, R. Ryanne Wu, Jing Xian Teo, Sonia Davila, Jyn Ling Kuan, Sock Hoai Chan, Nicolas Bertin, Cheng Xi Yang, Steve Rozen, Bin Tean Teh, Khung Keong Yeo, Stuart Alexander Cook, Saumya Shekhar Jamuar…

    Citation: Genome Medicine 2021 13:3

    Content type: Research

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  7. The apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for late onset Alzheimer’s disease, whilst the ε2 allele confers protection. Previous studies report differential DNA methylation of APOE

    Authors: Rosie M. Walker, Kadi Vaher, Mairead L. Bermingham, Stewart W. Morris, Andrew D. Bretherick, Yanni Zeng, Konrad Rawlik, Carmen Amador, Archie Campbell, Chris S. Haley, Caroline Hayward, David J. Porteous, Andrew M. McIntosh, Riccardo E. Marioni and Kathryn L. Evans

    Citation: Genome Medicine 2021 13:1

    Content type: Research

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  8. The identification of genetic variation that directly impacts infection susceptibility to SARS-CoV-2 and disease severity of COVID-19 is an important step towards risk stratification, personalized treatment pl...

    Authors: Yu-Chung Lin, Jennifer D. Brooks, Shelley B. Bull, France Gagnon, Celia M. T. Greenwood, Rayjean J. Hung, Jerald Lawless, Andrew D. Paterson, Lei Sun and Lisa J. Strug

    Citation: Genome Medicine 2020 12:115

    Content type: Correspondence

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  9. Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in...

    Authors: Gary Napier, Susana Campino, Yared Merid, Markos Abebe, Yimtubezinash Woldeamanuel, Abraham Aseffa, Martin L. Hibberd, Jody Phelan and Taane G. Clark

    Citation: Genome Medicine 2020 12:114

    Content type: Research

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  10. Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, and pneumonia, driven mainly by the emergence of successful high-risk ...

    Authors: Stefan E. Heiden, Nils-Olaf Hübner, Jürgen A. Bohnert, Claus-Dieter Heidecke, Axel Kramer, Veronika Balau, Wolfgang Gierer, Stephan Schaefer, Tim Eckmanns, Sören Gatermann, Elias Eger, Sebastian Guenther, Karsten Becker and Katharina Schaufler

    Citation: Genome Medicine 2020 12:113

    Content type: Research

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  11. Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little...

    Authors: Trine Line Hauge Okholm, Shashank Sathe, Samuel S. Park, Andreas Bjerregaard Kamstrup, Asta Mannstaedt Rasmussen, Archana Shankar, Zong Ming Chua, Niels Fristrup, Morten Muhlig Nielsen, Søren Vang, Lars Dyrskjøt, Stefan Aigner, Christian Kroun Damgaard, Gene W. Yeo and Jakob Skou Pedersen

    Citation: Genome Medicine 2020 12:112

    Content type: Research

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  12. The recent emergence and dissemination of high-level mobile tigecycline resistance Tet(X) challenge the clinical effectiveness of tigecycline, one of the last-resort therapeutic options for complicated infecti...

    Authors: Chong Chen, Chao-Yue Cui, Jun-Jun Yu, Qian He, Xiao-Ting Wu, Yu-Zhang He, Ze-Hua Cui, Cang Li, Qiu-Lin Jia, Xiang-Guang Shen, Ruan-Yang Sun, Xi-Ran Wang, Min-Ge Wang, Tian Tang, Yan Zhang, Xiao-Ping Liao…

    Citation: Genome Medicine 2020 12:111

    Content type: Research

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  13. Comprehensive molecular profiling has revealed somatic variations in cancer at genomic, epigenomic, transcriptomic, and proteomic levels. The accumulating data has shown clearly that molecular phenotypes of ca...

