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  1. As a result of multiple technological and practical advances, high-throughput sequencing, known more commonly as “next-generation” sequencing (NGS), can now be incorporated into standard clinical practice. Whe...

    Authors: Jeffrey Gagan and Eliezer M. Van Allen
    Citation: Genome Medicine 2015 7:80
    Content type: Review Published on:

  2. Expanded genetic carrier testing is changing clinical practice. Current experience highlights the need for rigorous curation of tens of thousands of variants as to their pathogenicity and phenotypic effects. T...

    Authors: Arthur L. Beaudet
    Citation: Genome Medicine 2015 7:79
    Content type: Comment Published on:

  3. Next-generation sequencing is revolutionizing medical genetics and in the near future will pervade all medical fields. To maximize the potential clinical utility of this approach, global data sharing and pheno...

    Authors: Joris A. Veltman and James R. Lupski
    Citation: Genome Medicine 2015 7:78
    Content type: Editorial Published on:

  4. Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGen...

    Authors: Jinlian Wang, Jun Liao, Jinglan Zhang, Wei-Yi Cheng, Jörg Hakenberg, Meng Ma, Bryn D. Webb, Rajasekar Ramasamudram-chakravarthi, Lisa Karger, Lakshmi Mehta, Ruth Kornreich, George A. Diaz, Shuyu Li, Lisa Edelmann and Rong Chen
    Citation: Genome Medicine 2015 7:77
    Content type: Software Published on:

  5. Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical d...

    Authors: Márton Münz, Elise Ruark, Anthony Renwick, Emma Ramsay, Matthew Clarke, Shazia Mahamdallie, Victoria Cloke, Sheila Seal, Ann Strydom, Gerton Lunter and Nazneen Rahman
    Citation: Genome Medicine 2015 7:76
    Content type: Method Published on:

  7. Reliable detection of somatic copy-number alterations (sCNAs) in tumors using whole-exome sequencing (WES) remains challenging owing to technical (inherent noise) and sample-associated variability in WES data....

    Authors: Vinay Varadan, Salendra Singh, Arman Nosrati, Lakshmeswari Ravi, James Lutterbaugh, Jill S. Barnholtz-Sloan, Sanford D. Markowitz, Joseph E. Willis and Kishore Guda
    Citation: Genome Medicine 2015 7:69
    Content type: Method Published on:

  9. Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. ...

    Authors: Anil Patwardhan, Jason Harris, Nan Leng, Gabor Bartha, Deanna M. Church, Shujun Luo, Christian Haudenschild, Mark Pratt, Justin Zook, Marc Salit, Jeanie Tirch, Massimo Morra, Stephen Chervitz, Ming Li, Michael Clark, Sarah Garcia…
    Citation: Genome Medicine 2015 7:71
    Content type: Research Published on:

  10. The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical geno...

    Authors: Simon P. Sadedin, Harriet Dashnow, Paul A. James, Melanie Bahlo, Denis C. Bauer, Andrew Lonie, Sebastian Lunke, Ivan Macciocca, Jason P. Ross, Kirby R. Siemering, Zornitza Stark, Susan M. White, Graham Taylor, Clara Gaff, Alicia Oshlack and Natalie P. Thorne
    Citation: Genome Medicine 2015 7:68
    Content type: Software Published on:

  11. In an effort to return actionable results from variant data to electronic health records (EHRs), participants in the Electronic Medical Records and Genomics (eMERGE) Network are being sequenced with the target...

    Authors: David R. Crosslin, Peggy D. Robertson, David S. Carrell, Adam S. Gordon, David S. Hanna, Amber Burt, Stephanie M. Fullerton, Aaron Scrol, James Ralston, Kathleen Leppig, Andrea Hartzler, Eric Baldwin, Mariza de Andrade, Iftikhar J. Kullo, Gerard Tromp, Kimberly F. Doheny…
    Citation: Genome Medicine 2015 7:67
    Content type: Research Published on:

  12. High-throughput genetic testing is increasingly applied in clinics. Next-Generation Sequencing (NGS) data analysis however still remains a great challenge. The interpretation of pathogenicity of single variant...

