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  1. Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown.

    Authors: Sjors Middelkamp, Judith M. Vlaar, Jacques Giltay, Jerome Korzelius, Nicolle Besselink, Sander Boymans, Roel Janssen, Lisanne de la Fonteijne, Ellen van Binsbergen, Markus J. van Roosmalen, Ron Hochstenbach, Daniela Giachino, Michael E. Talkowski, Wigard P. Kloosterman and Edwin Cuppen

    Citation: Genome Medicine 2019 11:79

    Content type: Research

    Published on:

  2. Precision oncology involves analysis of individual cancer samples to understand the genes and pathways involved in the development and progression of a cancer. To improve patient care, knowledge of diagnostic,...

    Authors: Jake Lever, Martin R. Jones, Arpad M. Danos, Kilannin Krysiak, Melika Bonakdar, Jasleen K. Grewal, Luka Culibrk, Obi L. Griffith, Malachi Griffith and Steven J. M. Jones

    Citation: Genome Medicine 2019 11:78

    Content type: Research

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  3. The 2015 American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines for clinical sequence variant interpretation state that “well-established” functio...

    Authors: Dona M. Kanavy, Shannon M. McNulty, Meera K. Jairath, Sarah E. Brnich, Chris Bizon, Bradford C. Powell and Jonathan S. Berg

    Citation: Genome Medicine 2019 11:77

    Content type: Research

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  4. Manually curated variant knowledgebases and their associated knowledge models are serving an increasingly important role in distributing and interpreting variants in cancer. These knowledgebases vary in their ...

    Authors: Arpad M. Danos, Kilannin Krysiak, Erica K. Barnell, Adam C. Coffman, Joshua F. McMichael, Susanna Kiwala, Nicholas C. Spies, Lana M. Sheta, Shahil P. Pema, Lynzey Kujan, Kaitlin A. Clark, Amber Z. Wollam, Shruti Rao, Deborah I. Ritter, Dmitriy Sonkin, Gordana Raca…

    Citation: Genome Medicine 2019 11:76

    Content type: Correspondence

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  5. Inherited susceptibility to common, complex diseases may be caused by rare, pathogenic variants (“monogenic”) or by the cumulative effect of numerous common variants (“polygenic”). Comprehensive genome interpr...

    Authors: Julian R. Homburger, Cynthia L. Neben, Gilad Mishne, Alicia Y. Zhou, Sekar Kathiresan and Amit V. Khera

    Citation: Genome Medicine 2019 11:74

    Content type: Research

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  6. Acute myeloid leukemia (AML), caused by the abnormal proliferation of immature myeloid cells in the blood or bone marrow, is one of the most common hematologic malignancies. Currently, the interactions between...

    Authors: Jian Zhang, Xihao Hu, Jin Wang, Avinash Das Sahu, David Cohen, Li Song, Zhangyi Ouyang, Jingyu Fan, Binbin Wang, Jingxin Fu, Shengqing Gu, Moshe Sade-Feldman, Nir Hacohen, Wuju Li, Xiaomin Ying, Bo Li…

    Citation: Genome Medicine 2019 11:73

    Content type: Research

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  7. Artificial intelligence (AI) is the development of computer systems that are able to perform tasks that normally require human intelligence. Advances in AI software and hardware, especially deep learning algor...

    Authors: Raquel Dias and Ali Torkamani

    Citation: Genome Medicine 2019 11:70

    Content type: Review

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  8. Group 1 pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite recent therapeutic advances. Pathogenic remodeling of pulmonary arterioles leads to increased pulmonary pressures, ri...

    Authors: Na Zhu, Michael W. Pauciulo, Carrie L. Welch, Katie A. Lutz, Anna W. Coleman, Claudia Gonzaga-Jauregui, Jiayao Wang, Joseph M. Grimes, Lisa J. Martin, Hua He, Yufeng Shen, Wendy K. Chung and William C. Nichols

    Citation: Genome Medicine 2019 11:69

    Content type: Research

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  9. Since different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) ra...

