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  1. Content type: Research

    Next-generation sequencing (NGS) of cancer gene panels are widely applied to enable personalized cancer therapy and to identify novel oncogenic mutations.

    Authors: Shuyu D. Li, Meng Ma, Hui Li, Aneta Waluszko, Tatyana Sidorenko, Eric E. Schadt, David Y. Zhang, Rong Chen and Fei Ye

    Citation: Genome Medicine 2017 9:89

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  2. Content type: Research

    The Wiskott–Aldrich syndrome protein (WASp) family of actin-nucleating factors are present in the cytoplasm and in the nucleus. The role of nuclear WASp for T cell development remains incompletely defined.

    Authors: Nikolai V. Kuznetsov, Bader Almuzzaini, Joanna S. Kritikou, Marisa A. P. Baptista, Mariana M. S. Oliveira, Marton Keszei, Scott B. Snapper, Piergiorgio Percipalle and Lisa S. Westerberg

    Citation: Genome Medicine 2017 9:91

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  3. Content type: Research

    Massively parallel DNA sequencing, such as exome sequencing, has become a routine clinical procedure to identify pathogenic variants responsible for a patient’s phenotype. Exome sequencing has the capability o...

    Authors: Hayk Barseghyan, Wilson Tang, Richard T. Wang, Miguel Almalvez, Eva Segura, Matthew S. Bramble, Allen Lipson, Emilie D. Douine, Hane Lee, Emmanuèle C. Délot, Stanley F. Nelson and Eric Vilain

    Citation: Genome Medicine 2017 9:90

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  4. Content type: Software

    The human leukocyte antigen (HLA) system is a genomic region involved in regulating the human immune system by encoding cell membrane major histocompatibility complex (MHC) proteins that are responsible for se...

    Authors: Martin L. Buchkovich, Chad C. Brown, Kimberly Robasky, Shengjie Chai, Sharon Westfall, Benjamin G. Vincent, Eric T. Weimer and Jason G. Powers

    Citation: Genome Medicine 2017 9:86

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  5. Content type: Comment

    Genome editing using clustered regularly interspersed short palindromic repeats (CRISPR) and CRISPR-associated proteins offers the potential to facilitate safe and effective treatment of genetic diseases refra...

    Authors: Dianne Nicol, Lisa Eckstein, Michael Morrison, Jacob S. Sherkow, Margaret Otlowski, Tess Whitton, Tania Bubela, Kathryn P. Burdon, Don Chalmers, Sarah Chan, Jac Charlesworth, Christine Critchley, Merlin Crossley, Sheryl de Lacey, Joanne L. Dickinson, Alex W. Hewitt…

    Citation: Genome Medicine 2017 9:85

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  6. Content type: Correspondence

    National and international public–private partnerships, consortia, and government initiatives are underway to collect and share genomic, personal, and healthcare data on a massive scale. Ideally, these efforts...

    Authors: Patricia A. Deverka, Mary A. Majumder, Angela G. Villanueva, Margaret Anderson, Annette C. Bakker, Jessica Bardill, Eric Boerwinkle, Tania Bubela, Barbara J. Evans, Nanibaa’ A. Garrison, Richard A. Gibbs, Robert Gentleman, David Glazer, Melissa M. Goldstein, Hank Greely, Crane Harris…

    Citation: Genome Medicine 2017 9:84

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  7. Content type: Research

    Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular ...

    Authors: Tomasz Gambin, Bo Yuan, Weimin Bi, Pengfei Liu, Jill A. Rosenfeld, Zeynep Coban-Akdemir, Amber N. Pursley, Sandesh C. S. Nagamani, Ronit Marom, Sailaja Golla, Lauren Dengle, Heather G. Petrie, Reuben Matalon, Lisa Emrick, Monica B. Proud, Diane Treadwell-Deering…

    Citation: Genome Medicine 2017 9:83

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  8. Content type: Research

    Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas.

    Authors: Chakkaphan Runcharoen, Kathy E. Raven, Sandra Reuter, Teemu Kallonen, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Beth Blane, Julian Parkhill, Sharon J. Peacock and Narisara Chantratita

    Citation: Genome Medicine 2017 9:81

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  9. Content type: Research

    Neoepitopes derived from tumor-specific somatic mutations are promising targets for immunotherapy in childhood cancers. However, the potential for such therapies in targeting these epitopes remains uncertain d...