    Authors: Sabine C. Mueller, Christina Backes, Olga V. Kalinina, Benjamin Meder, Daniel Stöckel, Hans-Peter Lenhof, Eckart Meese and Andreas Keller
    Citation: Genome Medicine 2015 7:65
    Content type: Research Published on:

  13. Classifiers based on molecular criteria such as gene expression signatures have been developed to distinguish Burkitt lymphoma and diffuse large B cell lymphoma, which help to explore the intermediate cases wh...

    Authors: Chulin Sha, Sharon Barrans, Matthew A. Care, David Cunningham, Reuben M. Tooze, Andrew Jack and David R. Westhead
    Citation: Genome Medicine 2015 7:64
    Content type: Research Published on:

  14. The oxidative DNA demethylase ALKBH3 targets single-stranded DNA (ssDNA) in order to perform DNA alkylation damage repair. ALKBH3 becomes upregulated during tumorigenesis and is necessary for proliferation. Ho...

    Authors: Robert Liefke, Indra M. Windhof-Jaidhauser, Jochen Gaedcke, Gabriela Salinas-Riester, Feizhen Wu, Michael Ghadimi and Sebastian Dango
    Citation: Genome Medicine 2015 7:66
    Content type: Research Published on:

  15. Evidence from several recent metabolomic studies suggests that increased concentrations of triacylglycerols with shorter (14–16 carbon atoms), saturated fatty acids are associated with insulin resistance and t...

    Authors: Michael Eiden, Albert Koulman, Mensud Hatunic, James A. West, Steven Murfitt, Michael Osei, Claire Adams, Xinzhu Wang, Yajing Chu, Luke Marney, Lee D. Roberts, Stephen O’Rahilly, Robert K. Semple, David B. Savage and Julian L. Griffin
    Citation: Genome Medicine 2015 7:63
    Content type: Research Published on:

  19. The human gut microbiome is associated with the development of colon cancer, and recent studies have found changes in the microbiome in cancer patients compared to healthy controls. Studying the microbial comm...

    Authors: Michael B. Burns, Joshua Lynch, Timothy K. Starr, Dan Knights and Ran Blekhman
    Citation: Genome Medicine 2015 7:55
    Content type: Research Published on:

  20. Age-related macular degeneration (AMD) is a leading cause of blindness. Most vision loss occurs following the transition from a disease of deposit formation and inflammation to a disease of neovascular fibrosi...

    Authors: Monte J. Radeke, Carolyn M. Radeke, Ying-Hsuan Shih, Jane Hu, Dean Bok, Lincoln V. Johnson and Pete J. Coffey
    Citation: Genome Medicine 2015 7:58
    Content type: Research Published on:

  21. Genetic analyses of autoimmune diseases have revealed hundreds of disease-associated DNA variants, but the identity and function of the causal variants are understudied and warrant deeper mechanistic studies. ...

    Authors: John P Ray and Nir Hacohen
    Citation: Genome Medicine 2015 7:57
    Content type: Comment Published on:

  22. The organic cation transporter OCT1 (SLC22A1) mediates the uptake of vitamin B1, cationic drugs, and xenobiotics into hepatocytes. Nine percent of Caucasians lack or have very low OCT1 activity due to loss-of-...

    Authors: Tina Seitz, Robert Stalmann, Nawar Dalila, Jiayin Chen, Sherin Pojar, Joao N. Dos Santos Pereira, Ralph Krätzner, Jürgen Brockmöller and Mladen V. Tzvetkov
    Citation: Genome Medicine 2015 7:56
    Content type: Research Published on:

  23. Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potentia...

    Authors: Tomasz Gambin, Shalini N. Jhangiani, Jennifer E. Below, Ian M. Campbell, Wojciech Wiszniewski, Donna M. Muzny, Jeffrey Staples, Alanna C. Morrison, Matthew N. Bainbridge, Samantha Penney, Amy L. McGuire, Richard A. Gibbs, James R. Lupski and Eric Boerwinkle
    Citation: Genome Medicine 2015 7:54
    Content type: Research Published on:

  25. We describe an approach for genotyping bacterial strains from low coverage genome datasets, including metagenomic data from complex samples. Sequence reads from unknown samples are aligned to a reference genom...

    Authors: Jason W. Sahl, James M. Schupp, David A. Rasko, Rebecca E. Colman, Jeffrey T. Foster and Paul Keim
    Citation: Genome Medicine 2015 7:52
    Content type: Method Published on:

  27. HIV/AIDS is a chronic and debilitating disease that cannot be cured with current antiretroviral drugs. While combinatorial antiretroviral therapy (cART) can potently suppress HIV-1 replication and delay the on...