    Authors: Anna Lindstrand, Jesper Eisfeldt, Maria Pettersson, Claudia M. B. Carvalho, Malin Kvarnung, Giedre Grigelioniene, Britt-Marie Anderlid, Olof Bjerin, Peter Gustavsson, Anna Hammarsjö, Patrik Georgii-Hemming, Erik Iwarsson, Maria Johansson-Soller, Kristina Lagerstedt-Robinson, Agne Lieden, Måns Magnusson…

    Citation: Genome Medicine 2019 11:68

    Content type: Research

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  10. Cancer neoantigens are expressed only in cancer cells and presented on the tumor cell surface in complex with major histocompatibility complex (MHC) class I proteins for recognition by cytotoxic T cells. Accur...

    Authors: Chi Zhou, Zhiting Wei, Zhanbing Zhang, Biyu Zhang, Chenyu Zhu, Ke Chen, Guohui Chuai, Sheng Qu, Lu Xie, Yong Gao and Qi Liu

    Citation: Genome Medicine 2019 11:67

    Content type: Software

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  11. Sepsis, a life-threatening organ dysfunction caused by a dysregulated systemic immune response to infection, associates with reduced responsiveness to subsequent infections. How such tolerance is acquired is n...

    Authors: Clara Lorente-Sorolla, Antonio Garcia-Gomez, Francesc Català-Moll, Víctor Toledano, Laura Ciudad, José Avendaño-Ortiz, Charbel Maroun-Eid, Alejandro Martín-Quirós, Mónica Martínez-Gallo, Adolfo Ruiz-Sanmartín, Álvaro García del Campo, Ricard Ferrer-Roca, Juan Carlos Ruiz-Rodriguez, Damiana Álvarez-Errico, Eduardo López-Collazo and Esteban Ballestar

    Citation: Genome Medicine 2019 11:66

    Content type: Research

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  12. Neurodevelopmental disorders (NDDs) such as autism spectrum disorder, intellectual disability, developmental disability, and epilepsy are characterized by abnormal brain development that may affect cognition, ...

    Authors: Julie Chow, Matthew Jensen, Hajar Amini, Farhad Hormozdiari, Osnat Penn, Sagiv Shifman, Santhosh Girirajan and Fereydoun Hormozdiari

    Citation: Genome Medicine 2019 11:65

    Content type: Research

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  13. Here, we present the Northeast Asian Reference Database (NARD), including whole-genome sequencing data of 1779 individuals from Korea, Mongolia, Japan, China, and Hong Kong. NARD provides the genetic diversity...

    Authors: Seong-Keun Yoo, Chang-Uk Kim, Hie Lim Kim, Sungjae Kim, Jong-Yeon Shin, Namcheol Kim, Joshua Sung Woo Yang, Kwok-Wai Lo, Belong Cho, Fumihiko Matsuda, Stephan C. Schuster, Changhoon Kim, Jong-Il Kim and Jeong-Sun Seo

    Citation: Genome Medicine 2019 11:64

    Content type: Database

    Published on:

  14. Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease, and gene expression profiling has identified several molecular subtypes with distinct biological and clinicopathological characteristics. While...

    Authors: Joep J. de Jong, Yang Liu, A. Gordon Robertson, Roland Seiler, Clarice S. Groeneveld, Michiel S. van der Heijden, Jonathan L. Wright, James Douglas, Marc Dall’Era, Simon J. Crabb, Bas W. G. van Rhijn, Kim E. M. van Kessel, Elai Davicioni, Mauro A. A. Castro, Yair Lotan, Ellen C. Zwarthoff…

    Citation: Genome Medicine 2019 11:60

    Content type: Research

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  15. Recent evidence suggests that immunotherapy efficacy in melanoma is modulated by gut microbiota. Few studies have examined this phenomenon in humans, and none have incorporated metatranscriptomics, important f...

    Authors: Brandilyn A. Peters, Melissa Wilson, Una Moran, Anna Pavlick, Allison Izsak, Todd Wechter, Jeffrey S. Weber, Iman Osman and Jiyoung Ahn

    Citation: Genome Medicine 2019 11:61

    Content type: Research

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  16. After years of concentrated research efforts, the exact cause of Crohn’s disease (CD) remains unknown. Its accurate diagnosis, however, helps in management and preventing the onset of disease. Genome-wide asso...

