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  1. Content type: Research

    Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains cha...

    Authors: Avinash V. Dharmadhikari, Rajarshi Ghosh, Bo Yuan, Pengfei Liu, Hongzheng Dai, Sami Al Masri, Jennifer Scull, Jennifer E. Posey, Allen H. Jiang, Weimin He, Francesco Vetrini, Alicia A. Braxton, Patricia Ward, Theodore Chiang, Chunjing Qu, Shen Gu…

    Citation: Genome Medicine 2019 11:30

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  2. Content type: Comment

    The nature of the tumor antigens that are detectable by T cells remains unclear. In melanoma, T cells were shown to react against major histocompatibility complex (MHC)-associated peptides (MAPs) that are deri...

    Authors: Grégory Ehx and Claude Perreault

    Citation: Genome Medicine 2019 11:29

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    The Research to this article has been published in Genome Medicine 2019 11:28

  3. Content type: Research

    Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach ...

    Authors: Markus W. Löffler, Christopher Mohr, Leon Bichmann, Lena Katharina Freudenmann, Mathias Walzer, Christopher M. Schroeder, Nico Trautwein, Franz J. Hilke, Raphael S. Zinser, Lena Mühlenbruch, Daniel J. Kowalewski, Heiko Schuster, Marc Sturm, Jakob Matthes, Olaf Riess, Stefan Czemmel…

    Citation: Genome Medicine 2019 11:28

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    The Comment to this article has been published in Genome Medicine 2019 11:29

  4. Content type: Research

    Germinal center-derived B cell lymphomas are tumors of the lymphoid tissues representing one of the most heterogeneous malignancies. Here we characterize the variety of transcriptomic phenotypes of this diseas...

    Authors: Henry Loeffler-Wirth, Markus Kreuz, Lydia Hopp, Arsen Arakelyan, Andrea Haake, Sergio B. Cogliatti, Alfred C. Feller, Martin-Leo Hansmann, Dido Lenze, Peter Möller, Hans Konrad Müller-Hermelink, Erik Fortenbacher, Edith Willscher, German Ott, Andreas Rosenwald, Christiane Pott…

    Citation: Genome Medicine 2019 11:27

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  5. Content type: Research

    Genome wide association studies have identified > 200 susceptibility loci accounting for much of the heritability of multiple sclerosis (MS). Epstein-Barr virus (EBV), a memory B cell tropic virus, has been id...

    Authors: Ali Afrasiabi, Grant P. Parnell, Nicole Fewings, Stephen D. Schibeci, Monica A. Basuki, Ramya Chandramohan, Yuan Zhou, Bruce Taylor, David A. Brown, Sanjay Swaminathan, Fiona C. McKay, Graeme J. Stewart and David R. Booth

    Citation: Genome Medicine 2019 11:26

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  6. Content type: Research

    Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, gene disruption, position effects, or fusion gene formation. Recently, post-zygotic de novo triplications adjace...

    Authors: Claudia M. B. Carvalho, Zeynep Coban-Akdemir, Hadia Hijazi, Bo Yuan, Matthew Pendleton, Eoghan Harrington, John Beaulaurier, Sissel Juul, Daniel J. Turner, Rupa S. Kanchi, Shalini N. Jhangiani, Donna M. Muzny, Richard A. Gibbs, Pawel Stankiewicz, John W. Belmont, Chad A. Shaw…

    Citation: Genome Medicine 2019 11:25

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  7. Content type: Research Highlight

    The contribution of distinct genes to overlapping phenotypes suggests that such genes share ancestral origins, membership of disease pathways, or molecular functions. A recent study by Liu and colleagues ident...

    Authors: Vijay Kumar Pounraja and Santhosh Girirajan

    Citation: Genome Medicine 2019 11:24

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    The Research to this article has been published in Genome Medicine 2019 11:12

  8. Content type: Research

    Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by al...

