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  1. Driven by high throughput next generation sequencing technologies and the pressing need to decipher cancer genomes, computational approaches for detecting somatic single nucleotide variants (sSNVs) have underg...

    Authors: Qingguo Wang, Peilin Jia, Fei Li, Haiquan Chen, Hongbin Ji, Donald Hucks, Kimberly Brown Dahlman, William Pao and Zhongming Zhao
    Citation: Genome Medicine 2013 5:91
    Content type: Research Published on:

  2. Differentiating true somatic mutations from artifacts in massively parallel sequencing data is an immense challenge. To develop methods for optimal somatic mutation detection and to identify factors influencin...

    Authors: David L Goode, Sally M Hunter, Maria A Doyle, Tao Ma, Simone M Rowley, David Choong, Georgina L Ryland and Ian G Campbell
    Citation: Genome Medicine 2013 5:90
    Content type: Method Published on:

  3. Whole-exome sequencing provides a cost-effective means to sequence protein coding regions within the genome, which are significantly enriched for etiological variants. We describe a panel of single nucleotide ...

    Authors: Reuben J Pengelly, Jane Gibson, Gaia Andreoletti, Andrew Collins, Christopher J Mattocks and Sarah Ennis
    Citation: Genome Medicine 2013 5:89
    Content type: Method Published on:

    The Erratum to this article has been published in Genome Medicine 2015 7:44

  5. Acetaminophen (APAP) is a commonly used analgesic. However, its use is associated with drug-induced liver injury (DILI). It is a prominent cause of acute liver failure, with APAP hepatotoxicity far exceeding o...

    Authors: Jürgen Borlak, Bijon Chatterji, Kishor B Londhe and Paul B Watkins
    Citation: Genome Medicine 2013 5:86
    Content type: Research Published on:

  6. Biomarkers of drug-induced liver injury (DILI) are essential for the diagnosis of severe cases of DILI in clinical trials and clinical practice, but the currently used biomarker paradigm detects damage after i...

    Authors: Jiri Aubrecht, Shelli J Schomaker and David E Amacher
    Citation: Genome Medicine 2013 5:85
    Content type: Research highlight Published on:

  7. Development of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This ...

    Authors: Ilse R Wiechers, Noah C Perin and Robert Cook-Deegan
    Citation: Genome Medicine 2013 5:83
    Content type: Research Published on:

  8. Traditional pathogen detection methods in public health infectious disease surveillance rely upon the identification of agents that are already known to be associated with a particular clinical syndrome. The e...

    Authors: Ruth R Miller, Vincent Montoya, Jennifer L Gardy, David M Patrick and Patrick Tang
    Citation: Genome Medicine 2013 5:81
    Content type: Review Published on:

  10. Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identif...

    Authors: Mark Hills, Kieran O’Neill, Ester Falconer, Ryan Brinkman and Peter M Lansdorp
    Citation: Genome Medicine 2013 5:82
    Content type: Software Published on:

  12. Pancreatic cancer is one of the most lethal and molecularly diverse malignancies. Repurposing of therapeutics that target specific molecular mechanisms in different disease types offers potential for rapid imp...

    Authors: Angela Chou, Nicola Waddell, Mark J Cowley, Anthony J Gill, David K Chang, Ann-Marie Patch, Katia Nones, Jianmin Wu, Mark Pinese, Amber L Johns, David K Miller, Karin S Kassahn, Adnan M Nagrial, Harpreet Wasan, David Goldstein, Christopher W Toon…
    Citation: Genome Medicine 2013 5:78
    Content type: Research Published on:

  13. The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, includ...

    Authors: Sachin Sah, Liangjing Chen, Jeffrey Houghton, Jon Kemppainen, Adam C Marko, Robert Zeigler and Gary J Latham
    Citation: Genome Medicine 2013 5:77
    Content type: Method Published on:

  14. Single-cell functional proteomics assays can connect genomic information to biological function through quantitative and multiplex protein measurements. Tools for single-cell proteomics have developed rapidly ...

