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  2. 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

    Published on:

  3. 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

    Published on:

  4. 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:

  5. 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:

  6. The concentrations of the highly atherogenic lipoprotein(a) [Lp(a)] are mainly genetically determined by the LPA gene locus. However, up to 70% of the coding sequence is located in the complex so-called kringle I...

    Authors: Silvia Di Maio, Rebecca Grüneis, Gertraud Streiter, Claudia Lamina, Manuel Maglione, Sebastian Schoenherr, Dietmar Öfner, Barbara Thorand, Annette Peters, Kai-Uwe Eckardt, Anna Köttgen, Florian Kronenberg and Stefan Coassin

    Citation: Genome Medicine 2020 12:74

    Content type: Research

    Published on:

  7. For circadian medicine to influence health, such as when to take a drug or undergo a procedure, a biomarker of molecular clock phase is required––one that is easily measured and generalizable across a broad po...

    Authors: Gang Wu, Marc D. Ruben, Lauren J. Francey, David F. Smith, Joseph D. Sherrill, John E. Oblong, Kevin J. Mills and John B. Hogenesch

    Citation: Genome Medicine 2020 12:73

    Content type: Research

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  8. DNA originating from degenerate tumour cells can be detected in the circulation in many tumour types, where it can be used as a marker of disease burden as well as to monitor treatment response. Although circu...

    Authors: Edmund Lau, Patrick McCoy, Fairleigh Reeves, Ken Chow, Michael Clarkson, Edmond M. Kwan, Kate Packwood, Helen Northen, Miao He, Zoya Kingsbury, Stefano Mangiola, Michael Kerger, Marc A. Furrer, Helen Crowe, Anthony J. Costello, David J. McBride…

    Citation: Genome Medicine 2020 12:72

    Content type: Research

    Published on:

  10. The ongoing COVID-19 pandemic has created an urgency to identify novel vaccine targets for protective immunity against SARS-CoV-2. Early reports identify protective roles for both humoral and cell-mediated imm...

    Authors: Asaf Poran, Dewi Harjanto, Matthew Malloy, Christina M. Arieta, Daniel A. Rothenberg, Divya Lenkala, Marit M. van Buuren, Terri A. Addona, Michael S. Rooney, Lakshmi Srinivasan and Richard B. Gaynor

    Citation: Genome Medicine 2020 12:70

    Content type: Research

    Published on:

  11. Current computational methods on Hi-C analysis focused on identifying Mb-size domains often failed to unveil the underlying functional and mechanistic relationship of chromatin structure and gene regulation. W...

    Authors: Yufan Zhou, Xiaolong Cheng, Yini Yang, Tian Li, Jingwei Li, Tim H.-M. Huang, Junbai Wang, Shili Lin and Victor X. Jin

    Citation: Genome Medicine 2020 12:69

    Content type: Method

    Published on:

  12. Many genetic/genomic disorders are caused by genomic rearrangements. Standard methods can often characterize these variations only partly, e.g., copy number changes or breakpoints. It is important to fully und...

    Authors: Satomi Mitsuhashi, Sachiko Ohori, Kazutaka Katoh, Martin C. Frith and Naomichi Matsumoto

    Citation: Genome Medicine 2020 12:67

    Content type: Research

    Published on:

  13. Although the microbiome is established as an important regulator of health and disease, the role of viruses that inhabit asymptomatic humans (collectively, the virome) is less defined. While we are still chara...

    Authors: Fatemeh Adiliaghdam and Kate L. Jeffrey

    Citation: Genome Medicine 2020 12:66

    Content type: Comment

    Published on:

  14. SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this...

    Authors: Andrew D. Davidson, Maia Kavanagh Williamson, Sebastian Lewis, Deborah Shoemark, Miles W. Carroll, Kate J. Heesom, Maria Zambon, Joanna Ellis, Philip A. Lewis, Julian A. Hiscox and David A. Matthews

    Citation: Genome Medicine 2020 12:68

    Content type: Research

    Published on:

  15. There is increasing evidence that the intestinal microbiota plays a crucial role in the maturation of the immune system and the prevention of diseases during childhood. Early-life short-course antibiotic use m...

    Authors: Ceren Ozkul, Victoria E. Ruiz, Thomas Battaglia, Joseph Xu, Claire Roubaud-Baudron, Ken Cadwell, Guillermo I. Perez-Perez and Martin J. Blaser

    Citation: Genome Medicine 2020 12:65

    Content type: Research

    Published on:

  16. A challenge in the post-GWAS era is to assign function to disease-associated variants. However, available resources do not include all tissues or environmental exposures that are relevant to all diseases. For ...

