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  1. Software

    ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants

    The success of the clinical use of sequencing based tests (from single gene to genomes) depends on the accuracy and consistency of variant interpretation. Aiming to improve the interpretation process through p...

    Ronak Y. Patel, Neethu Shah, Andrew R. Jackson, Rajarshi Ghosh, Piotr Pawliczek, Sameer Paithankar, Aaron Baker, Kevin Riehle, Hailin Chen, Sofia Milosavljevic, Chris Bizon, Shawn Rynearson, Tristan Nelson, Gail P. Jarvik, Heidi L. Rehm, Steven M. Harrison…

    Genome Medicine 2017 9:3

    Published on: 12 January 2017

  2. Research

    Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations

    Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has b...

    Jennifer A. Oberg, Julia L. Glade Bender, Maria Luisa Sulis, Danielle Pendrick, Anthony N. Sireci, Susan J. Hsiao, Andrew T. Turk, Filemon S. Dela Cruz, Hanina Hibshoosh, Helen Remotti, Rebecca J. Zylber, Jiuhong Pang, Daniel Diolaiti, Carrie Koval, Stuart J. Andrews, James H. Garvin…

    Genome Medicine 2016 8:133

    Published on: 23 December 2016

  3. Research

    Genomic landscape of colorectal cancer in Japan: clinical implications of comprehensive genomic sequencing for precision medicine

    Comprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been li...

    Masayuki Nagahashi, Toshifumi Wakai, Yoshifumi Shimada, Hiroshi Ichikawa, Hitoshi Kameyama, Takashi Kobayashi, Jun Sakata, Ryoma Yagi, Nobuaki Sato, Yuko Kitagawa, Hiroyuki Uetake, Kazuhiro Yoshida, Eiji Oki, Shin-ei Kudo, Hiroshi Izutsu, Keisuke Kodama…

    Genome Medicine 2016 8:136

    Published on: 22 December 2016

  4. Research

    The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

    The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resis...

    Jody Phelan, Denise M. O’Sullivan, Diana Machado, Jorge Ramos, Alexandra S. Whale, Justin O’Grady, Keertan Dheda, Susana Campino, Ruth McNerney, Miguel Viveiros, Jim F. Huggett and Taane G. Clark

    Genome Medicine 2016 8:132

    Published on: 22 December 2016

  5. Research

    Alternate-locus aware variant calling in whole genome sequencing

    The last two human genome assemblies have extended the previous linear golden-path paradigm of the human genome to a graph-like model to better represent regions with a high degree of structural variability. T...

    Marten Jäger, Max Schubach, Tomasz Zemojtel, Knut Reinert, Deanna M. Church and Peter N. Robinson

    Genome Medicine 2016 8:130

    Published on: 13 December 2016

  6. Research

    Non-coding single nucleotide variants affecting estrogen receptor binding and activity

    Estrogen receptor (ER) activity is critical for the development and progression of the majority of breast cancers. It is known that ER is differentially bound to DNA leading to transcriptomic and phenotypic ch...

    Amir Bahreini, Kevin Levine, Lucas Santana-Santos, Panayiotis V. Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich and Adrian V. Lee

    Genome Medicine 2016 8:128

    Published on: 13 December 2016

  7. Research

    Truncating de novo mutations in the Krüppel-type zinc-finger gene ZNF148 in patients with corpus callosum defects, developmental delay, short stature, and dysmorphisms

    Krüppel-type zinc finger genes (ZNF) constitute a large yet relatively poorly characterized gene family. ZNF genes encode proteins that recognize specific DNA motifs in gene promotors. They act as transcriptio...

    Servi J. C. Stevens, Anthonie J. van Essen, Conny M. A. van Ravenswaaij, Abdallah F. Elias, Jaclyn A. Haven, Stefan H. Lelieveld, Rolph Pfundt, Willy M. Nillesen, Helger G. Yntema, Kees van Roozendaal, Alexander P. Stegmann, Christian Gilissen and Han G. Brunner

    Genome Medicine 2016 8:131

    Published on: 13 December 2016

  8. Research

    Allele-specific expression in the human heart and its application to postoperative atrial fibrillation and myocardial ischemia

    Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from t...

    Martin I. Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S. Couper, Stanton K. Shernan, Jon G. Seidman, Simon C. Body and Jochen D. Muehlschlegel

    Genome Medicine 2016 8:127

    Published on: 6 December 2016

  9. Research

    Potential contribution of the uterine microbiome in the development of endometrial cancer

    Endometrial cancer studies have led to a number of well-defined but mechanistically unconnected genetic and environmental risk factors. One of the emerging modulators between environmental triggers and genetic...