    Authors: Maggie L Bobbin, John C Burnett and John J Rossi
    Citation: Genome Medicine 2015 7:50
    Content type: Review Published on:

  28. Lymphocyte receptor repertoires are continually shaped throughout the lifetime of an individual in response to environmental and pathogenic exposure. Thus, they may serve as a fingerprint of an individual’s on...

    Authors: Victor Greiff, Pooja Bhat, Skylar C. Cook, Ulrike Menzel, Wenjing Kang and Sai T. Reddy
    Citation: Genome Medicine 2015 7:49
    Content type: Research Published on:

  29. Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequenci...

    Authors: Francesc Coll, Ruth McNerney, Mark D Preston, José Afonso Guerra-Assunção, Andrew Warry, Grant Hill-Cawthorne, Kim Mallard, Mridul Nair, Anabela Miranda, Adriana Alves, João Perdigão, Miguel Viveiros, Isabel Portugal, Zahra Hasan, Rumina Hasan, Judith R Glynn…
    Citation: Genome Medicine 2015 7:51
    Content type: Method Published on:

  30. There are many challenges and opportunities for Africans in the emerging area of genome medicine. In particular, there is a need for investment in local education using real-world African genetic data sets. Cl...

    Authors: Geoffrey H Siwo, Scott M Williams and Jason H Moore
    Citation: Genome Medicine 2015 7:47
    Content type: Comment Published on:

    The Erratum to this article has been published in Genome Medicine 2015 7:70

  31. Mesenchymal stem cells (MSCs) are promising candidates for cellular therapies ranging from tissue repair in regenerative medicine to immunomodulation in graft versus host disease after allogeneic transplantati...

    Authors: Gerrit Erdmann, Michael Suchanek, Patrick Horn, Fabian Graf, Christian Volz, Thomas Horn, Xian Zhang, Wolfgang Wagner, Anthony D. Ho and Michael Boutros
    Citation: Genome Medicine 2015 7:46
    Content type: Method Published on:

  33. Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn’s disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling s...

    Authors: Aashiq H Mirza, Claus HB Berthelsen, Stefan E Seemann, Xiaoyong Pan, Klaus S Frederiksen, Mogens Vilien, Jan Gorodkin and Flemming Pociot
    Citation: Genome Medicine 2015 7:39
    Content type: Research Published on:

  35. This is an Erratum to Genome Medicine 2013, 5:89, highlighting an error in Table 1 of the original article. Please see related article:

    Authors: Reuben J Pengelly, Jane Gibson, Gaia Andreoletti, Andrew Collins, Christopher J Mattocks and Sarah Ennis
    Citation: Genome Medicine 2015 7:44
    Content type: Erratum Published on:

    The original article was published in Genome Medicine 2013 5:89

  36. The overwhelming majority (approximately 80%) of individuals with classic familial adenomatous polyposis (FAP) exhibit mutations in the coding sequence of the adenomatous polyposis coli (APC) tumor suppressor gen...

    Authors: Yiing Lin, Shin Lin, Melanie D Baxter, Lawrence Lin, Susan M Kennedy, Zhengyan Zhang, Paul J Goodfellow, William C Chapman and Nicholas O Davidson
    Citation: Genome Medicine 2015 7:42
    Content type: Research Published on:

  38. Aristolochic acid (AA) is a natural compound found in many plants of the Aristolochia genus, and these plants are widely used in traditional medicines for numerous conditions and for weight loss. Previous work ha...

    Authors: Song Ling Poon, Mi Ni Huang, Yang Choo, John R McPherson, Willie Yu, Hong Lee Heng, Anna Gan, Swe Swe Myint, Ee Yan Siew, Lian Dee Ler, Lay Guat Ng, Wen-Hui Weng, Cheng-Keng Chuang, John SP Yuen, See-Tong Pang, Patrick Tan…
    Citation: Genome Medicine 2015 7:38
    Content type: Research Published on:

  40. Periodontitis is a polymicrobial biofilm-induced inflammatory disease that affects 743 million people worldwide. The current model to explain periodontitis progression proposes that changes in the relative abu...