    Authors: Emma E. Thompson, Quynh Dang, Blair Mitchell-Handley, Kavitha Rajendran, Sumati Ram-Mohan, Julian Solway, Carole Ober and Ramaswamy Krishnan

    Citation: Genome Medicine 2020 12:64

    Content type: Research

    Published on:

  17. Small cell lung cancer (SCLC) is a more aggressive subtype of lung cancer that often results in rapid tumor growth, early metastasis, and acquired therapeutic resistance. Consequently, such phenotypical charac...

    Authors: Aileen Patricia Szczepanski, Zibo Zhao, Tori Sosnowski, Young Ah Goo, Elizabeth Thomas Bartom and Lu Wang

    Citation: Genome Medicine 2020 12:63

    Content type: Research

    Published on:

  18. When interpreting sequencing data from multiple spatial or longitudinal biopsies, detecting sample mix-ups is essential, yet more difficult than in studies of germline variation. In most genomic studies of tum...

    Authors: Brent S. Pedersen, Preetida J. Bhetariya, Joe Brown, Stephanie N. Kravitz, Gabor Marth, Randy L. Jensen, Mary P. Bronner, Hunter R. Underhill and Aaron R. Quinlan

    Citation: Genome Medicine 2020 12:62

    Content type: Software

    Published on:

  20. The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear...

    Authors: Robert F. Hillary, Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, Sven Erik Ojavee, Qian Zhang, David C. Liewald, Craig W. Ritchie, Kathryn L. Evans, Elliot M. Tucker-Drob, Naomi R. Wray, Allan F. McRae, Peter M. Visscher…

    Citation: Genome Medicine 2020 12:60

    Content type: Research

    Published on:

  21. Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consi...

    Authors: Richard Creswell, Jie Tan, Jonathan W. Leff, Brandon Brooks, Michael A. Mahowald, Ruth Thieroff-Ekerdt and Georg K. Gerber

    Citation: Genome Medicine 2020 12:59

    Content type: Research

    Published on:

  23. COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-...

    Authors: Minfeng Xiao, Xiaoqing Liu, Jingkai Ji, Min Li, Jiandong Li, Lin Yang, Wanying Sun, Peidi Ren, Guifang Yang, Jincun Zhao, Tianzhu Liang, Huahui Ren, Tian Chen, Huanzi Zhong, Wenchen Song, Yanqun Wang…

    Citation: Genome Medicine 2020 12:57

    Content type: Research

    Published on:

  25. Traditionally, the transcriptomic and proteomic characterisation of CD4+ T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA sequencing (scRNA-seq) ...

    Authors: Dominik Trzupek, Melanie Dunstan, Antony J. Cutler, Mercede Lee, Leila Godfrey, Lorna Jarvis, Daniel B. Rainbow, Dominik Aschenbrenner, Joanne L. Jones, Holm H. Uhlig, Linda S. Wicker, John A. Todd and Ricardo C. Ferreira

    Citation: Genome Medicine 2020 12:55

    Content type: Research

    Published on:

  26. Cell-free DNA (cfDNA) analysis has become essential in cancer diagnostics and prenatal testing. We present cfNOMe, a two-in-one method of measuring cfDNA cytosine methylation and nucleosome occupancy in a single ...

    Authors: Florian Erger, Deborah Nörling, Domenica Borchert, Esther Leenen, Sandra Habbig, Michael S. Wiesener, Malte P. Bartram, Andrea Wenzel, Christian Becker, Mohammad R. Toliat, Peter Nürnberg, Bodo B. Beck and Janine Altmüller

    Citation: Genome Medicine 2020 12:54

    Content type: Method

    Published on:

  27. The human plasma proteome is important for many biological processes and targets for diagnostics and therapy. It is therefore of great interest to understand the interplay of genetic and environmental factors ...

    Authors: Wen Zhong, Anders Gummesson, Abdellah Tebani, Max J. Karlsson, Mun-Gwan Hong, Jochen M. Schwenk, Fredrik Edfors, Göran Bergström, Linn Fagerberg and Mathias Uhlén

    Citation: Genome Medicine 2020 12:53

    Content type: Research

    Published on:

  28. Studies of cancer mutations have typically focused on identifying cancer driving mutations that confer growth advantage to cancer cells. However, cancer genomes accumulate a large number of passenger somatic m...

    Authors: Yoo-Ah Kim, Damian Wojtowicz, Rebecca Sarto Basso, Itay Sason, Welles Robinson, Dorit S. Hochbaum, Mark D. M. Leiserson, Roded Sharan, Fabio Vadin and Teresa M. Przytycka

    Citation: Genome Medicine 2020 12:52

    Content type: Research

    Published on:

  29. Distinct prevalence of inherited genetic predisposition may partially explain the difference of cancer risks across ancestries. Ancestry-specific analyses of germline genomes are required to inform cancer gene...

