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  1. Research

    Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

    High tumor mutational burden (TMB) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to PD-1 and PD-L1 blockade immuno...

    Zachary R. Chalmers, Caitlin F. Connelly, David Fabrizio, Laurie Gay, Siraj M. Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S. Lieber…

    Genome Medicine 2017 9:34

    Published on: 19 April 2017

  2. Method

    Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

    Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome seq...

    Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M. Rueda, Suet-Feung Chin and Carlos Caldas

    Genome Medicine 2017 9:35

    Published on: 18 April 2017

  3. Research

    Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas

    Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermeth...

    Davide Degli Esposti, Athena Sklias, Sheila C. Lima, Stéphanie Beghelli-de la Forest Divonne, Vincent Cahais, Nora Fernandez-Jimenez, Marie-Pierre Cros, Szilvia Ecsedi, Cyrille Cuenin, Liacine Bouaoun, Graham Byrnes, Rosita Accardi, Anne Sudaka, Valérie Giordanengo, Hector Hernandez-Vargas, Luis Felipe Ribeiro Pinto…

    Genome Medicine 2017 9:33

    Published on: 5 April 2017

  4. Research

    Ethnic and diet-related differences in the healthy infant microbiome

    The infant gut is rapidly colonized by microorganisms soon after birth, and the composition of the microbiota is dynamic in the first year of life. Although a stable microbiome may not be established until 1 t...

    Jennifer C. Stearns, Michael A. Zulyniak, Russell J. de Souza, Natalie C. Campbell, Michelle Fontes, Mateen Shaikh, Malcolm R. Sears, Allan B. Becker, Piushkumar J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, Milan Gupta, Joseph Beyene, Michael G. Surette and Sonia S. Anand

    Genome Medicine 2017 9:32

    Published on: 29 March 2017

  5. Research

    Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma

    Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Her...

    Vinodh Srinivasainagendra, Michael W. Sandel, Bhupendra Singh, Aishwarya Sundaresan, Ved P. Mooga, Prachi Bajpai, Hemant K. Tiwari and Keshav K. Singh

    Genome Medicine 2017 9:31

    Published on: 29 March 2017

  6. Research

    New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

    Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion a...

    Antoine Dara, Elliott F. Drábek, Mark A. Travassos, Kara A. Moser, Arthur L. Delcher, Qi Su, Timothy Hostelley, Drissa Coulibaly, Modibo Daou, Ahmadou Dembele, Issa Diarra, Abdoulaye K. Kone, Bourema Kouriba, Matthew B. Laurens, Amadou Niangaly, Karim Traore…

    Genome Medicine 2017 9:30

    Published on: 28 March 2017

  7. Research

    Genetic pleiotropy between age-related macular degeneration and 16 complex diseases and traits

    Age-related macular degeneration (AMD) is a common condition of vision loss with disease development strongly influenced by environmental and genetic factors. Recently, 34 loci were associated with AMD at geno...

    Felix Grassmann, Christina Kiel, Martina E. Zimmermann, Mathias Gorski, Veronika Grassmann, Klaus Stark, Iris M. Heid and Bernhard H. F. Weber

    Genome Medicine 2017 9:29

    Published on: 27 March 2017

  8. Research

    DNA methylation changes at infertility genes in newborn twins conceived by in vitro fertilisation

    The association of in vitro fertilisation (IVF) and DNA methylation has been studied predominantly at regulatory regions of imprinted genes and at just thousands of the ~28 million CpG sites in the human genome.

    Juan E. Castillo-Fernandez, Yuk Jing Loke, Sebastian Bass-Stringer, Fei Gao, Yudong Xia, Honglong Wu, Hanlin Lu, Yuan Liu, Jun Wang, Tim D. Spector, Richard Saffery, Jeffrey M. Craig and Jordana T. Bell

    Genome Medicine 2017 9:28

    Published on: 24 March 2017

  9. Research

    A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

    Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved...

    Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood, Romy B. Christmann, Harrison W. Farber, Robert A. Lafyatis, Christopher P. Denton, Monique E. Hinchcliff, Patricia A. Pioli, J. Matthew Mahoney and Michael L. Whitfield

    Genome Medicine 2017 9:27

    Published on: 23 March 2017

  10. Comment

    Schizophrenia and substance use comorbidity: a genome-wide perspective

    Dual diagnosis with substance use disorders (SUDs) consistently contributes to the premature mortality and increased disability observed in schizophrenia. Large genome-wide association studies are providing th...

    Renato Polimanti, Arpana Agrawal and Joel Gelernter

    Genome Medicine 2017 9:25

    Published on: 21 March 2017

  11. Research

    Lessons learned from additional research analyses of unsolved clinical exome cases

    Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene disc...

    Mohammad K. Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A. Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R. Lalani, Christian P. Schaaf…

    Genome Medicine 2017 9:26

    Published on: 21 March 2017

  12. Research

    Imiquimod has strain-dependent effects in mice and does not uniquely model human psoriasis

    Imiquimod (IMQ) produces a cutaneous phenotype in mice frequently studied as an acute model of human psoriasis. Whether this phenotype depends on strain or sex has never been systematically investigated on a l...

    William R. Swindell, Kellie A. Michaels, Andrew J. Sutter, Doina Diaconu, Yi Fritz, Xianying Xing, Mrinal K. Sarkar, Yun Liang, Alex Tsoi, Johann E. Gudjonsson and Nicole L. Ward

    Genome Medicine 2017 9:24

    Published on: 9 March 2017

  13. Research

    Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants

    The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from approximately 24,000 ad...

    Reka Nagy, Thibaud S. Boutin, Jonathan Marten, Jennifer E. Huffman, Shona M. Kerr, Archie Campbell, Louise Evenden, Jude Gibson, Carmen Amador, David M. Howard, Pau Navarro, Andrew Morris, Ian J. Deary, Lynne J. Hocking, Sandosh Padmanabhan, Blair H. Smith…

    Genome Medicine 2017 9:23

    Published on: 7 March 2017

  14. Research

    Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients

    Understanding longitudinal variability of the microbiome in ill patients is critical to moving microbiome-based measurements and therapeutics into clinical practice. However, the vast majority of data regardin...

    Jessica R. Galloway-Peña, Daniel P. Smith, Pranoti Sahasrabhojane, W. Duncan Wadsworth, Bryan M. Fellman, Nadim J. Ajami, Elizabeth J. Shpall, Naval Daver, Michele Guindani, Joseph F. Petrosino, Dimitrios P. Kontoyiannis and Samuel A. Shelburne

    Genome Medicine 2017 9:21

    Published on: 28 February 2017

  15. Research

    Genomic analysis of 63,220 tumors reveals insights into tumor uniqueness and targeted cancer immunotherapy strategies

    The integration of genomics with immunotherapy has potential value for cancer vaccine development. Given the clinical successes of immune checkpoint modulators, interest in cancer vaccines as therapeutic optio...

    Ryan J. Hartmaier, Jehad Charo, David Fabrizio, Michael E. Goldberg, Lee A. Albacker, William Pao and Juliann Chmielecki

    Genome Medicine 2017 9:16

    Published on: 24 February 2017

  16. Research

    A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus

    Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under i...

    Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H. A. Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun…

    Genome Medicine 2017 9:18

    Published on: 20 February 2017

  17. Research

    Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance

    Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblas...

    David J. Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G. Higgins and Walter Kolch

    Genome Medicine 2017 9:15

    Published on: 10 February 2017

  18. Research

    Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas

    While the role of the gut microbiome in inflammation and colorectal cancers has received much recent attention, there are few data to support an association between the oral microbiome and head and neck squamo...

    Hannah Wang, Pauline Funchain, Gurkan Bebek, Jessica Altemus, Huan Zhang, Farshad Niazi, Charissa Peterson, Walter T. Lee, Brian B. Burkey and Charis Eng

    Genome Medicine 2017 9:14

    Published on: 7 February 2017

  19. Research

    Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation

    The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is ...

    Yuya Kobayashi, Shan Yang, Keith Nykamp, John Garcia, Stephen E. Lincoln and Scott E. Topper

    Genome Medicine 2017 9:13

    Published on: 6 February 2017

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