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  1. 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,...

    Authors: 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
    Citation: Genome Medicine 2017 9:40
    Content type: Research Published on:

  2. 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...

    Authors: 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
    Citation: Genome Medicine 2017 9:38
    Content type: Software Published on:

  4. 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...

    Authors: 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…
    Citation: Genome Medicine 2017 9:34
    Content type: Research Published on:

  6. 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...

    Authors: Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M. Rueda, Suet-Feung Chin and Carlos Caldas
    Citation: Genome Medicine 2017 9:35
    Content type: Method Published on:

  7. 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...

    Authors: 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…
    Citation: Genome Medicine 2017 9:33
    Content type: Research Published on:

  8. 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...

    Authors: 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
    Citation: Genome Medicine 2017 9:32
    Content type: Research Published on:

  9. 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...

    Authors: Vinodh Srinivasainagendra, Michael W. Sandel, Bhupendra Singh, Aishwarya Sundaresan, Ved P. Mooga, Prachi Bajpai, Hemant K. Tiwari and Keshav K. Singh
    Citation: Genome Medicine 2017 9:31
    Content type: Research Published on:

  10. 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...

    Authors: 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…
    Citation: Genome Medicine 2017 9:30
    Content type: Research Published on:

  11. 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...

    Authors: Felix Grassmann, Christina Kiel, Martina E. Zimmermann, Mathias Gorski, Veronika Grassmann, Klaus Stark, Iris M. Heid and Bernhard H. F. Weber
    Citation: Genome Medicine 2017 9:29
    Content type: Research Published on:

  12. 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.

    Authors: 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
    Citation: Genome Medicine 2017 9:28
    Content type: Research Published on:

  13. 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...

    Authors: 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
    Citation: Genome Medicine 2017 9:27
    Content type: Research Published on:

  14. Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene disc...

    Authors: Mohammad K. Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A. Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R. Lalani, Christian P. Schaaf…
    Citation: Genome Medicine 2017 9:26
    Content type: Research Published on:

  16. Imiquimod (IMQ) produces a cutaneous phenotype in mice frequently studied as an acute model of human psoriasis. Whether this phenotype depends on strain or sex has never been systematically investigated on a l...

    Authors: William R. Swindell, Kellie A. Michaels, Andrew J. Sutter, Doina Diaconu, Yi Fritz, Xianying Xing, Mrinal K. Sarkar, Yun Liang, Alex Tsoi, Johann E. Gudjonsson and Nicole L. Ward
    Citation: Genome Medicine 2017 9:24
    Content type: Research Published on:

  17. The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from approximately 24,000 ad...

    Authors: Reka Nagy, Thibaud S. Boutin, Jonathan Marten, Jennifer E. Huffman, Shona M. Kerr, Archie Campbell, Louise Evenden, Jude Gibson, Carmen Amador, David M. Howard, Pau Navarro, Andrew Morris, Ian J. Deary, Lynne J. Hocking, Sandosh Padmanabhan, Blair H. Smith…
    Citation: Genome Medicine 2017 9:23
    Content type: Research Published on:

  19. Understanding longitudinal variability of the microbiome in ill patients is critical to moving microbiome-based measurements and therapeutics into clinical practice. However, the vast majority of data regardin...

    Authors: Jessica R. Galloway-Peña, Daniel P. Smith, Pranoti Sahasrabhojane, W. Duncan Wadsworth, Bryan M. Fellman, Nadim J. Ajami, Elizabeth J. Shpall, Naval Daver, Michele Guindani, Joseph F. Petrosino, Dimitrios P. Kontoyiannis and Samuel A. Shelburne
    Citation: Genome Medicine 2017 9:21
    Content type: Research Published on:

  21. The integration of genomics with immunotherapy has potential value for cancer vaccine development. Given the clinical successes of immune checkpoint modulators, interest in cancer vaccines as therapeutic optio...

    Authors: Ryan J. Hartmaier, Jehad Charo, David Fabrizio, Michael E. Goldberg, Lee A. Albacker, William Pao and Juliann Chmielecki
    Citation: Genome Medicine 2017 9:16
    Content type: Research Published on:

  23. Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under i...

    Authors: Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H. A. Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun…
    Citation: Genome Medicine 2017 9:18
    Content type: Research Published on:

  25. Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblas...

    Authors: David J. Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G. Higgins and Walter Kolch
    Citation: Genome Medicine 2017 9:15
    Content type: Research Published on:

  26. While the role of the gut microbiome in inflammation and colorectal cancers has received much recent attention, there are few data to support an association between the oral microbiome and head and neck squamo...