    Authors: Ti-Cheng Chang, Robert A. Carter, Yongjin Li, Yuxin Li, Hong Wang, Michael N. Edmonson, Xiang Chen, Paula Arnold, Terrence L. Geiger, Gang Wu, Junmin Peng, Michael Dyer, James R. Downing, Douglas R. Green, Paul G. Thomas and Jinghui Zhang

    Citation: Genome Medicine 2017 9:78

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  10. Content type: Method

    The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative...

    Authors: Zeynep Kalender Atak, Hana Imrichova, Dmitry Svetlichnyy, Gert Hulselmans, Valerie Christiaens, Joke Reumers, Hugo Ceulemans and Stein Aerts

    Citation: Genome Medicine 2017 9:80

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  11. Content type: Research

    Several articles suggest that DNA methylation levels in blood relate to Parkinson’s disease (PD) but there is a need for a large-scale study that involves suitable population based controls. The purposes of th...

    Authors: Yu-Hsuan Chuang, Kimberly C. Paul, Jeff M. Bronstein, Yvette Bordelon, Steve Horvath and Beate Ritz

    Citation: Genome Medicine 2017 9:76

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  12. Content type: Method

    A major aim of cancer genomics is to pinpoint which somatically mutated genes are involved in tumor initiation and progression. We introduce a new framework for uncovering cancer genes, differential mutation a...

    Authors: Pawel F. Przytycki and Mona Singh

    Citation: Genome Medicine 2017 9:79

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    The Correction to this article has been published in Genome Medicine 2018 10:35

  13. Content type: Review

    RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled mu...

    Authors: Ashraful Haque, Jessica Engel, Sarah A. Teichmann and Tapio Lönnberg

    Citation: Genome Medicine 2017 9:75

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  14. Content type: Comment

    Advances in molecular tools to characterize the microbiome have led to the discovery of unique roles for microbes in human disease. Findings that the female genital microbiome can influence HIV acquisition and...

    Authors: Lenine J. P. Liebenberg, Derseree Archary, Aida Sivro and Douglas S. Kwon

    Citation: Genome Medicine 2017 9:74

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  15. Content type: Research

    De novo missense variants in CDK13 have been described as the cause of syndromic congenital heart defects in seven individuals ascertained from a large congenital cardiovascular malformations cohort. We aimed to ...

    Authors: Bret L. Bostwick, Scott McLean, Jennifer E. Posey, Haley E. Streff, Karen W. Gripp, Alyssa Blesson, Nina Powell-Hamilton, Jessica Tusi, David A. Stevenson, Ellyn Farrelly, Louanne Hudgins, Yaping Yang, Fan Xia, Xia Wang, Pengfei Liu, Magdalena Walkiewicz…

    Citation: Genome Medicine 2017 9:73

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  16. Content type: Research

    Psychiatric disorders are multigenic diseases with complex etiology that contribute significantly to human morbidity and mortality. Although clinically distinct, several disorders share many symptoms, suggesti...

    Authors: Ryne C. Ramaker, Kevin M. Bowling, Brittany N. Lasseigne, Megan H. Hagenauer, Andrew A. Hardigan, Nicholas S. Davis, Jason Gertz, Preston M. Cartagena, David M. Walsh, Marquis P. Vawter, Edward G. Jones, Alan F. Schatzberg, Jack D. Barchas, Stanley J. Watson, Blynn G. Bunney, Huda Akil…

    Citation: Genome Medicine 2017 9:72

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  17. Content type: Research

    Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcare...

    Authors: Hayley J. Brodrick, Kathy E. Raven, Teemu Kallonen, Dorota Jamrozy, Beth Blane, Nicholas M. Brown, Veronique Martin, M. Estée Török, Julian Parkhill and Sharon J. Peacock

    Citation: Genome Medicine 2017 9:70

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  18. Content type: Research

    Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders.

    Authors: Claudio Reggiani, Sandra Coppens, Tayeb Sekhara, Ivan Dimov, Bruno Pichon, Nicolas Lufin, Marie-Claude Addor, Elga Fabia Belligni, Maria Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gerard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone…

    Citation: Genome Medicine 2017 9:67

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  19. Content type: Research

    Onco-proteogenomics aims to understand how changes in a cancer’s genome influences its proteome. One challenge in integrating these molecular data is the identification of aberrant protein products from mass-s...