    Authors: Ninad Oak, Andrew D. Cherniack, R. Jay Mashl, Fred R. Hirsch, Li Ding, Rameen Beroukhim, Zeynep H. Gümüş, Sharon E. Plon and Kuan-lin Huang

    Citation: Genome Medicine 2020 12:51

    Content type: Research

    Published on:

  30. Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read...

    Authors: Soumaya Zlitni, Alex Bishara, Eli L. Moss, Ekaterina Tkachenko, Joyce B. Kang, Rebecca N. Culver, Tessa M. Andermann, Ziming Weng, Christina Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou and Ami S. Bhatt

    Citation: Genome Medicine 2020 12:50

    Content type: Research

    Published on:

  31. Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of...

    Authors: Francesc Muyas, Luis Zapata, Roderic Guigó and Stephan Ossowski

    Citation: Genome Medicine 2020 12:49

    Content type: Research

    Published on:

  32. Clinical whole-genome sequencing (WGS) offers clear diagnostic benefits for patients with rare disease. However, there are barriers to its widespread adoption, including a lack of standards for clinical practi...

    Authors: Christian R. Marshall, David Bick, John W. Belmont, Stacie L. Taylor, Euan Ashley, David Dimmock, Vaidehi Jobanputra, Hutton M. Kearney, Shashikant Kulkarni and Heidi Rehm

    Citation: Genome Medicine 2020 12:48

    Content type: Comment

    Published on:

  33. Tumor cell-intrinsic mechanisms and complex interactions with the tumor microenvironment contribute to therapeutic failure via tumor evolution. It may be possible to overcome treatment resistance by developing...

    Authors: Hye Won Lee, Woosung Chung, Hae-Ock Lee, Da Eun Jeong, Areum Jo, Joung Eun Lim, Jeong Hee Hong, Do-Hyun Nam, Byong Chang Jeong, Se Hoon Park, Kyeung-Min Joo and Woong-Yang Park

    Citation: Genome Medicine 2020 12:47

    Content type: Research

    Published on:

  34. Hutchinson-Gilford progeria syndrome (HGPS) is a progeroid disease characterized by the early onset of age-related phenotypes including arthritis, loss of body fat and hair, and atherosclerosis. Cells from aff...

    Authors: Florian Köhler, Felix Bormann, Günter Raddatz, Julian Gutekunst, Samuel Corless, Tanja Musch, Anke S. Lonsdorf, Sylvia Erhardt, Frank Lyko and Manuel Rodríguez-Paredes

    Citation: Genome Medicine 2020 12:46

    Content type: Research

    Published on:

  35. Immune checkpoint blockade (ICB) with antibodies inhibiting cytotoxic T lymphocyte-associated protein-4 (CTLA-4) and programmed cell death protein-1 (PD-1) (or its ligand (PD-L1)) can stimulate immune response...

    Authors: Aaron M. Goodman, Andrea Castro, Rachel Marty Pyke, Ryosuke Okamura, Shumei Kato, Paul Riviere, Garrett Frampton, Ethan Sokol, Xinlian Zhang, Edward D. Ball, Hannah Carter and Razelle Kurzrock

    Citation: Genome Medicine 2020 12:45

    Content type: Research

    Published on:

  37. Cyclophosphamide, doxorubicin, vincristine, and prednisolone (CHOP)/CHOP-like chemotherapy is widely used in peripheral T cell lymphoma (PTCL). Here we conducted a phase 2, multicenter, randomized, controlled ...

    Authors: Ming-Ci Cai, Shu Cheng, Xin Wang, Jian-Da Hu, Yong-Ping Song, Yao-Hui Huang, Zi-Xun Yan, Yu-Jie Jiang, Xiao-Sheng Fang, Xiao-Yun Zheng, Li-Hua Dong, Meng-Meng Ji, Li Wang, Peng-Peng Xu and Wei-Li Zhao

    Citation: Genome Medicine 2020 12:41

    Content type: Research

    Published on:

  39. The contribution of somatic mosaicism, or genetic mutations arising after oocyte fertilization, to congenital heart disease (CHD) is not well understood. Further, the relationship between mosaicism in blood an...

    Authors: Alexander Hsieh, Sarah U. Morton, Jon A. L. Willcox, Joshua M. Gorham, Angela C. Tai, Hongjian Qi, Steven DePalma, David McKean, Emily Griffin, Kathryn B. Manheimer, Daniel Bernstein, Richard W. Kim, Jane W. Newburger, George A. Porter Jr, Deepak Srivastava, Martin Tristani-Firouzi…

    Citation: Genome Medicine 2020 12:42

    Content type: Research

    Published on:

  40. Endogenous retroelements (EREs) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. The dominant paradigm holds that EREs are expressed i...

