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From genomics to disease mechanisms

Guest editor: Jay Shendure

Genome Medicine presents a special issue on ‘From genomics to disease mechanisms’. Now that sequencing has moved into the clinic, researchers and clinicians are working together to understand the genomic mechanisms that underlie disease. We are moving from an era of association studies to functional studies that are beginning to reveal the cause of the clinical phenotype. A multi-disciplinary and multi-omic approach will be required to explain how genotypes give rise to phenotypes.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editor declares no competing interests.

  1. Content type: Editorial

    Gene finding is a finite exercise, and a means to an end, rather than an end in itself. The field of human genetics should increasingly shift its attention from disease gene identification to following through...

    Authors: Jay Shendure

    Citation: Genome Medicine 2014 6:86

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  2. Content type: Research

    INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library p...

    Authors: Han Fang, Yiyang Wu, Giuseppe Narzisi, Jason A ORawe, Laura T Jimenez Barrón, Julie Rosenbaum, Michael Ronemus, Ivan Iossifov, Michael C Schatz and Gholson J Lyon

    Citation: Genome Medicine 2014 6:89

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  3. Content type: Research

    Although genome-wide association studies (GWAS) have identified hundreds of variants associated with a risk for autoimmune and immune-related disorders (AID), our understanding of the disease mechanisms is sti...

    Authors: Barbara Hrdlickova, Vinod Kumar, Kartiek Kanduri, Daria V Zhernakova, Subhash Tripathi, Juha Karjalainen, Riikka J Lund, Yang Li, Ubaid Ullah, Rutger Modderman, Wayel Abdulahad, Harri Lähdesmäki, Lude Franke, Riitta Lahesmaa, Cisca Wijmenga and Sebo Withoff

    Citation: Genome Medicine 2014 6:88

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  4. Content type: Review

    Gene enhancer elements are noncoding segments of DNA that play a central role in regulating transcriptional programs that control development, cell identity, and evolutionary processes. Recent studies have sho...

    Authors: Olivia Corradin and Peter C Scacheri

    Citation: Genome Medicine 2014 6:85

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  5. Content type: Research

    Neoadjuvant chemotherapy for breast cancer leads to considerable variability in clinical responses, with only 10 to 20% of cases achieving complete pathologic responses (pCR). Biological and clinical factors t...

    Authors: Angela Alistar, Jeff W Chou, Srikanth Nagalla, Michael A Black, Ralph D’Agostino and Lance D Miller

    Citation: Genome Medicine 2014 6:80

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  6. Content type: Review

    Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but...

    Authors: Mika Gustafsson, Colm E Nestor, Huan Zhang, Albert-László Barabási, Sergio Baranzini, Sören Brunak, Kian Fan Chung, Howard J Federoff, Anne-Claude Gavin, Richard R Meehan, Paola Picotti, Miguel Ángel Pujana, Nikolaus Rajewsky, Kenneth GC Smith, Peter J Sterk, Pablo Villoslada…

    Citation: Genome Medicine 2014 6:82

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  7. Content type: Research

    Recently, a number of large-scale cancer genome sequencing projects have generated a large volume of somatic mutations; however, identifying the functional consequences and roles of somatic mutations in tumori...

    Authors: Huy Vuong, Feixiong Cheng, Chen-Ching Lin and Zhongming Zhao

    Citation: Genome Medicine 2014 6:81

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  8. Content type: Software

    Identifying functional non-coding variants is one of the greatest unmet challenges in genetics. To help address this, we introduce an R package, SuRFR, which integrates functional annotation and prior biologic...

    Authors: Niamh M Ryan, Stewart W Morris, David J Porteous, Martin S Taylor and Kathryn L Evans

    Citation: Genome Medicine 2014 6:79

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  9. Content type: Research

    Common genetic variation and rare mutations in genes encoding calcium channel subunits have pleiotropic effects on risk for multiple neuropsychiatric disorders, including autism spectrum disorder (ASD) and sch...

    Authors: Yuan Tian, Irina Voineagu, Sergiu P Paşca, Hyejung Won, Vijayendran Chandran, Steve Horvath, Ricardo E Dolmetsch and Daniel H Geschwind

    Citation: Genome Medicine 2014 6:75

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  10. Content type: Research

    There are 481 ultra-conserved regions (UCRs) longer than 200 bases in the genomes of human, mouse and rat. These DNA sequences are absolutely conserved and show 100% identity with no insertions or deletions. A...

    Authors: Marco Galasso, Paola Dama, Maurizio Previati, Sukhinder Sandhu, Jeff Palatini, Vincenzo Coppola, Sarah Warner, Maria E Sana, Riccardo Zanella, Ramzey Abujarour, Caroline Desponts, Michael A Teitell, Ramiro Garzon, George Calin, Carlo M Croce and Stefano Volinia

    Citation: Genome Medicine 2014 6:76

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  11. Content type: Software

    Interpretation of the multitude of variants obtained from next generation sequencing (NGS) is labor intensive and complex. Web-based interfaces such as Galaxy streamline the generation of variant lists but lac...

    Authors: Geert Vandeweyer, Lut Van Laer, Bart Loeys, Tim Van den Bulcke and R Frank Kooy

    Citation: Genome Medicine 2014 6:74

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