    Authors: Quanyi Zhao, Robert Wirka, Trieu Nguyen, Manabu Nagao, Paul Cheng, Clint L. Miller, Juyong Brian Kim, Milos Pjanic and Thomas Quertermous

    Citation: Genome Medicine 2019 11:23

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  9. Content type: Method

    CRISPR/Cas9 has revolutionized cancer mouse models. Although loss-of-function genetics by CRISPR/Cas9 is well-established, generating gain-of-function alleles in somatic cancer models is still challenging beca...

    Authors: Haiwei Mou, Deniz M. Ozata, Jordan L. Smith, Ankur Sheel, Suet-Yan Kwan, Soren Hough, Alper Kucukural, Zachary Kennedy, Yueying Cao and Wen Xue

    Citation: Genome Medicine 2019 11:21

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  10. Content type: Research

    Genome-wide association studies (GWAS) have identified several hundred susceptibility loci for type 2 diabetes (T2D). One critical, but unresolved, issue concerns the extent to which the mechanisms through whi...

    Authors: Juan Fernández-Tajes, Kyle J. Gaulton, Martijn van de Bunt, Jason Torres, Matthias Thurner, Anubha Mahajan, Anna L. Gloyn, Kasper Lage and Mark I. McCarthy

    Citation: Genome Medicine 2019 11:19

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  11. Content type: Research Highlight

    As trials of immune checkpoint inhibitor (ICI) therapies demonstrate responses in only a minority of pleural mesotheliomas (PlMs) and largely exclude patients with the related peritoneal mesothelioma (PeM), cl...

    Authors: Marc Ladanyi, Francisco Sanchez Vega and Marjorie Zauderer

    Citation: Genome Medicine 2019 11:18

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    The Research to this article has been published in Genome Medicine 2019 11:8

  12. Content type: Correction

    It was highlighted that the original article [1] contained a typographical error in the Results section. Subject 17 was incorrectly cited as Subject 1. This Correction article shows the revised statement. The ...

    Authors: Francesco Vetrini, Shane McKee, Jill A. Rosenfeld, Mohnish Suri, Andrea M. Lewis, Kimberly Margaret Nugent, Elizabeth Roeder, Rebecca O. Littlejohn, Sue Holder, Wenmiao Zhu, Joseph T. Alaimo, Brett Graham, Jill M. Harris, James B. Gibson, Matthew Pastore, Kim L. McBride…

    Citation: Genome Medicine 2019 11:16

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    The original article was published in Genome Medicine 2019 11:12

  13. Content type: Correction

    It was highlighted that in the original article [1] the Availability of data and materials section was incorrect.

    Authors: Patricia C. Galipeau, Kenji M. Oman, Thomas G. Paulson, Carissa A. Sanchez, Qing Zhang, Jerry A. Marty, Jeffrey J. Delrow, Mary K. Kuhner, Thomas L. Vaughan, Brian J. Reid and Xiaohong Li

    Citation: Genome Medicine 2019 11:14

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    The original article was published in Genome Medicine 2018 10:17

  14. Content type: Research

    Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormaliti...

    Authors: Francesco Vetrini, Shane McKee, Jill A. Rosenfeld, Mohnish Suri, Andrea M. Lewis, Kimberly Margaret Nugent, Elizabeth Roeder, Rebecca O. Littlejohn, Sue Holder, Wenmiao Zhu, Joseph T. Alaimo, Brett Graham, Jill M. Harris, James B. Gibson, Matthew Pastore, Kim L. McBride…

    Citation: Genome Medicine 2019 11:12

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    The Correction to this article has been published in Genome Medicine 2019 11:16

    The Research Highlight to this article has been published in Genome Medicine 2019 11:24

  15. Content type: Research

    Increasing numbers of healthy individuals are undergoing predispositional personal genome sequencing. Here we describe the design and early outcomes of the PeopleSeq Consortium, a multi-cohort collaboration of...