    Authors: Wei Wei, Young Shik Shin, Chao Ma, Jun Wang, Meltem Elitas, Rong Fan and James R Heath
    Citation: Genome Medicine 2013 5:75
    Content type: Review Published on:

  16. For cancer patients, the current approach to prognosis relies on clinicopathological staging, but usually this provides little information about the individual response to treatment. Therefore, there is a trem...

    Authors: Ellen Heitzer, Martina Auer, Peter Ulz, Jochen B Geigl and Michael R Speicher
    Citation: Genome Medicine 2013 5:73
    Content type: Review Published on:

  17. It is often assumed that rare genetic variants will improve available risk prediction scores. We aimed to estimate the added predictive ability of rare variants for risk prediction of common diseases in hypoth...

    Authors: Raluca Mihaescu, Michael J Pencina, Alvaro Alonso, Kathryn L Lunetta, Susan R Heckbert, Emelia J Benjamin and A Cecile JW Janssens
    Citation: Genome Medicine 2013 5:76
    Content type: Research Published on:

  19. Preimplantation genetic diagnosis (PGD) aims to help couples with heritable genetic disorders to avoid the birth of diseased offspring or the recurrence of loss of conception. Following in vitro fertilization, on...

    Authors: Niels Van der Aa, Masoud Zamani Esteki, Joris R Vermeesch and Thierry Voet
    Citation: Genome Medicine 2013 5:71
    Content type: Review Published on:

  21. With exome sequencing becoming a tool for mutation detection in routine diagnostics there is an increasing need for platform-independent methods of quality control. We present a genotype-weighted metric that a...

    Authors: Verena Heinrich, Tom Kamphans, Jens Stange, Dmitri Parkhomchuk, Jochen Hecht, Thorsten Dickhaus, Peter N Robinson and Peter M Krawitz
    Citation: Genome Medicine 2013 5:69
    Content type: Method Published on:

  22. The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influe...

    Authors: Daniela Börnigen, Xochitl C Morgan, Eric A Franzosa, Boyu Ren, Ramnik J Xavier, Wendy S Garrett and Curtis Huttenhower
    Citation: Genome Medicine 2013 5:65
    Content type: Review Published on:

  24. The mycobiome, referring primarily to the fungal biota in an environment, is an important component of the human microbiome. Despite its importance, it has remained understudied. New culture-independent approa...

    Authors: Lijia Cui, Alison Morris and Elodie Ghedin
    Citation: Genome Medicine 2013 5:63
    Content type: Review Published on:

  27. New strategies to combat complex human disease require systems approaches to biology that integrate experiments from cell lines, primary tissues and model organisms. We have developed Pathprint, a functional a...

    Authors: Gabriel M Altschuler, Oliver Hofmann, Irina Kalatskaya, Rebecca Payne, Shannan J Ho Sui, Uma Saxena, Andrei V Krivtsov, Scott A Armstrong, Tianxi Cai, Lincoln Stein and Winston A Hide
    Citation: Genome Medicine 2013 5:68
    Content type: Method Published on:

  28. Whole-exome sequencing has identified the causes of several Mendelian diseases by analyzing multiple unrelated cases, but it is more challenging to resolve the cause of extremely rare and suspected Mendelian d...

    Authors: Kai Wang, Cecilia Kim, Jonathan Bradfield, Yunfei Guo, Elina Toskala, Frederick G Otieno, Cuiping Hou, Kelly Thomas, Christopher Cardinale, Gholson J Lyon, Ryan Golhar and Hakon Hakonarson
    Citation: Genome Medicine 2013 5:67
    Content type: Research Published on:

  31. Biological therapies have been introduced for the treatment of chronic inflammatory diseases including rheumatoid arthritis (RA) and Crohn's disease (CD). The efficacy of biologics differs from patient to pati...