    Authors: Javier A. Alfaro, Alexandr Ignatchenko, Vladimir Ignatchenko, Ankit Sinha, Paul C. Boutros and Thomas Kislinger

    Citation: Genome Medicine 2017 9:62

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  20. Content type: Research

    Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes (T2D). However, the underlying biological mechanisms for many of these associations remain unkn...

    Authors: Maykel López Rodríguez, Dorota Kaminska, Kati Lappalainen, Jussi Pihlajamäki, Minna U. Kaikkonen and Markku Laakso

    Citation: Genome Medicine 2017 9:63

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  21. Content type: Software

    A key step in cancer genome analysis is the identification of somatic mutations in the tumor. This is typically done by comparing the genome of the tumor to the reference genome sequence derived from a normal ...

    Authors: Irina Kalatskaya, Quang M. Trinh, Melanie Spears, John D. McPherson, John M. S. Bartlett and Lincoln Stein

    Citation: Genome Medicine 2017 9:59

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  22. Content type: Opinion

    Biomedical research is becoming increasingly large-scale and international. Cloud computing enables the comprehensive integration of genomic and clinical data, and the global sharing and collaborative processi...

    Authors: Fruzsina Molnár-Gábor, Rupert Lueck, Sergei Yakneen and Jan O. Korbel

    Citation: Genome Medicine 2017 9:58

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  23. Content type: Research

    Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole ...

    Authors: Stephanie U. Greer, Lincoln D. Nadauld, Billy T. Lau, Jiamin Chen, Christina Wood-Bouwens, James M. Ford, Calvin J. Kuo and Hanlee P. Ji

    Citation: Genome Medicine 2017 9:57

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  24. Content type: Comment

    Recent advances in genome sequencing of single microbial cells enable the assignment of functional roles to members of the human microbiome that cannot currently be cultured. This approach can reveal the genom...

    Authors: Andrew C. Tolonen and Ramnik J. Xavier

    Citation: Genome Medicine 2017 9:56

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  25. Content type: Software

    The pathogenesis of neurological and mental health disorders often involves multiple genes, complex interactions, as well as brain- and development-specific biological mechanisms. These characteristics make id...

    Authors: Saskia Freytag, Rosemary Burgess, Karen L. Oliver and Melanie Bahlo

    Citation: Genome Medicine 2017 9:55

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  26. Content type: Research

    Profiles of DNA methylation of many tissues relevant in human disease have been obtained from microarrays and are publicly available. These can be used to generate maps of chromatin compartmentalization, demar...

    Authors: Poppy Simmonds, Erick Loomis and Edward Curry

    Citation: Genome Medicine 2017 9:54

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  27. Content type: Research

    It is frequently assumed that pre-invasive lesions are simpler precursors of cancer and will contain a limited subset of the genomic changes seen in their associated invasive disease. Driver mutations are thou...

    Authors: Henry M. Wood, Catherine Daly, Rebecca Chalkley, Burcu Senguven, Lisa Ross, Philip Egan, Preetha Chengot, Jennifer Graham, Neeraj Sethi, Thian K. Ong, Kenneth MacLennan, Pamela Rabbitts and Caroline Conway

    Citation: Genome Medicine 2017 9:53

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  28. Content type: Research

    Genome-wide loss-of-function profiling is widely used for systematic identification of genetic dependencies in cancer cells; however, the poor reproducibility of RNA interference (RNAi) screens has been a majo...

    Authors: Alok Jaiswal, Gopal Peddinti, Yevhen Akimov, Krister Wennerberg, Sergey Kuznetsov, Jing Tang and Tero Aittokallio

    Citation: Genome Medicine 2017 9:51

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  29. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2017 9:50

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  30. Content type: Review

    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 ...

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

    Citation: Genome Medicine 2017 9:49

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  31. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2017 9:43

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  32. Content type: Research

    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 ...

    Authors: Yael Silberberg, Martin Kupiec and Roded Sharan

    Citation: Genome Medicine 2017 9:48

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  33. Content type: Research

    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...

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

    Citation: Genome Medicine 2017 9:47

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  34. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2017 9:46

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  35. Content type: Comment

    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...

    Authors: Solomon Afelik and Meritxell Rovira

    Citation: Genome Medicine 2017 9:42

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

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