    Authors: Emilie S. Zoltick, Michael D. Linderman, Molly A. McGinniss, Erica Ramos, Madeleine P. Ball, George M. Church, Debra G. B. Leonard, Stacey Pereira, Amy L. McGuire, C. Thomas Caskey, Saskia C. Sanderson, Eric E. Schadt, Daiva E. Nielsen, Scott D. Crawford and Robert C. Green

    Citation: Genome Medicine 2019 11:10

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  16. Content type: Review

    In recent years, the number of studies investigating the impact of the gut microbiome in colorectal cancer (CRC) has risen sharply. As a result, we now know that various microbes (and microbial communities) ar...

    Authors: Jawara Allen and Cynthia L. Sears

    Citation: Genome Medicine 2019 11:11

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  17. Content type: Comment

    Genomic medicine has considerable potential to provide novel diagnostic and therapeutic solutions for patients who have molecularly complex diseases and who are not responding to existing therapies. To bridge ...

    Authors: Huan Zhang, Lars Klareskog, Andreas Matussek, Stefan M. Pfister and Mikael Benson

    Citation: Genome Medicine 2019 11:9

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  18. Content type: Research

    Malignant peritoneal mesothelioma (PeM) is a rare and fatal cancer that originates from the peritoneal lining of the abdomen. Standard treatment of PeM is limited to cytoreductive surgery and/or chemotherapy, ...

    Authors: Raunak Shrestha, Noushin Nabavi, Yen-Yi Lin, Fan Mo, Shawn Anderson, Stanislav Volik, Hans H. Adomat, Dong Lin, Hui Xue, Xin Dong, Robert Shukin, Robert H. Bell, Brian McConeghy, Anne Haegert, Sonal Brahmbhatt, Estelle Li…

    Citation: Genome Medicine 2019 11:8

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    The Research Highlight to this article has been published in Genome Medicine 2019 11:18

  19. Content type: Research

    The extent to which changes in gene expression can influence cardiovascular disease risk across different tissue types has not yet been systematically explored. We have developed an analysis pipeline that inte...

    Authors: Kurt Taylor, George Davey Smith, Caroline L. Relton, Tom R. Gaunt and Tom G. Richardson

    Citation: Genome Medicine 2019 11:6

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  20. Content type: Research

    International guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false-positive rate over test sensitivity and...

    Authors: Roddy Walsh, Francesco Mazzarotto, Nicola Whiffin, Rachel Buchan, William Midwinter, Alicja Wilk, Nicholas Li, Leanne Felkin, Nathan Ingold, Risha Govind, Mian Ahmad, Erica Mazaika, Mona Allouba, Xiaolei Zhang, Antonio de Marvao, Sharlene M. Day…

    Citation: Genome Medicine 2019 11:5

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  21. Content type: Research

    Human kidney organoids hold promise for studying development, disease modelling and drug screening. However, the utility of stem cell-derived kidney tissues will depend on how faithfully these replicate normal...

    Authors: Alexander N. Combes, Luke Zappia, Pei Xuan Er, Alicia Oshlack and Melissa H. Little

    Citation: Genome Medicine 2019 11:3

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  22. Content type: Method

    Circulating tumour DNA (ctDNA) detection and monitoring have enormous potential clinical utility in oncology. We describe here a fast, flexible and cost-effective method to profile multiple genes simultaneousl...

    Authors: Meiling Gao, Maurizio Callari, Emma Beddowes, Stephen-John Sammut, Marta Grzelak, Heather Biggs, Linda Jones, Abdelhamid Boumertit, Sabine C. Linn, Javier Cortes, Mafalda Oliveira, Richard Baird, Suet-Feung Chin and Carlos Caldas

    Citation: Genome Medicine 2019 11:1

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  23. Content type: Research Highlight

    A new study highlights the biases and inaccuracies of polygenic risk scores (PRS) when predicting disease risk in individuals from populations other than those used in their derivation. The design bias of work...

