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

    Integrator complex subunit 6 (INTS6) inhibits hepatocellular carcinoma growth by Wnt pathway and serve as a prognostic marker

    Integrator complex subunit 6 (INTS6) was found to play a tumour suppressing role in certain types of solid tumours. In this study, we wanted to determine the expression level of INTS6 in hepatocellular carcino...

    Ka Yin Lui, Hui Zhao, Chunhui Qiu, Chuo Li, Zhigang Zhang, Haoran Peng, Rongdang Fu, Hu-an Chen and Min-qiang Lu

    BMC Cancer 2017 17:644

    Published on: 12 September 2017

  2. Research article

    BRCA2 carriers with male breast cancer show elevated tumour methylation

    Male breast cancer (MBC) represents a poorly characterised group of tumours, the management of which is largely based on practices established for female breast cancer. However, recent studies demonstrate biol...

    Siddhartha Deb, Kylie L. Gorringe, Jia-Min B. Pang, David J. Byrne, Elena A. Takano, kConFab Investigators, Alexander Dobrovic and Stephen B. Fox

    BMC Cancer 2017 17:641

    Published on: 11 September 2017

  3. Research article

    Involvement of DPP9 in gene fusions in serous ovarian carcinoma

    A fusion gene is a hybrid gene consisting of parts from two previously independent genes. Chromosomal rearrangements leading to gene breakage are frequent in high-grade serous ovarian carcinomas and have been ...

    Marianne Lislerud Smebye, Antonio Agostini, Bjarne Johannessen, Jim Thorsen, Ben Davidson, Claes Göran Tropé, Sverre Heim, Rolf Inge Skotheim and Francesca Micci

    BMC Cancer 2017 17:642

    Published on: 11 September 2017

  4. Research article

    Disease-stabilizing treatment based on all-trans retinoic acid and valproic acid in acute myeloid leukemia – identification of responders by gene expression profiling of pretreatment leukemic cells

    Acute myeloid leukemia (AML) is an aggressive malignancy only cured by intensive therapy. However, many elderly and unfit patients cannot receive such treatment due to an unacceptable risk of treatment-related...

    Håkon Reikvam, Randi Hovland, Rakel Brendsdal Forthun, Sigrid Erdal, Bjørn Tore Gjertsen, Hanne Fredly and Øystein Bruserud

    BMC Cancer 2017 17:630

    Published on: 6 September 2017

  5. Research article

    A survey of the clinicopathological and molecular characteristics of patients with suspected Lynch syndrome in Latin America

    Genetic counselling and testing for Lynch syndrome (LS) have recently been introduced in several Latin America countries. We aimed to characterize the clinical, molecular and mismatch repair (MMR) variants spe...

    Benedito Mauro Rossi, Edenir Inêz Palmero, Francisco López-Kostner, Carlos Sarroca, Carlos Alberto Vaccaro, Florencia Spirandelli, Patricia Ashton-Prolla, Yenni Rodriguez, Henrique de Campos Reis Galvão, Rui Manuel Reis, André Escremim de Paula, Luis Gustavo Capochin Romagnolo, Karin Alvarez, Adriana Della Valle, Florencia Neffa, Pablo German Kalfayan…

    BMC Cancer 2017 17:623

    Published on: 5 September 2017

  6. Research article

    Stress alters the expression of cancer-related genes in the prostate

    Prostate cancer is a major contributor to mortality worldwide, and significant efforts are being undertaken to decipher specific cellular and molecular pathways underlying the disease. Chronic stress is known ...

    Ivan E. Flores, Jorge A. Sierra-Fonseca, Olinamyr Davalos, Luis A. Saenz, Maria M. Castellanos, Jaidee K. Zavala and Kristin L. Gosselink

    BMC Cancer 2017 17:621

    Published on: 5 September 2017

  7. Research article

    CHEK2 c.1100delC mutation is associated with an increased risk for male breast cancer in Finnish patient population

    Several susceptibility genes have been established for female breast cancer, of which mutations in BRCA1 and especially in BRCA2 are also known risk factors for male breast cancer (MBC). The role of other breast ...

    Sanna Hallamies, Liisa M. Pelttari, Paula Poikonen-Saksela, Antti Jekunen, Arja Jukkola-Vuorinen, Päivi Auvinen, Carl Blomqvist, Kristiina Aittomäki, Johanna Mattson and Heli Nevanlinna

    BMC Cancer 2017 17:620

    Published on: 5 September 2017

  8. Research article

    Comprehensive genomic profiling in routine clinical practice leads to a low rate of benefit from genotype-directed therapy

    Describe a single-center real-world experience with comprehensive genomic profiling (CGP) to identify genotype directed therapy (GDT) options for patients with malignancies refractory to standard treatment opt...

    Talal Hilal, Mary Nakazawa, Jacob Hodskins, John L. Villano, Aju Mathew, Guarav Goel, Lars Wagner, Susanne M. Arnold, Philip DeSimone, Lowell B. Anthony and Peter J. Hosein

    BMC Cancer 2017 17:602

    Published on: 30 August 2017

  9. Research article

    Tumoral LINE-1 hypomethylation is associated with poor survival of patients with intrahepatic cholangiocarcinoma

    DNA methylation changes occurring in cancer cells are featured with both promoter CpG island hypermethylation and diffuse genomic hypomethylation. Long interspersed element-1 (LINE-1) is repeated in an intersp...

    Seorin Jeong, Kyoungbun Lee, Xianyu Wen, Younghoon Kim, Nam-Yun Cho, Ja-June Jang and Gyeong Hoon Kang

    BMC Cancer 2017 17:588

    Published on: 29 August 2017

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

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