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  1. Content type: Research

    Neoantigens that arise as a consequence of tumor-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumor types, a high number ...

    Authors: Giuseppe Rospo, Annalisa Lorenzato, Nabil Amirouchene-Angelozzi, Alessandro Magrì, Carlotta Cancelliere, Giorgio Corti, Carola Negrino, Vito Amodio, Monica Montone, Alice Bartolini, Ludovic Barault, Luca Novara, Claudio Isella, Enzo Medico, Andrea Bertotti, Livio Trusolino…

    Citation: Genome Medicine 2019 11:42

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  2. Content type: Software

    Mycobacterium tuberculosis resistance to anti-tuberculosis drugs is a major threat to global public health. Whole genome sequencing (WGS) is rapidly gaining traction as a diagnostic tool for clinical tuberculosis...

    Authors: Jody E. Phelan, Denise M. O’Sullivan, Diana Machado, Jorge Ramos, Yaa E. A. Oppong, Susana Campino, Justin O’Grady, Ruth McNerney, Martin L. Hibberd, Miguel Viveiros, Jim F. Huggett and Taane G. Clark

    Citation: Genome Medicine 2019 11:41

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  3. Content type: Opinion

    The expression of antigens that are recognized by self-reactive T cells is essential for immune-mediated tumor rejection by immune checkpoint blockade (ICB) therapy. Growing evidence suggests that mutation-ass...

    Authors: Claire Lhuillier, Nils-Petter Rudqvist, Olivier Elemento, Silvia C. Formenti and Sandra Demaria

    Citation: Genome Medicine 2019 11:40

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  4. Content type: Comment

    Personalized care of cancer patients undergoing treatment with immune checkpoint inhibitors will require approaches that can predict their susceptibility to immune-related adverse events. Understanding the rol...

    Authors: Zia Khan, Christian Hammer, Ellie Guardino, G. Scott Chandler and Matthew L. Albert

    Citation: Genome Medicine 2019 11:39

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  5. Content type: Research

    Diagnosis of primary immunodeficiencies (PIDs) is complex and cumbersome yet important for the clinical management of the disease. Exome sequencing may provide a genetic diagnosis in a significant number of pa...

    Authors: Peer Arts, Annet Simons, Mofareh S. AlZahrani, Elanur Yilmaz, Eman AlIdrissi, Koen J. van Aerde, Njood Alenezi, Hamza A. AlGhamdi, Hadeel A. AlJubab, Abdulrahman A. Al-Hussaini, Fahad AlManjomi, Alaa B. Alsaad, Badr Alsaleem, Abdulrahman A. Andijani, Ali Asery, Walid Ballourah…

    Citation: Genome Medicine 2019 11:38

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  6. Content type: Research

    Measures of the adaptive immune response have prognostic and predictive associations in melanoma and other cancer types. Specifically, intratumoral T cell density and function have considerable prognostic and ...

    Authors: Sara R. Selitsky, Lisle E. Mose, Christof C. Smith, Shengjie Chai, Katherine A. Hoadley, Dirk P. Dittmer, Stergios J. Moschos, Joel S. Parker and Benjamin G. Vincent

    Citation: Genome Medicine 2019 11:36

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  7. Content type: Comment

    Recent sequencing studies on healthy skin and esophagus have found that, as we age, these tissues become colonized by mutant clones of cells carrying driver mutations in traditional cancer genes. This comment ...

    Authors: Inigo Martincorena

    Citation: Genome Medicine 2019 11:35

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  8. Content type: Research

    Somatic genetic testing is rapidly becoming the standard of care in many adult and pediatric cancers. Previously, the standard approach was single-gene or focused multigene testing, but many centers have moved...

    Authors: Lea F. Surrey, Suzanne P. MacFarland, Fengqi Chang, Kajia Cao, Komal S. Rathi, Gozde T. Akgumus, Daniel Gallo, Fumin Lin, Adam Gleason, Pichai Raman, Richard Aplenc, Rochelle Bagatell, Jane Minturn, Yael Mosse, Mariarita Santi, Sarah K. Tasian…

    Citation: Genome Medicine 2019 11:32

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  9. Content type: Method

    We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry...

    Authors: Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Zuzana Loncova, Wilfried Posch, Doris Wilflingseder, Sieghart Sopper, Marieke Ijsselsteijn, Thomas P. Brouwer, Douglas Johnson, Yaomin Xu, Yu Wang…

    Citation: Genome Medicine 2019 11:34

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  10. Content type: Opinion

    As epigenetic studies become more common and lead to new insights into health and disease, the return of individual epigenetic results to research participants, in particular in large-scale epigenomic studies,...

    Authors: Stephanie O. M. Dyke, Katie M. Saulnier, Charles Dupras, Amy P. Webster, Karen Maschke, Mark Rothstein, Reiner Siebert, Jörn Walter, Stephan Beck, Tomi Pastinen and Yann Joly

    Citation: Genome Medicine 2019 11:31

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  11. 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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  12. 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

  13. 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

  14. 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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  15. 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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  16. 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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  17. 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

  18. 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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  19. 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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  20. 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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  21. 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

  22. 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

  23. 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

  24. 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

  25. 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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  26. 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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  27. 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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  28. 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

  29. 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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  30. 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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  31. 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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  32. 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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  33. 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

  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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