    Authors: Francisco M. De La Vega and Carlos D. Bustamante

    Citation: Genome Medicine 2018 10:100

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    The Research to this article has been published in Genome Biology 2018 19:179

  24. Content type: Research

    Prior research has established that the prevalence of pathogenic/likely pathogenic (P/LP) variants across all of the American College of Medical Genetics (ACMG) Secondary Findings (SF) genes is approximately 0...

    Authors: Jung Kim, Wen Luo, Mingyi Wang, Talia Wegman-Ostrosky, Megan N. Frone, Jennifer J. Johnston, Michael L. Nickerson, Melissa Rotunno, Shengchao A. Li, Maria I. Achatz, Seth A. Brodie, Michael Dean, Kelvin C. de Andrade, Fernanda P. Fortes, Matthew Gianferante, Payal Khincha…

    Citation: Genome Medicine 2018 10:99

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  25. Content type: Research

    In recent years, research has consistently proven the occurrence of genetic overlap across autoimmune diseases, which supports the existence of common pathogenic mechanisms in autoimmunity. The objective of th...

    Authors: Ana Márquez, Martin Kerick, Alexandra Zhernakova, Javier Gutierrez-Achury, Wei-Min Chen, Suna Onengut-Gumuscu, Isidoro González-Álvaro, Luis Rodriguez-Rodriguez, Raquel Rios-Fernández, Miguel A. González-Gay, Maureen D. Mayes, Soumya Raychaudhuri, Stephen S. Rich, Cisca Wijmenga and Javier Martín

    Citation: Genome Medicine 2018 10:97

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  26. Content type: Opinion

    Only a small fraction of patients respond to the drug prescribed to treat their disease, which means that most are at risk of unnecessary exposure to side effects through ineffective drugs. This inter-individu...

    Authors: Monique G. P. van der Wijst, Dylan H. de Vries, Harm Brugge, Harm-Jan Westra and Lude Franke

    Citation: Genome Medicine 2018 10:96

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  27. Content type: Research

    Studies have shown that complex structural variants (cxSVs) contribute to human genomic variation and can cause Mendelian disease. We aimed to identify cxSVs relevant to Mendelian disease using short-read whol...

    Authors: Alba Sanchis-Juan, Jonathan Stephens, Courtney E. French, Nicholas Gleadall, Karyn Mégy, Christopher Penkett, Olga Shamardina, Kathleen Stirrups, Isabelle Delon, Eleanor Dewhurst, Helen Dolling, Marie Erwood, Detelina Grozeva, Luca Stefanucci, Gavin Arno, Andrew R. Webster…

    Citation: Genome Medicine 2018 10:95

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  28. Content type: Research

    Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical significance. However, it remains a challenge to define disease biology solely based on gene expression because tumor bi...

    Authors: Wei Tang, Ming Zhou, Tiffany H. Dorsey, DaRue A. Prieto, Xin W. Wang, Eytan Ruppin, Timothy D. Veenstra and Stefan Ambs

    Citation: Genome Medicine 2018 10:94

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  29. Content type: Research

    Based on promising phase II data, the histone deacetylase inhibitor entinostat is in phase III trials for patients with metastatic estrogen receptor-positive breast cancer. Predictors of sensitivity and resist...

    Authors: Maki Tanioka, Kevin R. Mott, Daniel P. Hollern, Cheng Fan, David B. Darr and Charles M. Perou

    Citation: Genome Medicine 2018 10:86

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  30. Content type: Review

    Immune checkpoint blockade (ICB) therapies, which potentiate the body’s natural immune response against tumor cells, have shown immense promise in the treatment of various cancers. Currently, tumor mutational ...

    Authors: Jake R. Conway, Eric Kofman, Shirley S. Mo, Haitham Elmarakeby and Eliezer Van Allen

    Citation: Genome Medicine 2018 10:93

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  31. Content type: Research

    Chemotherapeutic agents such as anthracyclines and taxanes are commonly used in the neoadjuvant setting. Bevacizumab is an antibody which binds to vascular endothelial growth factor A (VEGFA) and inhibits its ...

