Genetics, genomics and epigenetics

Section edited by Ian Cree

This section considers articles on all aspects of genome-scale analysis, functional genomics, genetic association studies, pharmacogenomics and epigenetics in relation to cancer biology, diagnosis and therapy.

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  1. Research article

    Succinate dehydrogenase deficiency in a PDGFRA mutated GIST

    Most gastrointestinal stromal tumors (GISTs) harbor mutually exclusive gain of function mutations in the receptor tyrosine kinase (RTK) KIT (70–80%) or in the related receptor PDGFRA (~10%). These GISTs genera...

    Martin G. Belinsky, Kathy Q. Cai, Yan Zhou, Biao Luo, Jianming Pei, Lori Rink and Margaret von Mehren

    BMC Cancer 2017 17:512

    Published on: 2 August 2017

  2. Study protocol

    Psychosocial and behavioral impact of breast cancer risk assessed by testing for common risk variants: protocol of a prospective study

    The ‘common variant, common disease’ model predicts that a significant component of hereditary breast cancer unexplained by pathogenic variants in moderate or high-penetrance genes is due to the cumulative eff...

    Tatiane Yanes, Bettina Meiser, Mary-Anne Young, Rajneesh Kaur, Gillian Mitchell, Kristine Barlow-Stewart, Tony Roscioli, Jane Halliday and Paul James

    BMC Cancer 2017 17:491

    Published on: 18 July 2017

  3. Research article

    Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition

    The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in a subset of breast and lung cancers. To understand the role of DIP2C in tumour development we studied the gene in...

    Chatarina Larsson, Muhammad Akhtar Ali, Tatjana Pandzic, Anders M. Lindroth, Liqun He and Tobias Sjöblom

    BMC Cancer 2017 17:487

    Published on: 17 July 2017

  4. Research article

    Quantitation of DNA methylation in Epstein-Barr virus–associated nasopharyngeal carcinoma by bisulfite amplicon sequencing

    Epigenetic changes, including DNA methylation, disrupt normal cell function, thus contributing to multiple steps of carcinogenesis. Nasopharyngeal carcinoma (NPC) is endemic in southern China and is highly ass...

    Weilin Zhao, Yingxi Mo, Shumin Wang, Kaoru Midorikawa, Ning Ma, Yusuke Hiraku, Shinji Oikawa, Guangwu Huang, Zhe Zhang, Mariko Murata and Kazuhiko Takeuchi

    BMC Cancer 2017 17:489

    Published on: 17 July 2017

  5. Research article

    CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer

    DNA repair of alkylation damage is defective in various cancers. This occurs through somatically acquired inactivation of the MGMT gene in various cancer types, including breast cancers. In addition to MGMT, t...

    Olafur Andri Stefansson, Stefan Hermanowicz, Jasper van der Horst, Holmfridur Hilmarsdottir, Zuzanna Staszczak, Jon Gunnlaugur Jonasson, Laufey Tryggvadottir, Thorkell Gudjonsson and Stefan Sigurdsson

    BMC Cancer 2017 17:469

    Published on: 5 July 2017

  6. Research article

    Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications

    Sequencing analysis of circulating tumor cells (CTCs) enables “liquid biopsy” to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to error...

    Shonan Sho, Colin M. Court, Paul Winograd, Sangjun Lee, Shuang Hou, Thomas G. Graeber, Hsian-Rong Tseng and James S. Tomlinson

    BMC Cancer 2017 17:457

    Published on: 1 July 2017

  7. Research article

    Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration

    Epithelial to mesenchymal transition (EMT) is the process by which stationary epithelial cells transdifferentiate to mesenchymal cells with increased motility. EMT is integral in early stages of development an...

    Princy Parsana, Sarah R. Amend, James Hernandez, Kenneth J. Pienta and Alexis Battle

    BMC Cancer 2017 17:447

    Published on: 26 June 2017

  8. Research article

    Current guidelines for BRCA testing of breast cancer patients are insufficient to detect all mutation carriers

    Identification of BRCA mutations in breast cancer (BC) patients influences treatment and survival and may be of importance for their relatives. Testing is often restricted to women fulfilling high-risk criteria. ...

    Eli Marie Grindedal, Cecilie Heramb, Inga Karsrud, Sarah Louise Ariansen, Lovise Mæhle, Dag Erik Undlien, Jan Norum and Ellen Schlichting

    BMC Cancer 2017 17:438

    Published on: 21 June 2017

  9. Research article

    African-American esophageal squamous cell carcinoma expression profile reveals dysregulation of stress response and detox networks

    Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is largely unresponsive to therapy. African-Americans have an increased risk for esophageal squamous cell carcinoma (ESCC...