    Authors: Bertalan Mesko, Szilard Poliska, Andrea Váncsa, Zoltan Szekanecz, Karoly Palatka, Zsolt Hollo, Attila Horvath, Laszlo Steiner, Gabor Zahuczky, Janos Podani and and Laszlo Nagy
    Citation: Genome Medicine 2013 5:59
    Content type: Research Published on:

  34. Whole genome sequencing is poised to revolutionize personalized medicine, providing the capacity to classify individuals into risk categories for a wide range of diseases. Here we begin to explore how whole ge...

    Authors: Chirag J Patel, Ambily Sivadas, Rubina Tabassum, Thanawadee Preeprem, Jing Zhao, Dalia Arafat, Rong Chen, Alexander A Morgan, Gregory S Martin, Kenneth L Brigham, Atul J Butte and Greg Gibson
    Citation: Genome Medicine 2013 5:58
    Content type: Research Published on:

  35. The debate regarding the relative merits of whole genome sequencing (WGS) versus exome sequencing (ES) centers around comparative cost, average depth of coverage for each interrogated base, and their relative ...

    Authors: James R Lupski, Claudia Gonzaga-Jauregui, Yaping Yang, Matthew N Bainbridge, Shalini Jhangiani, Christian J Buhay, Christie L Kovar, Min Wang, Alicia C Hawes, Jeffrey G Reid, Christine Eng, Donna M Muzny and Richard A Gibbs
    Citation: Genome Medicine 2013 5:57
    Content type: Research Published on:

  36. Integration of clinical evaluations and whole-genome sequence data from eight individuals in a recent study demonstrates that genetic and clinical information can be combined and applied to preventive medicine...

    Authors: Nicholas J Schork
    Citation: Genome Medicine 2013 5:54
    Content type: Research highlight Published on:

  37. Proteomic technology has advanced steadily since the development of 'soft-ionization' techniques for mass-spectrometry-based molecular identification more than two decades ago. Now, the large-scale analysis of...

    Authors: John P Savaryn, Adam D Catherman, Paul M Thomas, Michael M Abecassis and Neil L Kelleher
    Citation: Genome Medicine 2013 5:53
    Content type: Opinion Published on:

  40. Target enrichment technologies utilize single-stranded oligonucleotide probes to capture candidate genomic regions from a DNA sample before sequencing. We describe target capture using double-stranded probes, ...

    Authors: Peidong Shen, Wenyi Wang, Aung-Kyaw Chi, Yu Fan, Ronald W Davis and Curt Scharfe
    Citation: Genome Medicine 2013 5:50
    Content type: Method Published on:

  41. Human papillomavirus positive (HPV+) head and neck squamous cell carcinoma (HNSCC) is an emerging disease, representing a distinct clinical and epidemiological entity. Understanding the genetic basis of this s...

    Authors: Matthias Lechner, Garrett M Frampton, Tim Fenton, Andrew Feber, Gary Palmer, Amrita Jay, Nischalan Pillay, Martin Forster, Maureen T Cronin, Doron Lipson, Vincent A Miller, Timothy A Brennan, Stephen Henderson, Francis Vaz, Paul O'Flynn, Nicholas Kalavrezos…
    Citation: Genome Medicine 2013 5:49
    Content type: Research Published on:

  47. Transcriptional studies suggest Alzheimer's disease (AD) involves dysfunction of many cellular pathways, including synaptic transmission, cytoskeletal dynamics, energetics, and apoptosis. Despite known progres...

    Authors: Jeremy A Miller, Randall L Woltjer, Jeff M Goodenbour, Steve Horvath and Daniel H Geschwind
    Citation: Genome Medicine 2013 5:48
    Content type: Research Published on:

  50. A DNA methylation signature has been characterized that distinguishes rheumatoid arthritis (RA) fibroblast like synoviocytes (FLS) from osteoarthritis (OA) FLS. The presence of epigenetic changes in long-term ...

    Authors: John W Whitaker, Robert Shoemaker, David L Boyle, Josh Hillman, David Anderson, Wei Wang and Gary S Firestein
    Citation: Genome Medicine 2013 5:40
    Content type: Research Published on:
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Genome Medicine

ISSN: 1756-994X

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