    Authors: Hannah Wang, Pauline Funchain, Gurkan Bebek, Jessica Altemus, Huan Zhang, Farshad Niazi, Charissa Peterson, Walter T. Lee, Brian B. Burkey and Charis Eng
    Citation: Genome Medicine 2017 9:14
    Content type: Research Published on:

  27. The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is ...

    Authors: Yuya Kobayashi, Shan Yang, Keith Nykamp, John Garcia, Stephen E. Lincoln and Scott E. Topper
    Citation: Genome Medicine 2017 9:13
    Content type: Research Published on:

  28. Glioblastoma multiforme (GBM) constitutes nearly half of all malignant brain tumors and has a median survival of 15 months. The standard treatment for these lesions includes maximal resection, radiotherapy, an...

    Authors: E. Zeynep Erson-Omay, Octavian Henegariu, S. Bülent Omay, Akdes Serin Harmancı, Mark W. Youngblood, Ketu Mishra-Gorur, Jie Li, Koray Özduman, Geneive Carrión-Grant, Victoria E. Clark, Caner ÇaÄŸlar, Mehmet BakırcıoÄŸlu, M. Necmettin Pamir, Viviane Tabar, Alexander O. Vortmeyer, Kaya Bilguvar…
    Citation: Genome Medicine 2017 9:12
    Content type: Research Published on:

  29. Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A...

    Authors: Daniel O’Connor, Elizabeth A. Clutterbuck, Amber J. Thompson, Matthew D. Snape, Maheshi N. Ramasamy, Dominic F. Kelly and Andrew J. Pollard
    Citation: Genome Medicine 2017 9:11
    Content type: Research Published on:

  31. Germline chromothripsis causes complex genomic rearrangements that are likely to affect multiple genes and their regulatory contexts. The contribution of individual rearrangements and affected genes to the phe...

    Authors: Sjors Middelkamp, Sebastiaan van Heesch, A. Koen Braat, Joep de Ligt, Maarten van Iterson, Marieke Simonis, Markus J. van Roosmalen, Martijn J. E. Kelder, Evelien Kruisselbrink, Ron Hochstenbach, Nienke E. Verbeek, Elly F. Ippel, Youri Adolfs, R. Jeroen Pasterkamp, Wigard P. Kloosterman, Ewart W. Kuijk…
    Citation: Genome Medicine 2017 9:9
    Content type: Research Published on:

  32. Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disease of the gastrointestinal tract which includes ulcerative colitis and Crohn's disease. Genetic risk factors for IBD are not well unde...

    Authors: Shinichi Takahashi, Gaia Andreoletti, Rui Chen, Yoichi Munehira, Akshay Batra, Nadeem A. Afzal, R. Mark Beattie, Jonathan A. Bernstein, Sarah Ennis and Michael Snyder
    Citation: Genome Medicine 2017 9:8
    Content type: Research Published on:

  33. Clinical genomic testing is dependent on the robust identification and reporting of variant-level information in relation to disease. With the shift to high-throughput sequencing, a major challenge for clinica...

    Authors: Jennifer L. Yen, Sarah Garcia, Aldrin Montana, Jason Harris, Stephen Chervitz, Massimo Morra, John West, Richard Chen and Deanna M. Church
    Citation: Genome Medicine 2017 9:7
    Content type: Research Published on:

  34. Klebsiella pneumoniae is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recentl...

    Authors: Chakkaphan Runcharoen, Danesh Moradigaravand, Beth Blane, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Julian Parkhill, Narisara Chantratita and Sharon J. Peacock
    Citation: Genome Medicine 2017 9:6
    Content type: Research Published on:

  35. As public health interventions drive parasite populations to elimination, genetic epidemiology models that incorporate population genomics can be powerful tools for evaluating the effectiveness of continued in...

    Authors: Wesley Wong, Allison D. Griggs, Rachel F. Daniels, Stephen F. Schaffner, Daouda Ndiaye, Amy K. Bei, Awa B. Deme, Bronwyn MacInnis, Sarah K. Volkman, Daniel L. Hartl, Daniel E. Neafsey and Dyann F. Wirth
    Citation: Genome Medicine 2017 9:5
    Content type: Research Published on:

  36. Many mutations in cancer are of unknown functional significance. Standard methods use statistically significant recurrence of mutations in tumor samples as an indicator of functional impact. We extend such ana...

    Authors: Jianjiong Gao, Matthew T. Chang, Hannah C. Johnsen, Sizhi Paul Gao, Brooke E. Sylvester, Selcuk Onur Sumer, Hongxin Zhang, David B. Solit, Barry S. Taylor, Nikolaus Schultz and Chris Sander
    Citation: Genome Medicine 2017 9:4
    Content type: Method Published on:

  37. The success of the clinical use of sequencing based tests (from single gene to genomes) depends on the accuracy and consistency of variant interpretation. Aiming to improve the interpretation process through p...