    Authors: Yanran Wang, Maximilian Miller, Yuri Astrakhan, Britt-Sabina Petersen, Stefan Schreiber, Andre Franke and Yana Bromberg

    Citation: Genome Medicine 2019 11:59

    Content type: Research

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  17. As the number of stroke survivors continues to increase, identification of therapeutic targets for stroke recovery has become a priority in stroke genomics research. The introduction of high-throughput genotyp...

    Authors: Julián N. Acosta, Stacy C. Brown and Guido J. Falcone

    Citation: Genome Medicine 2019 11:58

    Content type: Comment

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  18. Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T cell recognition. Recently, researchers and clinicians have leveraged next generation sequenci...

    Authors: Megan M. Richters, Huiming Xia, Katie M. Campbell, William E. Gillanders, Obi L. Griffith and Malachi Griffith

    Citation: Genome Medicine 2019 11:56

    Content type: Review

    Published on:

  19. Human cancer cell lines are fundamental models for cancer research and therapeutic strategy development. However, there is no characterization of circular RNAs (circRNAs) in a large number of cancer cell lines.

    Authors: Hang Ruan, Yu Xiang, Junsuk Ko, Shengli Li, Ying Jing, Xiaoyu Zhu, Youqiong Ye, Zhao Zhang, Tingting Mills, Jing Feng, Chun-Jie Liu, Ji Jing, Jin Cao, Bingying Zhou, Li Wang, Yubin Zhou…

    Citation: Genome Medicine 2019 11:55

    Content type: Research

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  20. DNA methylation changes with age. Chronological age predictors built from DNA methylation are termed ‘epigenetic clocks’. The deviation of predicted age from the actual age (‘age acceleration residual’, AAR) h...

    Authors: Qian Zhang, Costanza L. Vallerga, Rosie M. Walker, Tian Lin, Anjali K. Henders, Grant W. Montgomery, Ji He, Dongsheng Fan, Javed Fowdar, Martin Kennedy, Toni Pitcher, John Pearson, Glenda Halliday, John B. Kwok, Ian Hickie, Simon Lewis…

    Citation: Genome Medicine 2019 11:54

    Content type: Research

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  21. Clinical laboratories implement a variety of measures to classify somatic sequence variants and identify clinically significant variants to facilitate the implementation of precision medicine. To standardize t...

    Authors: Max M. He, Quan Li, Muqing Yan, Hui Cao, Yue Hu, Karen Y. He, Kajia Cao, Marilyn M. Li and Kai Wang

    Citation: Genome Medicine 2019 11:53

    Content type: Software

    Published on:

  22. Chemogenetic profiling enables the identification of gene mutations that enhance or suppress the activity of chemical compounds. This knowledge provides insights into drug mechanism of action, genetic vulnerab...

    Authors: Medina Colic, Gang Wang, Michal Zimmermann, Keith Mascall, Megan McLaughlin, Lori Bertolet, W. Frank Lenoir, Jason Moffat, Stephane Angers, Daniel Durocher and Traver Hart

    Citation: Genome Medicine 2019 11:52

    Content type: Software

    Published on:

  23. Genomic medicine has paved the way for identifying biomarkers and therapeutically actionable targets for complex diseases, but is complicated by the involvement of thousands of variably expressed genes across ...

    Authors: Danuta R. Gawel, Jordi Serra-Musach, Sandra Lilja, Jesper Aagesen, Alex Arenas, Bengt Asking, Malin Bengnér, Janne Björkander, Sophie Biggs, Jan Ernerudh, Henrik Hjortswang, Jan-Erik Karlsson, Mattias Köpsen, Eun Jung Lee, Antonio Lentini, Xinxiu Li…

    Citation: Genome Medicine 2019 11:47

    Content type: Research

    Published on:

  24. It was highlighted that the original article [1] contained a typesetting mistake in the name of Noel Filipe da Cunha Carvalho de Miranda. This was incorrectly captured as Noel Filipe da Cunha Carvahlo de Miran...