    Authors: Arshi Arora, Adam B. Olshen, Venkatraman E. Seshan and Ronglai Shen

    Citation: Genome Medicine 2020 12:110

    Content type: Research

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  14. Whole exome sequencing has been increasingly used in human disease studies. Prioritization based on appropriate functional annotations has been used as an indispensable step to select candidate variants. Here ...

    Authors: Xiaoming Liu, Chang Li, Chengcheng Mou, Yibo Dong and Yicheng Tu

    Citation: Genome Medicine 2020 12:103

    Content type: Database

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  15. The rising prevalence of type 2 diabetes (T2D) poses a major global challenge. It remains unresolved to what extent transcriptomic signatures of metabolic dysregulation and T2D can be observed in easily access...

    Authors: Valborg Gudmundsdottir, Helle Krogh Pedersen, Gianluca Mazzoni, Kristine H. Allin, Anna Artati, Joline W. Beulens, Karina Banasik, Caroline Brorsson, Henna Cederberg, Elizaveta Chabanova, Federico De Masi, Petra J. Elders, Ian Forgie, Giuseppe N. Giordano, Harald Grallert, Ramneek Gupta…

    Citation: Genome Medicine 2020 12:109

    Content type: Research

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  16. Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic d...

    Authors: Melanie Hennart, Leonardo G. Panunzi, Carla Rodrigues, Quentin Gaday, Sarah L. Baines, Marina Barros-Pinkelnig, Annick Carmi-Leroy, Melody Dazas, Anne Marie Wehenkel, Xavier Didelot, Julie Toubiana, Edgar Badell and Sylvain Brisse

    Citation: Genome Medicine 2020 12:107

    Content type: Research

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  17. Genome-wide association studies (GWAS) have identified pervasive sharing of genetic architectures across multiple immune-mediated diseases (IMD). By learning the genetic basis of IMD risk from common diseases,...

    Authors: Oliver S. Burren, Guillermo Reales, Limy Wong, John Bowes, James C. Lee, Anne Barton, Paul A. Lyons, Kenneth G. C. Smith, Wendy Thomson, Paul D. W. Kirk and Chris Wallace

    Citation: Genome Medicine 2020 12:106

    Content type: Research

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  18. DNA methylation has been shown to be associated with adiposity in adulthood. However, whether similar DNA methylation patterns are associated with childhood and adolescent body mass index (BMI) is largely unkn...

    Authors: Florianne O. L. Vehmeijer, Leanne K. Küpers, Gemma C. Sharp, Lucas A. Salas, Samantha Lent, Dereje D. Jima, Gwen Tindula, Sarah Reese, Cancan Qi, Olena Gruzieva, Christian Page, Faisal I. Rezwan, Philip E. Melton, Ellen Nohr, Geòrgia Escaramís, Peter Rzehak…

    Citation: Genome Medicine 2020 12:105

    Content type: Research

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  19. Multidrug-resistant (MDR) Mycobacterium tuberculosis complex strains not detected by commercial molecular drug susceptibility testing (mDST) assays due to the RpoB I491F resistance mutation are threatening the co...

    Authors: Patrick Beckert, Elisabeth Sanchez-Padilla, Matthias Merker, Viola Dreyer, Thomas A. Kohl, Christian Utpatel, Claudio U. Köser, Ivan Barilar, Nazir Ismail, Shaheed Vally Omar, Marisa Klopper, Robin M. Warren, Harald Hoffmann, Gugu Maphalala, Elisa Ardizzoni, Bouke C. de Jong…

    Citation: Genome Medicine 2020 12:104

    Content type: Research

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  20. The gut-liver axis plays a pivotal role in the pathogenesis of hepatocellular carcinoma (HCC). However, the correlations between the gut microbiome and the liver tumor transcriptome in patients with HCC and th...