    Marina R. S. Walther-António, Jun Chen, Francesco Multinu, Alexis Hokenstad, Tammy J. Distad, E. Heidi Cheek, Gary L. Keeney, Douglas J. Creedon, Heidi Nelson, Andrea Mariani and Nicholas Chia

    Genome Medicine 2016 8:122

    Published on: 25 November 2016

  10. Opinion

    Looking beyond the cancer cell for effective drug combinations

    Combinations of therapies are being actively pursued to expand therapeutic options and deal with cancer’s pervasive resistance to treatment. Research efforts to discover effective combination treatments have f...

    Jonathan R. Dry, Mi Yang and Julio Saez-Rodriguez

    Genome Medicine 2016 8:125

    Published on: 25 November 2016

  11. Research

    High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis

    Twin studies are powerful models to elucidate epigenetic modifications resulting from gene–environment interactions. Yet, commonly a limited number of clinical twin samples are available, leading to an underpo...

    David Gomez-Cabrero, Malin Almgren, Louise K. Sjöholm, Aase H. Hensvold, Mikael V. Ringh, Rakel Tryggvadottir, Juha Kere, Annika Scheynius, Nathalie Acevedo, Lovisa Reinius, Margaret A. Taub, Carolina Montano, Martin J. Aryee, Jason I. Feinberg, Andrew P. Feinberg, Jesper Tegnér…

    Genome Medicine 2016 8:124

    Published on: 22 November 2016

  12. Method

    Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

    Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describ...

    Tanjina Kader, David L. Goode, Stephen Q. Wong, Jacquie Connaughton, Simone M. Rowley, Lisa Devereux, David Byrne, Stephen B. Fox, Gisela Mir Arnau, Richard W. Tothill, Ian G. Campbell and Kylie L. Gorringe

    Genome Medicine 2016 8:121

    Published on: 15 November 2016

  13. Research

    Low heritability in pharmacokinetics of talinolol: a pharmacogenetic twin study on the heritability of the pharmacokinetics of talinolol, a putative probe drug of MDR1 and other membrane transporters

    Efflux transporters like MDR1 and MRP2 may modulate the pharmacokinetics of about 50 % of all drugs. It is currently unknown how much of the variation in the activities of important drug membrane transporters ...

    Johannes Matthaei, Mladen V. Tzvetkov, Valerie Gal, Cordula Sachse-Seeboth, Daniel Sehrt, Jakob B. Hjelmborg, Ute Hofmann, Matthias Schwab, Reinhold Kerb and Jürgen Brockmöller

    Genome Medicine 2016 8:119

    Published on: 8 November 2016

  14. Research

    Somatic cancer variant curation and harmonization through consensus minimum variant level data

    To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (C...

    Deborah I. Ritter, Sameek Roychowdhury, Angshumoy Roy, Shruti Rao, Melissa J. Landrum, Dmitriy Sonkin, Mamatha Shekar, Caleb F. Davis, Reece K. Hart, Christine Micheel, Meredith Weaver, Eliezer M. Van Allen, Donald W. Parsons, Howard L. McLeod, Michael S. Watson, Sharon E. Plon…

    Genome Medicine 2016 8:117

    Published on: 4 November 2016

  15. Research

    Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease

    Alzheimer’s disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. However, despite extensive clinical and genomic studies, the molecular bas...

    Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen J. Brennand, Gabriele C. De Luca, John F. Crary, Patrizia Casaccia, Joseph D. Buxbaum, Michelle Ehrlich, Sam Gandy, Alison Goate, Pavel Katsel, Eric Schadt, Vahram Haroutunian…

    Genome Medicine 2016 8:104

    Published on: 1 November 2016

  16. Research

    MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death

    Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial...

    Mohammad K. Eldomery, Zeynep C. Akdemir, F.-Nora Vögtle, Wu-Lin Charng, Patrycja Mulica, Jill A. Rosenfeld, Tomasz Gambin, Shen Gu, Lindsay C. Burrage, Aisha Al Shamsi, Samantha Penney, Shalini N. Jhangiani, Holly H. Zimmerman, Donna M. Muzny, Xia Wang, Jia Tang…

    Genome Medicine 2016 8:106

    Published on: 1 November 2016

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