    Authors: Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Zuzana Loncova, Wilfried Posch, Doris Wilflingseder, Sieghart Sopper, Marieke Ijsselsteijn, Thomas P. Brouwer, Douglas Johnson, Yaomin Xu, Yu Wang…

    Citation: Genome Medicine 2019 11:50

    Content type: Correction

    Published on:

    The original article was published in Genome Medicine 2019 11:34

  25. Knowing the activity of the mutational processes shaping a cancer genome may provide insight into tumorigenesis and personalized therapy. It is thus important to characterize the signatures of active mutationa...

    Authors: Damian Wojtowicz, Itay Sason, Xiaoqing Huang, Yoo-Ah Kim, Mark D. M. Leiserson, Teresa M. Przytycka and Roded Sharan

    Citation: Genome Medicine 2019 11:49

    Content type: Method

    Published on:

  26. Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have ...

    Authors: Ye Cao, Mari J. Tokita, Edward S. Chen, Rajarshi Ghosh, Tiansheng Chen, Yanming Feng, Elizabeth Gorman, Federica Gibellini, Patricia A. Ward, Alicia Braxton, Xia Wang, Linyan Meng, Rui Xiao, Weimin Bi, Fan Xia, Christine M. Eng…

    Citation: Genome Medicine 2019 11:48

    Content type: Research

    Published on:

  27. A multi-disciplinary approach to promote engagement, inform decision-making and support clinicians and patients is increasingly advocated to realise the potential of genome-scale sequencing in the clinic for p...

    Authors: John Taylor, Jude Craft, Edward Blair, Sarah Wordsworth, David Beeson, Saleel Chandratre, Judith Cossins, Tracy Lester, Andrea H. Németh, Elizabeth Ormondroyd, Smita Y. Patel, Alistair T. Pagnamenta, Jenny C. Taylor, Kate L. Thomson, Hugh Watkins, Andrew O. M. Wilkie…

    Citation: Genome Medicine 2019 11:46

    Content type: Research

    Published on:

  28. Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative ...

    Authors: Keira A. Cohen, Abigail L. Manson, Christopher A. Desjardins, Thomas Abeel and Ashlee M. Earl

    Citation: Genome Medicine 2019 11:45

    Content type: Review

    Published on:

  29. Next-generation sequencing has allowed for the identification of different genetic variations, which are known to contribute to diseases. Of these, insertions and deletions are the second most abundant type of...

    Authors: Jing Hao Wong, Daichi Shigemizu, Yukiko Yoshii, Shintaro Akiyama, Azusa Tanaka, Hidewaki Nakagawa, Shu Narumiya and Akihiro Fujimoto

    Citation: Genome Medicine 2019 11:44

    Content type: Research

    Published on:

  30. Neoantigens that arise as a consequence of tumor-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumor types, a high number ...

    Authors: Giuseppe Rospo, Annalisa Lorenzato, Nabil Amirouchene-Angelozzi, Alessandro Magrì, Carlotta Cancelliere, Giorgio Corti, Carola Negrino, Vito Amodio, Monica Montone, Alice Bartolini, Ludovic Barault, Luca Novara, Claudio Isella, Enzo Medico, Andrea Bertotti, Livio Trusolino…

    Citation: Genome Medicine 2019 11:42

    Content type: Research

    Published on:

  31. Mycobacterium tuberculosis resistance to anti-tuberculosis drugs is a major threat to global public health. Whole genome sequencing (WGS) is rapidly gaining traction as a diagnostic tool for clinical tuberculosis...

    Authors: Jody E. Phelan, Denise M. O’Sullivan, Diana Machado, Jorge Ramos, Yaa E. A. Oppong, Susana Campino, Justin O’Grady, Ruth McNerney, Martin L. Hibberd, Miguel Viveiros, Jim F. Huggett and Taane G. Clark

    Citation: Genome Medicine 2019 11:41

    Content type: Software

    Published on:

  32. The expression of antigens that are recognized by self-reactive T cells is essential for immune-mediated tumor rejection by immune checkpoint blockade (ICB) therapy. Growing evidence suggests that mutation-ass...