    Authors: Susan Yost, Ana E Duran-Pinedo, Ricardo Teles, Keerthana Krishnan and Jorge Frias-Lopez
    Citation: Genome Medicine 2015 7:27
    Content type: Research Published on:

    The Erratum to this article has been published in Genome Medicine 2015 7:111

  41. There has been considerable progress in the management of acute lymphoblastic leukemia (ALL) but further improvement is needed to increase long-term survival. The thiopurine agent 6-mercaptopurine (6-MP) used ...

    Authors: Laurent Chouchana, Ana Aurora Fernández-Ramos, Florent Dumont, Catherine Marchetti, Irène Ceballos-Picot, Philippe Beaune, David Gurwitz and Marie-Anne Loriot
    Citation: Genome Medicine 2015 7:37
    Content type: Research Published on:

  42. Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing usin...

    Authors: Sarah K Westbury, Ernest Turro, Daniel Greene, Claire Lentaigne, Anne M Kelly, Tadbir K Bariana, Ilenia Simeoni, Xavier Pillois, Antony Attwood, Steve Austin, Sjoert BG Jansen, Tamam Bakchoul, Abi Crisp-Hihn, Wendy N Erber, Rémi Favier, Nicola Foad…
    Citation: Genome Medicine 2015 7:36
    Content type: Research Published on:

  43. All cells in an individual are related to one another by a bifurcating lineage tree, in which each node is an ancestral cell that divided into two, each branch connects two nodes, and the root is the zygote. W...

    Authors: Ziming Weng, Noah Spies, Shirley X Zhu, Daniel E Newburger, Dorna Kashef-Haghighi, Serafim Batzoglou, Arend Sidow and Robert B West
    Citation: Genome Medicine 2015 7:28
    Content type: Research Published on:

  44. Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availabili...

    Authors: Akash Kumar, Allison Ryan, Jacob O Kitzman, Nina Wemmer, Matthew W Snyder, Styrmir Sigurjonsson, Choli Lee, Milena Banjevic, Paul W Zarutskie, Alexandra P Lewis, Jay Shendure and Matthew Rabinowitz
    Citation: Genome Medicine 2015 7:35
    Content type: Research Published on:

  45. Applying genomics to patient care demands sensitive, unambiguous and rapid characterization of a known set of clinically relevant variants in patients’ samples, an objective substantially different from the st...

    Authors: Wanding Zhou, Hao Zhao, Zechen Chong, Routbort J Mark, Agda K Eterovic, Funda Meric-Bernstam and Ken Chen
    Citation: Genome Medicine 2015 7:34
    Content type: Method Published on:

  46. With the prevalence of cardio-metabolic disorders reaching pandemic proportions, the search for modifiable causative factors has intensified. One such potential factor is the vast microbial community inhabitin...

    Authors: Tue H Hansen, Rikke J Gøbel, Torben Hansen and Oluf Pedersen
    Citation: Genome Medicine 2015 7:33
    Content type: Review Published on:

  47. Three-dimensional organotypic culture models show great promise as a tool for cancer precision medicine, with potential applications for oncogene modeling, gene discovery and chemosensitivity studies.

    Authors: Michael A Cantrell and Calvin J Kuo
    Citation: Genome Medicine 2015 7:32
    Content type: Comment Published on:

  48. Most pediatric tumors have only very few somatic mutations. However, a recent study revealed that a subset of tumors from children with congenital biallelic deficiency of DNA mismatch repair exhibits a mutatio...

    Authors: Matthias Schlesner and Roland Eils
    Citation: Genome Medicine 2015 7:31
    Content type: Research highlight Published on:

  49. RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through alle...

    Authors: Patrick Deelen, Daria V Zhernakova, Mark de Haan, Marijke van der Sijde, Marc Jan Bonder, Juha Karjalainen, K Joeri van der Velde, Kristin M Abbott, Jingyuan Fu, Cisca Wijmenga, Richard J Sinke, Morris A Swertz and Lude Franke
    Citation: Genome Medicine 2015 7:30
    Content type: Research Published on:

  50. Recent twin studies highlight the astonishing impact of non-heritable contributions to our immune health and wellbeing. Immunologists, long familiar with heterogeneity generated from within cells, must now gra...

    Authors: Alan G Baxter and Philip D Hodgkin
    Citation: Genome Medicine 2015 7:29
    Content type: Research highlight Published on:
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Genome Medicine

ISSN: 1756-994X

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