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  1. Research

    A pharmacogenetic signature of high response to Copaxone in late-phase clinical-trial cohorts of multiple sclerosis

    Copaxone is an efficacious and safe therapy that has demonstrated clinical benefit for over two decades in patients with relapsing forms of multiple sclerosis (MS). On an individual level, patients show variab...

    Colin J. Ross, Fadi Towfic, Jyoti Shankar, Daphna Laifenfeld, Mathis Thoma, Matthew Davis, Brian Weiner, Rebecca Kusko, Ben Zeskind, Volker Knappertz, Iris Grossman and Michael R. Hayden

    Genome Medicine 2017 9:50

    Published on: 31 May 2017

  2. Review

    Genome annotation for clinical genomic diagnostics: strengths and weaknesses

    The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number ...

    Charles A. Steward, Alasdair P. J. Parker, Berge A. Minassian, Sanjay M. Sisodiya, Adam Frankish and Jennifer Harrow

    Genome Medicine 2017 9:49

    Published on: 30 May 2017

  3. Research

    Genomic diagnosis for children with intellectual disability and/or developmental delay

    Developmental disabilities have diverse genetic causes that must be identified to facilitate precise diagnoses. We describe genomic data from 371 affected individuals, 309 of which were sequenced as proband-pa...

    Kevin M. Bowling, Michelle L. Thompson, Michelle D. Amaral, Candice R. Finnila, Susan M. Hiatt, Krysta L. Engel, J. Nicholas Cochran, Kyle B. Brothers, Kelly M. East, David E. Gray, Whitley V. Kelley, Neil E. Lamb, Edward J. Lose, Carla A. Rich, Shirley Simmons, Jana S. Whittle…

    Genome Medicine 2017 9:43

    Published on: 30 May 2017

  4. Research

    GLADIATOR: a global approach for elucidating disease modules

    Understanding the genetic basis of disease is an important challenge in biology and medicine. The observation that disease-related proteins often interact with one another has motivated numerous network-based ...

    Yael Silberberg, Martin Kupiec and Roded Sharan

    Genome Medicine 2017 9:48

    Published on: 26 May 2017

  5. Research

    Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes

    Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to th...

    Leif Väremo, Tora Ida Henriksen, Camilla Scheele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen and Jens Nielsen

    Genome Medicine 2017 9:47

    Published on: 25 May 2017

  6. Research

    Multilevel genomics of colorectal cancers with microsatellite instability—clinical impact of JAK1 mutations and consensus molecular subtype 1

    Approximately 15% of primary colorectal cancers have DNA mismatch repair deficiency, causing a complex genome with thousands of small mutations—the microsatellite instability (MSI) phenotype. We investigated m...

    Anita Sveen, Bjarne Johannessen, Torstein Tengs, Stine A. Danielsen, Ina A. Eilertsen, Guro E. Lind, Kaja C. G. Berg, Edward Leithe, Leonardo A. Meza-Zepeda, Enric Domingo, Ola Myklebost, David Kerr, Ian Tomlinson, Arild Nesbakken, Rolf I. Skotheim and Ragnhild A. Lothe

    Genome Medicine 2017 9:46

    Published on: 24 May 2017

  7. Comment

    Pancreatic β-cell regeneration: advances in understanding the genes and signaling pathways involved

    Recent advances in β-cell regeneration in vivo are providing insights into the mechanisms involved in the conversion of distinct pancreatic cell lineages into β cells. These mechanisms mostly involve reactivat...

    Solomon Afelik and Meritxell Rovira

    Genome Medicine 2017 9:42

    Published on: 16 May 2017

    The Erratum to this article has been published in Genome Medicine 2017 9:52

  8. Research

    Lost in translation: returning germline genetic results in genome-scale cancer research

    The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have...

    Amber L. Johns, Skye H. McKay, Jeremy L. Humphris, Mark Pinese, Lorraine A. Chantrill, R. Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda A. High, Katia Nones, Ann-Marie Patch, Neil D. Merrett, Nick Pavlakis, Karin S. Kassahn…

    Genome Medicine 2017 9:41

    Published on: 28 April 2017

  9. Research

    Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

    Parkinson’s disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the...

    J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork and U. Wüllner

    Genome Medicine 2017 9:39

    Published on: 28 April 2017

    The Erratum to this article has been published in Genome Medicine 2017 9:61

  10. Research

    Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes

    The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components,...

    Mumtahena Rahman, Shelley M. MacNeil, David F. Jenkins, Gajendra Shrestha, Sydney R. Wyatt, Jasmine A. McQuerry, Stephen R. Piccolo, Laura M. Heiser, Joe W. Gray, W. Evan Johnson and Andrea H. Bild

    Genome Medicine 2017 9:40

    Published on: 26 April 2017

  11. Software

    PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories

    The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical dia...