    Hayriye Verda Erkizan, Kory Johnson, Svetlana Ghimbovschi, Deepa Karkera, Gregory Trachiotis, Houtan Adib, Eric P. Hoffman and Robert G. Wadleigh

    BMC Cancer 2017 17:426

    Published on: 19 June 2017

  10. Research article

    Whole exome sequencing of an asbestos-induced wild-type murine model of malignant mesothelioma

    Malignant mesothelioma (MM) is an aggressive cancer of the pleural and peritoneal cavities caused by exposure to asbestos. Asbestos-induced mesotheliomas in wild-type mice have been used extensively as a precl...

    Sophie Sneddon, Ann-Marie Patch, Ian M. Dick, Stephen Kazakoff, John V. Pearson, Nicola Waddell, Richard J. N. Allcock, Robert A. Holt, Bruce W. S. Robinson and Jenette Creaney

    BMC Cancer 2017 17:396

    Published on: 2 June 2017

  11. Research article

    Use of the QIAGEN GeneReader NGS system for detection of KRAS mutations, validated by the QIAGEN Therascreen PCR kit and alternative NGS platform

    The detection of somatic mutations in primary tumors is critical for the understanding of cancer evolution and targeting therapy. Multiple technologies have been developed to enable the detection of such mutat...

    Agus Darwanto, Anne-Mette Hein, Sascha Strauss, Yi Kong, Andrew Sheridan, Dan Richards, Eric Lader, Monika Ngowe, Timothy Pelletier, Danielle Adams, Austin Ricker, Nishit Patel, Andreas Kühne, Simon Hughes, Dan Shiffman, Dirk Zimmermann…

    BMC Cancer 2017 17:358

    Published on: 22 May 2017

  12. Research article

    Investigation of DNA repair-related SNPs underlying susceptibility to papillary thyroid carcinoma reveals MGMT as a novel candidate gene in Belarusian children exposed to radiation

    Genetic factors may influence an individual’s sensitivity to ionising radiation and therefore modify his/her risk of developing papillary thyroid carcinoma (PTC). Previously, we reported that common single nuc...

    Christine Lonjou, Francesca Damiola, Monika Moissonnier, Geoffroy Durand, Irina Malakhova, Vladimir Masyakin, Florence Le Calvez-Kelm, Elisabeth Cardis, Graham Byrnes, Ausrele Kesminiene and Fabienne Lesueur

    BMC Cancer 2017 17:328

    Published on: 12 May 2017

  13. Research article

    Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

    Current diagnostic tools for prostate cancer lack specificity and sensitivity for detecting very early lesions. DNA methylation is a stable genomic modification that is detectable in peripheral patient fluids ...

    Marie K. Kirby, Ryne C. Ramaker, Brian S. Roberts, Brittany N. Lasseigne, David S. Gunther, Todd C. Burwell, Nicholas S. Davis, Zulfiqar G. Gulzar, Devin M. Absher, Sara J. Cooper, James D. Brooks and Richard M. Myers

    BMC Cancer 2017 17:273

    Published on: 17 April 2017

  14. Research article

    Hypermethylation of CDKN2A exon 2 in tumor, tumor-adjacent and tumor-distant tissues from breast cancer patients

    Breast carcinogenesis is a multistep process involving genetic and epigenetic changes. Tumor tissues are frequently characterized by gene-specific hypermethylation and global DNA hypomethylation. Aberrant DNA ...

    Melanie Spitzwieser, Elisabeth Entfellner, Bettina Werner, Walter Pulverer, Georg Pfeiler, Stefan Hacker and Margit Cichna-Markl

    BMC Cancer 2017 17:260

    Published on: 12 April 2017

  15. Research article

    Global analysis of H3K27me3 as an epigenetic marker in prostate cancer progression

    H3K27me3 histone marks shape the inhibition of gene transcription. In prostate cancer, the deregulation of H3K27me3 marks might play a role in prostate tumor progression.

    Marjolaine Ngollo, Andre Lebert, Marine Daures, Gaelle Judes, Khaldoun Rifai, Lucas Dubois, Jean-Louis Kemeny, Frederique Penault-Llorca, Yves-Jean Bignon, Laurent Guy and Dominique Bernard-Gallon

    BMC Cancer 2017 17:261

    Published on: 12 April 2017

  16. Research article

    MUC1 in lung adenocarcinoma: cross-sectional genetic and serological study

    Mucin 1 (MUC1) contributes to the growth and metastasis of various cancers, including lung cancer, and MUC1 gene length polymorphisms are associated with susceptibility to lung cancer and its prognosis. In contra...

    Yasushi Horimasu, Nobuhisa Ishikawa, Sonosuke Tanaka, Chihiro Hirano, Hiroshi Iwamoto, Shinichiro Ohshimo, Kazunori Fujitaka, Hironobu Hamada, Noboru Hattori and Nobuoki Kohno

    BMC Cancer 2017 17:263

    Published on: 12 April 2017

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