    Authors: Jean-David Larouche, Assya Trofimov, Leslie Hesnard, Gregory Ehx, Qingchuan Zhao, Krystel Vincent, Chantal Durette, Patrick Gendron, Jean-Philippe Laverdure, Éric Bonneil, Caroline Côté, Sébastien Lemieux, Pierre Thibault and Claude Perreault

    Citation: Genome Medicine 2020 12:40

    Content type: Research

    Published on:

  41. Large numbers of autosomal sites are found differentially methylated in the aging genome. Due to analytical difficulties in dealing with sex differences in X-chromosome content and X-inactivation (XCI) in fema...

    Authors: Shuxia Li, Jesper B. Lund, Kaare Christensen, Jan Baumbach, Jonas Mengel-From, Torben Kruse, Weilong Li, Afsaneh Mohammadnejad, Alison Pattie, Riccardo E. Marioni, Ian J. Deary and Qihua Tan

    Citation: Genome Medicine 2020 12:39

    Content type: Research

    Published on:

  42. Pancreatic neuroendocrine tumors (PANETs) are rare, slow growing cancers that often present with local and distant metastasis upon detection. PANETS contain distinct karyotypes, epigenetic dysregulation, and r...

    Authors: Rene Quevedo, Anna Spreafico, Jeff Bruce, Arnavaz Danesh, Samah El Ghamrasni, Amanda Giesler, Youstina Hanna, Cherry Have, Tiantian Li, S. Y. Cindy Yang, Tong Zhang, Sylvia L. Asa, Benjamin Haibe-Kains, Monika Krzyzanowska, Adam C. Smith, Simron Singh…

    Citation: Genome Medicine 2020 12:38

    Content type: Research

    Published on:

  43. An amendment to this paper has been published and can be accessed via the original article.

    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 2020 12:37

    Content type: Correction

    Published on:

    The original article was published in Genome Medicine 2019 11:47

  44. Clinical exome sequencing is frequently used to identify gene-disrupting variants in individuals with neurodevelopmental disorders. While splice-disrupting variants are known to contribute to these disorders, ...

    Authors: Stephan J. Sanders, Grace B. Schwartz and Kyle Kai-How Farh

    Citation: Genome Medicine 2020 12:36

    Content type: Comment

    Published on:

  45. Accurate lung cancer classification is crucial to guide therapeutic decisions. However, histological subtyping by pathologists requires tumor tissue—a necessity that is often intrinsically associated with proc...

    Authors: Lennart Raman, Malaïka Van der Linden, Kim Van der Eecken, Karim Vermaelen, Ingel Demedts, Veerle Surmont, Ulrike Himpe, Franceska Dedeurwaerdere, Liesbeth Ferdinande, Yolande Lievens, Kathleen Claes, Björn Menten and Jo Van Dorpe

    Citation: Genome Medicine 2020 12:35

    Content type: Research

    Published on:

  46. Reprogramming human induced pluripotent stem cells (iPSCs) from somatic cells and generating three-dimensional brain organoids from these iPSCs provide access to live human neuronal tissue with disease-specifi...

    Authors: Annie Kathuria, Kara Lopez-Lengowski, Magdalena Vater, Donna McPhie, Bruce M. Cohen and Rakesh Karmacharya

    Citation: Genome Medicine 2020 12:34

    Content type: Research

    Published on:

  47. Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as...

    Authors: Mary A. Wood, Benjamin R. Weeder, Julianne K. David, Abhinav Nellore and Reid F. Thompson

    Citation: Genome Medicine 2020 12:33

    Content type: Research

    Published on:

  48. Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a w...

    Authors: Anna Reustle, Moreno Di Marco, Carolin Meyerhoff, Annika Nelde, Juliane S. Walz, Stefan Winter, Siahei Kandabarau, Florian Büttner, Mathias Haag, Linus Backert, Daniel J. Kowalewski, Steffen Rausch, Jörg Hennenlotter, Viktoria Stühler, Marcus Scharpf, Falko Fend…

    Citation: Genome Medicine 2020 12:32

    Content type: Research

    Published on:

  50. In cancer, normal epigenetic patterns are disturbed and contribute to gene expression changes, disease onset, and progression. The cancer epigenome is composed of the epigenetic patterns present in the tumor-i...

    Authors: Justyna A. Wierzbinska, Reka Toth, Naveed Ishaque, Karsten Rippe, Jan-Philipp Mallm, Lara C. Klett, Daniel Mertens, Thorsten Zenz, Thomas Hielscher, Marc Seifert, Ralf Küppers, Yassen Assenov, Pavlo Lutsik, Stephan Stilgenbauer, Philipp M. Roessner, Martina Seiffert…

    Citation: Genome Medicine 2020 12:29

    Content type: Research

    Published on:

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