    Kenneth D. Doig, Andrew Fellowes, Anthony H. Bell, Andrei Seleznev, David Ma, Jason Ellul, Jason Li, Maria A. Doyle, Ella R. Thompson, Amit Kumar, Luis Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T. Papenfuss and Stephen B. Fox

    Genome Medicine 2017 9:38

    Published on: 24 April 2017

  12. Research

    Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

    High tumor mutational burden (TMB) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to PD-1 and PD-L1 blockade immuno...

    Zachary R. Chalmers, Caitlin F. Connelly, David Fabrizio, Laurie Gay, Siraj M. Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S. Lieber…

    Genome Medicine 2017 9:34

    Published on: 19 April 2017

  13. Method

    Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

    Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome seq...

    Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M. Rueda, Suet-Feung Chin and Carlos Caldas

    Genome Medicine 2017 9:35

    Published on: 18 April 2017

  14. Research

    Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas

    Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermeth...

    Davide Degli Esposti, Athena Sklias, Sheila C. Lima, Stéphanie Beghelli-de la Forest Divonne, Vincent Cahais, Nora Fernandez-Jimenez, Marie-Pierre Cros, Szilvia Ecsedi, Cyrille Cuenin, Liacine Bouaoun, Graham Byrnes, Rosita Accardi, Anne Sudaka, Valérie Giordanengo, Hector Hernandez-Vargas, Luis Felipe Ribeiro Pinto…

    Genome Medicine 2017 9:33

    Published on: 5 April 2017

  15. Research

    Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma

    Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Her...

    Vinodh Srinivasainagendra, Michael W. Sandel, Bhupendra Singh, Aishwarya Sundaresan, Ved P. Mooga, Prachi Bajpai, Hemant K. Tiwari and Keshav K. Singh

    Genome Medicine 2017 9:31

    Published on: 29 March 2017

  16. Research

    Ethnic and diet-related differences in the healthy infant microbiome

    The infant gut is rapidly colonized by microorganisms soon after birth, and the composition of the microbiota is dynamic in the first year of life. Although a stable microbiome may not be established until 1 t...

    Jennifer C. Stearns, Michael A. Zulyniak, Russell J. de Souza, Natalie C. Campbell, Michelle Fontes, Mateen Shaikh, Malcolm R. Sears, Allan B. Becker, Piushkumar J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, Milan Gupta, Joseph Beyene, Michael G. Surette and Sonia S. Anand

    Genome Medicine 2017 9:32

    Published on: 29 March 2017

  17. Research

    New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

    Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion a...

    Antoine Dara, Elliott F. Drábek, Mark A. Travassos, Kara A. Moser, Arthur L. Delcher, Qi Su, Timothy Hostelley, Drissa Coulibaly, Modibo Daou, Ahmadou Dembele, Issa Diarra, Abdoulaye K. Kone, Bourema Kouriba, Matthew B. Laurens, Amadou Niangaly, Karim Traore…

    Genome Medicine 2017 9:30

    Published on: 28 March 2017

  18. Research

    Genetic pleiotropy between age-related macular degeneration and 16 complex diseases and traits

    Age-related macular degeneration (AMD) is a common condition of vision loss with disease development strongly influenced by environmental and genetic factors. Recently, 34 loci were associated with AMD at geno...

    Felix Grassmann, Christina Kiel, Martina E. Zimmermann, Mathias Gorski, Veronika Grassmann, Klaus Stark, Iris M. Heid and Bernhard H. F. Weber

    Genome Medicine 2017 9:29

    Published on: 27 March 2017

  19. Research

    DNA methylation changes at infertility genes in newborn twins conceived by in vitro fertilisation

    The association of in vitro fertilisation (IVF) and DNA methylation has been studied predominantly at regulatory regions of imprinted genes and at just thousands of the ~28 million CpG sites in the human genome.

    Juan E. Castillo-Fernandez, Yuk Jing Loke, Sebastian Bass-Stringer, Fei Gao, Yudong Xia, Honglong Wu, Hanlin Lu, Yuan Liu, Jun Wang, Tim D. Spector, Richard Saffery, Jeffrey M. Craig and Jordana T. Bell

    Genome Medicine 2017 9:28

    Published on: 24 March 2017

  20. Research

    A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

    Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved...

    Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood, Romy B. Christmann, Harrison W. Farber, Robert A. Lafyatis, Christopher P. Denton, Monique E. Hinchcliff, Patricia A. Pioli, J. Matthew Mahoney and Michael L. Whitfield

    Genome Medicine 2017 9:27

    Published on: 23 March 2017

  21. Comment

    Schizophrenia and substance use comorbidity: a genome-wide perspective

    Dual diagnosis with substance use disorders (SUDs) consistently contributes to the premature mortality and increased disability observed in schizophrenia. Large genome-wide association studies are providing th...

    Renato Polimanti, Arpana Agrawal and Joel Gelernter

    Genome Medicine 2017 9:25

    Published on: 21 March 2017

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