    Authors: Hechen Huang, Zhigang Ren, Xingxing Gao, Xiaoyi Hu, Yuan Zhou, Jianwen Jiang, Haifeng Lu, Shengyong Yin, Junfang Ji, Lin Zhou and Shusen Zheng

    Citation: Genome Medicine 2020 12:102

    Content type: Research

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  21. Heat shock proteins (HSPs), a representative family of chaperone genes, play crucial roles in malignant progression and are pursued as attractive anti-cancer therapeutic targets. Despite tremendous efforts to ...

    Authors: Zhao Zhang, Ji Jing, Youqiong Ye, Zhiao Chen, Ying Jing, Shengli Li, Wei Hong, Hang Ruan, Yaoming Liu, Qingsong Hu, Jun Wang, Wenbo Li, Chunru Lin, Lixia Diao, Yubin Zhou and Leng Han

    Citation: Genome Medicine 2020 12:101

    Content type: Research

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  22. Polygenic risk scores (PRSs) are a summarization of an individual’s genetic risk for a disease or trait. These scores are being generated in research and commercial settings to study how they may be used to gu...

    Authors: Shang-Fu Chen, Raquel Dias, Doug Evans, Elias L. Salfati, Shuchen Liu, Nathan E. Wineinger and Ali Torkamani

    Citation: Genome Medicine 2020 12:100

    Content type: Research

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  23. Tight regulatory loops orchestrate commitment to B cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic ...

    Authors: Juha Mehtonen, Susanna Teppo, Mari Lahnalampi, Aleksi Kokko, Riina Kaukonen, Laura Oksa, Maria Bouvy-Liivrand, Alena Malyukova, Artturi Mäkinen, Saara Laukkanen, Petri I. Mäkinen, Samuli Rounioja, Pekka Ruusuvuori, Olle Sangfelt, Riikka Lund, Tapio Lönnberg…

    Citation: Genome Medicine 2020 12:99

    Content type: Research

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  24. One of the major challenges in obesity treatment is to explain the high variability in the individual’s response to specific dietary and physical activity interventions. With this study, we tested the hypothes...

    Authors: Maria Keller, Anat Yaskolka Meir, Stephan H. Bernhart, Yftach Gepner, Ilan Shelef, Dan Schwarzfuchs, Gal Tsaban, Hila Zelicha, Lydia Hopp, Luise Müller, Kerstin Rohde, Yvonne Böttcher, Peter F. Stadler, Michael Stumvoll, Matthias Blüher, Peter Kovacs…

    Citation: Genome Medicine 2020 12:97

    Content type: Research

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  25. Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection preven...

    Authors: Ana Berbel Caban, Theodore R. Pak, Ajay Obla, Amy C. Dupper, Kieran I. Chacko, Lindsey Fox, Alexandra Mills, Brianne Ciferri, Irina Oussenko, Colleen Beckford, Marilyn Chung, Robert Sebra, Melissa Smith, Sarah Conolly, Gopi Patel, Andrew Kasarskis…

    Citation: Genome Medicine 2020 12:96

    Content type: Research

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  26. Genomic studies of patients with COVID-19, or exposed to it, are underway to delineate host factors associated with variability in susceptibility, infectivity, and disease severity. Here, we highlight the ethi...

    Authors: Gail Geller, Priya Duggal, Chloe L. Thio, Debra Mathews, Jeffrey P. Kahn, Lisa L. Maragakis and Brian T. Garibaldi

    Citation: Genome Medicine 2020 12:95

    Content type: Comment

    Published on:

  27. High-grade serous ovarian cancer (HGSOC) is a major unmet need in oncology. The remaining uncertainty on its originating tissue has hampered the discovery of molecular oncogenic pathways and the development of...

    Authors: Pietro Lo Riso, Carlo Emanuele Villa, Gilles Gasparoni, Andrea Vingiani, Raffaele Luongo, Anna Manfredi, Annemarie Jungmann, Alessia Bertolotti, Francesca Borgo, Annalisa Garbi, Michela Lupia, Pasquale Laise, Vivek Das, Giancarlo Pruneri, Giuseppe Viale, Nicoletta Colombo…

    Citation: Genome Medicine 2020 12:94

    Content type: Research

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  28. Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiol...