    Authors: Elen Kristine Höglander, Silje Nord, David C. Wedge, Ole Christian Lingjærde, Laxmi Silwal-Pandit, Hedda vdL Gythfeldt, Hans Kristian Moen Vollan, Thomas Fleischer, Marit Krohn, Ellen Schlitchting, Elin Borgen, Øystein Garred, Marit M. Holmen, Erik Wist, Bjørn Naume, Peter Van Loo…

    Citation: Genome Medicine 2018 10:92

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  32. Content type: Research

    Mutations in KRAS are frequent in human cancer, yet effective targeted therapeutics for these cancers are still lacking. Attempts to drug the MEK kinases downstream of KRAS have had limited success in clinical tr...

    Authors: Tonći Šuštić, Sake van Wageningen, Evert Bosdriesz, Robert J. D. Reid, John Dittmar, Cor Lieftink, Roderick L. Beijersbergen, Lodewyk F. A. Wessels, Rodney Rothstein and René Bernards

    Citation: Genome Medicine 2018 10:90

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  33. Content type: Comment

    Telomere crisis is linked with many of the genomic alterations found in cancer genomes. A new understanding of how these alterations arise points towards an active role for innate immune sensors during crisis ...

    Authors: Patrick von Morgen and John Maciejowski

    Citation: Genome Medicine 2018 10:89

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  34. Content type: Comment

    Immunotherapy has revolutionized the management of numerous cancers; however, a substantial proportion that initially respond subsequently acquire means of immune escape and relapse. Analysis of recent clinica...

    Authors: J. Bryan Iorgulescu, David Braun, Giacomo Oliveira, Derin B. Keskin and Catherine J. Wu

    Citation: Genome Medicine 2018 10:87

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  35. Content type: Research

    There are multiple existing and emerging therapeutic avenues for metastatic prostate cancer, with a common denominator, which is the need for predictive biomarkers. Circulating tumor DNA (ctDNA) has the potent...

    Authors: Markus Mayrhofer, Bram De Laere, Tom Whitington, Peter Van Oyen, Christophe Ghysel, Jozef Ampe, Piet Ost, Wim Demey, Lucien Hoekx, Dirk Schrijvers, Barbara Brouwers, Willem Lybaert, Els Everaert, Daan De Maeseneer, Michiel Strijbos, Alain Bols…

    Citation: Genome Medicine 2018 10:85

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  36. Content type: Research

    Major histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide to MHC-II binding are trained on binding affinity data, ...

    Authors: Carolina Barra, Bruno Alvarez, Sinu Paul, Alessandro Sette, Bjoern Peters, Massimo Andreatta, Søren Buus and Morten Nielsen

    Citation: Genome Medicine 2018 10:84

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  37. Content type: Research

    Comprehensive mutational profiling data now available on all major cancers have led to proposals of novel molecular tumor classifications that modify or replace the established organ- and tissue-based tumor ty...

    Authors: Daniel Heim, Grégoire Montavon, Peter Hufnagl, Klaus-Robert Müller and Frederick Klauschen

    Citation: Genome Medicine 2018 10:83

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  38. Content type: Research

    Staphylococcus aureus is an opportunistic pathogen and a leading cause of nosocomial infections. It can acquire resistance to all the antibiotics that entered the clinics to date, and the World Health Organizatio...

    Authors: Serena Manara, Edoardo Pasolli, Daniela Dolce, Novella Ravenni, Silvia Campana, Federica Armanini, Francesco Asnicar, Alessio Mengoni, Luisa Galli, Carlotta Montagnani, Elisabetta Venturini, Omar Rota-Stabelli, Guido Grandi, Giovanni Taccetti and Nicola Segata

    Citation: Genome Medicine 2018 10:82

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