    Authors: Ronak Y. Patel, Neethu Shah, Andrew R. Jackson, Rajarshi Ghosh, Piotr Pawliczek, Sameer Paithankar, Aaron Baker, Kevin Riehle, Hailin Chen, Sofia Milosavljevic, Chris Bizon, Shawn Rynearson, Tristan Nelson, Gail P. Jarvik, Heidi L. Rehm, Steven M. Harrison…
    Citation: Genome Medicine 2017 9:3
    Content type: Software Published on:

  40. Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has b...

    Authors: Jennifer A. Oberg, Julia L. Glade Bender, Maria Luisa Sulis, Danielle Pendrick, Anthony N. Sireci, Susan J. Hsiao, Andrew T. Turk, Filemon S. Dela Cruz, Hanina Hibshoosh, Helen Remotti, Rebecca J. Zylber, Jiuhong Pang, Daniel Diolaiti, Carrie Koval, Stuart J. Andrews, James H. Garvin…
    Citation: Genome Medicine 2016 8:133
    Content type: Research Published on:

  41. Comprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been li...

    Authors: Masayuki Nagahashi, Toshifumi Wakai, Yoshifumi Shimada, Hiroshi Ichikawa, Hitoshi Kameyama, Takashi Kobayashi, Jun Sakata, Ryoma Yagi, Nobuaki Sato, Yuko Kitagawa, Hiroyuki Uetake, Kazuhiro Yoshida, Eiji Oki, Shin-ei Kudo, Hiroshi Izutsu, Keisuke Kodama…
    Citation: Genome Medicine 2016 8:136
    Content type: Research Published on:

  42. Cancer results from the acquisition of somatic driver mutations. Several computational tools can predict driver genes from population-scale genomic data, but tools for analyzing personal cancer genomes are und...

    Authors: Chengliang Dong, Yunfei Guo, Hui Yang, Zeyu He, Xiaoming Liu and Kai Wang
    Citation: Genome Medicine 2016 8:135
    Content type: Method Published on:

  43. The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resis...

    Authors: Jody Phelan, Denise M. O’Sullivan, Diana Machado, Jorge Ramos, Alexandra S. Whale, Justin O’Grady, Keertan Dheda, Susana Campino, Ruth McNerney, Miguel Viveiros, Jim F. Huggett and Taane G. Clark
    Citation: Genome Medicine 2016 8:132
    Content type: Research Published on:

  45. Krüppel-type zinc finger genes (ZNF) constitute a large yet relatively poorly characterized gene family. ZNF genes encode proteins that recognize specific DNA motifs in gene promotors. They act as transcriptio...

    Authors: Servi J. C. Stevens, Anthonie J. van Essen, Conny M. A. van Ravenswaaij, Abdallah F. Elias, Jaclyn A. Haven, Stefan H. Lelieveld, Rolph Pfundt, Willy M. Nillesen, Helger G. Yntema, Kees van Roozendaal, Alexander P. Stegmann, Christian Gilissen and Han G. Brunner
    Citation: Genome Medicine 2016 8:131
    Content type: Research Published on:

  46. The last two human genome assemblies have extended the previous linear golden-path paradigm of the human genome to a graph-like model to better represent regions with a high degree of structural variability. T...

    Authors: Marten Jäger, Max Schubach, Tomasz Zemojtel, Knut Reinert, Deanna M. Church and Peter N. Robinson
    Citation: Genome Medicine 2016 8:130
    Content type: Research Published on:

  47. Biological interpretation of genomic summary data such as those resulting from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies is one of the major bottlenecks in me...

    Authors: Hai Fang, Bogdan Knezevic, Katie L. Burnham and Julian C. Knight
    Citation: Genome Medicine 2016 8:129
    Content type: Software Published on:

  48. Estrogen receptor (ER) activity is critical for the development and progression of the majority of breast cancers. It is known that ER is differentially bound to DNA leading to transcriptomic and phenotypic ch...

    Authors: Amir Bahreini, Kevin Levine, Lucas Santana-Santos, Panayiotis V. Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich and Adrian V. Lee
    Citation: Genome Medicine 2016 8:128
    Content type: Research Published on:

  49. Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from t...

    Authors: Martin I. Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S. Couper, Stanton K. Shernan, Jon G. Seidman, Simon C. Body and Jochen D. Muehlschlegel
    Citation: Genome Medicine 2016 8:127
    Content type: Research Published on:
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Genome Medicine

ISSN: 1756-994X

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