    Authors: Linda Kachuri, Stephen S. Francis, Maike L. Morrison, George A. Wendt, Yohan Bossé, Taylor B. Cavazos, Sara R. Rashkin, Elad Ziv and John S. Witte

    Citation: Genome Medicine 2020 12:93

    Content type: Research

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  29. Multiple studies suggest a key role for gut microbiota in IgE-mediated food allergy (FA) development, but to date, none has studied it in the persistent state.

    Authors: Michael R. Goldberg, Hadar Mor, Dafna Magid Neriya, Faiga Magzal, Efrat Muller, Michael Y. Appel, Liat Nachshon, Elhanan Borenstein, Snait Tamir, Yoram Louzoun, Ilan Youngster, Arnon Elizur and Omry Koren

    Citation: Genome Medicine 2020 12:92

    Content type: Research

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  30. Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs ...

    Authors: Shiyang Liu, Nathan Harmston, Trudy Lee Glaser, Yunka Wong, Zheng Zhong, Babita Madan, David M. Virshup and Enrico Petretto

    Citation: Genome Medicine 2020 12:89

    Content type: Research

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  31. Autism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. The neonatal epigenome has the potential to reflect past interactions between genetic a...

    Authors: Charles E. Mordaunt, Julia M. Jianu, Benjamin I. Laufer, Yihui Zhu, Hyeyeon Hwang, Keith W. Dunaway, Kelly M. Bakulski, Jason I. Feinberg, Heather E. Volk, Kristen Lyall, Lisa A. Croen, Craig J. Newschaffer, Sally Ozonoff, Irva Hertz-Picciotto, M. Daniele Fallin, Rebecca J. Schmidt…

    Citation: Genome Medicine 2020 12:88

    Content type: Research

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  32. During aging, there is a physiological decline, an increase of morbidity and mortality, and a natural change in the gut microbiome. In this study, we investigated the influence of the gut microbiome on differe...

    Authors: Dana Binyamin, Nir Werbner, Meital Nuriel-Ohayon, Atara Uzan, Hadar Mor, Atallah Abbas, Oren Ziv, Raffaele Teperino, Roee Gutman and Omry Koren

    Citation: Genome Medicine 2020 12:87

    Content type: Research

    Published on:

  33. Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases. While numerous methods can quantify immune or stromal cells in human tissue samples from ...

    Authors: Florent Petitprez, Sacha Levy, Cheng-Ming Sun, Maxime Meylan, Christophe Linhard, Etienne Becht, Nabila Elarouci, David Tavel, Lubka T. Roumenina, Mira Ayadi, Catherine Sautès-Fridman, Wolf H. Fridman and Aurélien de Reyniès

    Citation: Genome Medicine 2020 12:86

    Content type: Method

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  34. Solid tumors such as pancreatic ductal adenocarcinoma (PDAC) comprise not just tumor cells but also a microenvironment with which the tumor cells constantly interact. Detailed characterization of the cellular ...

    Authors: Wei Lin, Pawan Noel, Erkut H. Borazanci, Jeeyun Lee, Albert Amini, In Woong Han, Jin Seok Heo, Gayle S. Jameson, Cory Fraser, Margaux Steinbach, Yanghee Woo, Yuman Fong, Derek Cridebring, Daniel D. Von Hoff, Joon Oh Park and Haiyong Han

    Citation: Genome Medicine 2020 12:80

    Content type: Research

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  35. APOBEC-driven mutagenesis and functional positive selection of mutated genes may synergistically drive the higher frequency of some hotspot driver mutations compared to other mutations within the same gene, as...

    Authors: Ming-Jun Shi, Xiang-Yu Meng, Jacqueline Fontugne, Chun-Long Chen, François Radvanyi and Isabelle Bernard-Pierrot

    Citation: Genome Medicine 2020 12:85

    Content type: Research

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  36. Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currentl...

