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

    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

  2. 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

  3. 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

  4. 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

  5. Research article

    The germline variants in DNA repair genes in pediatric medulloblastoma: a challenge for current therapeutic strategies

    The defects in DNA repair genes are potentially linked to development and response to therapy in medulloblastoma. Therefore the purpose of this study was to establish the spectrum and frequency of germline varian...

    Joanna Trubicka, Tomasz Żemojtel, Jochen Hecht, Katarzyna Falana, Dorota Piekutowska- Abramczuk, Rafał Płoski, Marta Perek-Polnik, Monika Drogosiewicz, Wiesława Grajkowska, Elżbieta Ciara, Elżbieta Moszczyńska, Bożenna Dembowska-Bagińska, Danuta Perek, Krystyna H. Chrzanowska, Małgorzata Krajewska-Walasek and Maria Łastowska

    BMC Cancer 2017 17:239

    Published on: 4 April 2017

  6. Research article

    Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

    Triple negative breast cancer (TNBC) is a heterogeneous disease that lacks unifying molecular alterations that can guide therapy decisions. We previously identified distinct molecular subtypes of TNBC (TNBCtyp...

    Bojana Jovanović, Quanhu Sheng, Robert S. Seitz, Kasey D. Lawrence, Stephan W. Morris, Lance R. Thomas, David R. Hout, Brock L. Schweitzer, Yan Guo, Jennifer A. Pietenpol and Brian D. Lehmann

    BMC Cancer 2017 17:241

    Published on: 4 April 2017

  7. Research article

    Aberrant expression of ALK and EZH2 in Merkel cell carcinoma

    Distinct characteristic features categorize Merkel cell carcinoma (MCC) into two subgroups according to the Merkel cell polyomavirus infection. Many mutational studies on MCC have been carried out in recent ye...

    Tuukka Veija, Virve Koljonen, Tom Bohling, Mia Kero, Sakari Knuutila and Virinder Kaur Sarhadi

    BMC Cancer 2017 17:236

    Published on: 31 March 2017

  8. Research article

    Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer

    Aberrant DNA methylation profiles are a characteristic of all known cancer types, epitomized by the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). Hypermethylation has been observed at CpG ...

    Tyler McInnes, Donghui Zou, Dasari S. Rao, Francesca M. Munro, Vicky L. Phillips, John L. McCall, Michael A. Black, Anthony E. Reeve and Parry J. Guilford

    BMC Cancer 2017 17:228

    Published on: 28 March 2017

  9. Research article

    A genetic variant in long non-coding RNA MALAT1 associated with survival outcome among patients with advanced lung adenocarcinoma: a survival cohort analysis

    Recently studies have demonstrated that the long non-coding RNA (lncRNA) metastasis associated lung adenocarcinoma transcript 1 (MALAT1) may participate in the development and progression of lung cancer. In th...

    Jian-Zhong Wang, Jing-Jun Xiang, Li-Ge Wu, Yan-Sen Bai, Zhuo-Wang Chen, Xiang-Qian Yin, Qing Wang, Wen-Hao Guo, Ying Peng, Huan Guo and Ping Xu

    BMC Cancer 2017 17:167

    Published on: 3 March 2017

  10. Research article

    A novel FOXO1-mediated dedifferentiation blocking role for DKK3 in adrenocortical carcinogenesis

    Dysregulated WNT signaling dominates adrenocortical malignancies. This study investigates whether silencing of the WNT negative regulator DKK3 (Dickkopf-related protein 3), an implicated adrenocortical differe...

    Joyce Y. Cheng, Taylor C. Brown, Timothy D. Murtha, Adam Stenman, C. Christofer Juhlin, Catharina Larsson, James M. Healy, Manju L. Prasad, Wolfram T. Knoefel, Andreas Krieg, Ute I. Scholl, Reju Korah and Tobias Carling

    BMC Cancer 2017 17:164

    Published on: 1 March 2017

  11. Research article

    Validation of an NGS mutation detection panel for melanoma

    Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are dr...

    Anne Reiman, Hugh Kikuchi, Daniela Scocchia, Peter Smith, Yee Wah Tsang, David Snead and Ian A Cree

    BMC Cancer 2017 17:150

    Published on: 22 February 2017

  12. Research article

    Characterization of BRCA1 and BRCA2 variants in multi-ethnic Asian cohort from a Malaysian case-control study

    Genetic testing for BRCA1 and BRCA2 has led to the accurate identification of individuals at higher risk of cancer and the development of new therapies. Approximately 10-20% of the genetic testing for BRCA1 and B...

    Kah Nyin Lai, Weang Kee Ho, In Nee Kang, Peter Choon Eng Kang, Sze Yee Phuah, Shivaani Mariapun, Cheng-Har Yip, Nur Aishah Mohd Taib and Soo-Hwang Teo

    BMC Cancer 2017 17:149

    Published on: 22 February 2017

  13. Research article

    Identification of somatic and germ-line DICER1 mutations in pleuropulmonary blastoma, cystic nephroma and rhabdomyosarcoma tumors within a DICER1 syndrome pedigree

    DICER1 syndrome is a pediatric cancer predisposition condition causing a variety of tumor types in children and young adults. In this report we studied a family with two relatives presenting a variety of neopl...

    Lorena Fernández-Martínez, José Antonio Villegas, Íñigo Santamaría, Ana S. Pitiot, Marta G. Alvarado, Soledad Fernández, Héctor Torres, Ángeles Paredes, Pilar Blay and Milagros Balbín

    BMC Cancer 2017 17:146

    Published on: 21 February 2017

  14. Research article

    Clinical performance evaluation of a sensitive, rapid low-throughput test for KRAS mutation analysis using formalin-fixed, paraffin-embedded tissue samples

    Testing for KRAS mutations in metastatic colorectal cancer (mCRC) on formalin-fixed, paraffin embedded (FFPE) tumor tissue has become standard of care. Different molecular methods exist to determine hotspot KRAS ...

    Christine Weyn, Sofie Van Raemdonck, Robina Dendooven, Vincent Maes, Karen Zwaenepoel, Suzan Lambin and Patrick Pauwels

    BMC Cancer 2017 17:139

    Published on: 16 February 2017

  15. Research article

    Viral E6 is overexpressed via high viral load in invasive cervical cancer with episomal HPV16

    The integration of HR-HPV genome into host DNA is regarded as a key step for the development of cervical cancer. However, HR-HPV genome indeed exists as episome except for integrant. It may be alternative mech...

    Die Hong, Jia Liu, Ying Hu, Xiaonan Lu, Baohua Li, Yang Li, Dongxiao Hu, Weiguo Lu, Xing Xie and Xiaodong Cheng

    BMC Cancer 2017 17:136

    Published on: 15 February 2017

  16. Case report

    First insight into the somatic mutation burden of neurofibromatosis type 2-associated grade I and grade II meningiomas: a case report comprehensive genomic study of two cranial meningiomas with vastly different clinical presentation

    Neurofibromatosis type 2 (NF2) is a rare autosomal dominant nervous system tumor predisposition disorder caused by constitutive inactivation of one of the two copies of NF2. Meningiomas affect about one half of N...

    Ramita Dewan, Alexander Pemov, Amalia S. Dutra, Evgenia D. Pak, Nancy A. Edwards, Abhik Ray-Chaudhury, Nancy F. Hansen, Settara C. Chandrasekharappa, James C. Mullikin, Ashok R. Asthagiri, John D. Heiss, Douglas R. Stewart and Anand V. Germanwala

    BMC Cancer 2017 17:127

    Published on: 13 February 2017

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