    Authors: Claire Lhuillier, Nils-Petter Rudqvist, Olivier Elemento, Silvia C. Formenti and Sandra Demaria

    Citation: Genome Medicine 2019 11:40

    Content type: Opinion

    Published on:

  33. Personalized care of cancer patients undergoing treatment with immune checkpoint inhibitors will require approaches that can predict their susceptibility to immune-related adverse events. Understanding the rol...

    Authors: Zia Khan, Christian Hammer, Ellie Guardino, G. Scott Chandler and Matthew L. Albert

    Citation: Genome Medicine 2019 11:39

    Content type: Comment

    Published on:

  34. Diagnosis of primary immunodeficiencies (PIDs) is complex and cumbersome yet important for the clinical management of the disease. Exome sequencing may provide a genetic diagnosis in a significant number of pa...

    Authors: Peer Arts, Annet Simons, Mofareh S. AlZahrani, Elanur Yilmaz, Eman AlIdrissi, Koen J. van Aerde, Njood Alenezi, Hamza A. AlGhamdi, Hadeel A. AlJubab, Abdulrahman A. Al-Hussaini, Fahad AlManjomi, Alaa B. Alsaad, Badr Alsaleem, Abdulrahman A. Andijani, Ali Asery, Walid Ballourah…

    Citation: Genome Medicine 2019 11:38

    Content type: Research

    Published on:

  35. Measures of the adaptive immune response have prognostic and predictive associations in melanoma and other cancer types. Specifically, intratumoral T cell density and function have considerable prognostic and ...

    Authors: Sara R. Selitsky, Lisle E. Mose, Christof C. Smith, Shengjie Chai, Katherine A. Hoadley, Dirk P. Dittmer, Stergios J. Moschos, Joel S. Parker and Benjamin G. Vincent

    Citation: Genome Medicine 2019 11:36

    Content type: Research

    Published on:

  36. Recent sequencing studies on healthy skin and esophagus have found that, as we age, these tissues become colonized by mutant clones of cells carrying driver mutations in traditional cancer genes. This comment ...

    Authors: Inigo Martincorena

    Citation: Genome Medicine 2019 11:35

    Content type: Comment

    Published on:

  37. Somatic genetic testing is rapidly becoming the standard of care in many adult and pediatric cancers. Previously, the standard approach was single-gene or focused multigene testing, but many centers have moved...

    Authors: Lea F. Surrey, Suzanne P. MacFarland, Fengqi Chang, Kajia Cao, Komal S. Rathi, Gozde T. Akgumus, Daniel Gallo, Fumin Lin, Adam Gleason, Pichai Raman, Richard Aplenc, Rochelle Bagatell, Jane Minturn, Yael Mosse, Mariarita Santi, Sarah K. Tasian…

    Citation: Genome Medicine 2019 11:32

    Content type: Research

    Published on:

  38. We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry...

    Authors: Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Zuzana Loncova, Wilfried Posch, Doris Wilflingseder, Sieghart Sopper, Marieke Ijsselsteijn, Thomas P. Brouwer, Douglas Johnson, Yaomin Xu, Yu Wang…

    Citation: Genome Medicine 2019 11:34

    Content type: Method

    Published on:

    The Correction to this article has been published in Genome Medicine 2019 11:50

  39. As epigenetic studies become more common and lead to new insights into health and disease, the return of individual epigenetic results to research participants, in particular in large-scale epigenomic studies,...

    Authors: Stephanie O. M. Dyke, Katie M. Saulnier, Charles Dupras, Amy P. Webster, Karen Maschke, Mark Rothstein, Reiner Siebert, Jörn Walter, Stephan Beck, Tomi Pastinen and Yann Joly

    Citation: Genome Medicine 2019 11:31

    Content type: Opinion

    Published on:

  40. Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains cha...

    Authors: Avinash V. Dharmadhikari, Rajarshi Ghosh, Bo Yuan, Pengfei Liu, Hongzheng Dai, Sami Al Masri, Jennifer Scull, Jennifer E. Posey, Allen H. Jiang, Weimin He, Francesco Vetrini, Alicia A. Braxton, Patricia Ward, Theodore Chiang, Chunjing Qu, Shen Gu…

    Citation: Genome Medicine 2019 11:30

    Content type: Research

    Published on:

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