    Authors: Christina A. Castellani, Ryan J. Longchamps, Jason A. Sumpter, Charles E. Newcomb, John A. Lane, Megan L. Grove, Jan Bressler, Jennifer A. Brody, James S. Floyd, Traci M. Bartz, Kent D. Taylor, Penglong Wang, Adrienne Tin, Josef Coresh, James S. Pankow, Myriam Fornage…

    Citation: Genome Medicine 2020 12:84

    Content type: Research

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  37. Immune checkpoint blockade (ICB) therapy has demonstrated considerable clinical benefit in several malignancies, but has shown favorable response in only a small proportion of cancer patients. Recent studies h...

    Authors: Youqiong Ye, Xinwei Kuang, Zuozhong Xie, Long Liang, Zhao Zhang, Yongchang Zhang, Fangyu Ma, Qian Gao, Ruimin Chang, Heng-Huan Lee, Shuang Zhao, Juan Su, Hui Li, Jingbo Peng, Huifang Chen, Minzhu Yin…

    Citation: Genome Medicine 2020 12:83

    Content type: Research

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  38. Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the princ...

    Authors: Tianlu Li, Lourdes Ortiz-Fernández, Eduardo Andrés-León, Laura Ciudad, Biola M. Javierre, Elena López-Isac, Alfredo Guillén-Del-Castillo, Carmen Pilar Simeón-Aznar, Esteban Ballestar and Javier Martin

    Citation: Genome Medicine 2020 12:81

    Content type: Research

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  39. Identification of actionable genomic vulnerabilities is key to precision oncology. Utilizing a large-scale drug screening in patient-derived xenografts, we uncover driver gene alteration connections, derive dr...

    Authors: Lidia Mateo, Miquel Duran-Frigola, Albert Gris-Oliver, Marta Palafox, Maurizio Scaltriti, Pedram Razavi, Sarat Chandarlapaty, Joaquin Arribas, Meritxell Bellet, Violeta Serra and Patrick Aloy

    Citation: Genome Medicine 2020 12:78

    Content type: Method

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  40. Long non-coding RNAs (lncRNAs) are extensively intricate in the tumorigenesis and metastasis of various cancer types. Nevertheless, the detailed molecular mechanisms of lncRNA in non-small cell lung cancer (NS...

    Authors: Cheng-Cao Sun, Wei Zhu, Shu-Jun Li, Wei Hu, Jian Zhang, Yue Zhuo, Han Zhang, Juan Wang, Yu Zhang, Shao-Xin Huang, Qi-Qiang He and De-Jia Li

    Citation: Genome Medicine 2020 12:77

    Content type: Research

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  41. Congenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disea...

    Authors: Jose M. G. Izarzugaza, Sabrina G. Ellesøe, Canan Doganli, Natasja Spring Ehlers, Marlene D. Dalgaard, Enrique Audain, Gregor Dombrowsky, Karina Banasik, Alejandro Sifrim, Anna Wilsdon, Bernard Thienpont, Jeroen Breckpot, Marc Gewillig, J. David Brook, Marc-Phillip Hitz, Lars A. Larsen…

    Citation: Genome Medicine 2020 12:76

    Content type: Research

    Published on:

  42. Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational predicti...

    Authors: Shuang Li, K. Joeri van der Velde, Dick de Ridder, Aalt D. J. van Dijk, Dimitrios Soudis, Leslie R. Zwerwer, Patrick Deelen, Dennis Hendriksen, Bart Charbon, Marielle E. van Gijn, Kristin Abbott, Birgit Sikkema-Raddatz, Cleo C. van Diemen, Wilhelmina S. Kerstjens-Frederikse, Richard J. Sinke and Morris A. Swertz

    Citation: Genome Medicine 2020 12:75

    Content type: Method

    Published on:

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