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Genetics, genomics and epigenetics

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. Ependymal tumors are pathologically defined intrinsic neoplasms originating in the intracranial compartments or the spinal cord that affect both children and adults. The recently integrated classification of e...

    Authors: Shaoyan Xi, Ke Sai, Wanming Hu, Fang Wang, Yinsheng Chen, Jing Wang, Jing Zeng and Zhongping Chen

    Citation: BMC Cancer 2019 19:717

    Content type: Research article

    Published on:

  2. The rapid development of single-cell RNA sequencing (scRNA-seq) provides unprecedented opportunities to study the tumor ecosystem that involves a heterogeneous mixture of cell types. However, the majority of p...

    Authors: Xiaoqing Yu, Y. Ann Chen, Jose R. Conejo-Garcia, Christine H. Chung and Xuefeng Wang

    Citation: BMC Cancer 2019 19:715

    Content type: Research article

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  4. Genetic profiling of cancers for variations in copy number, structure or expression of certain genes has improved diagnosis, risk-stratification and therapeutic decision-making. However the tumor-restricted na...

    Authors: Jordan Mandel, Huabo Wang, Daniel P. Normolle, Wei Chen, Qi Yan, Peter C. Lucas, Panayiotis V. Benos and Edward V. Prochownik

    Citation: BMC Cancer 2019 19:686

    Content type: Research article

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  5. Sterol-regulatory element binding protein 1 (SREBP1), an intracellular cholesterol sensor located in the endoplasmic reticulum, regulates the intracellular cholesterol by the Insig-Srebp-Scap pathway. Over-exp...

    Authors: Yuyan Gao, Xianxiu Nan, Xinjue Shi, Xiaoqin Mu, Binbin Liu, Huifen Zhu, Bingqing Yao, Xinyi Liu, Tianyue Yang, Yiting Hu and Shulin Liu

    Citation: BMC Cancer 2019 19:685

    Content type: Research article

    Published on:

  6. Canonical WNT signalling plays a critical role in the regulation of ovarian development; mis-regulation of this key pathway in the adult ovary is associated with subfertility and tumourigenesis. The roles of A...

    Authors: Noha-Ehssan Mohamed, Trevor Hay, Karen R. Reed, Matthew J. Smalley and Alan R. Clarke

    Citation: BMC Cancer 2019 19:677

    Content type: Research article

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  7. Analysis of melanomas for actionable mutations has become the standard of care. Recently, a classification scheme has been proposed that categorizes BRAF mutations based on their mechanisms for activation of the ...

    Authors: Parvez M. Lokhandwala, Li-Hui Tseng, Erika Rodriguez, Gang Zheng, Aparna Pallavajjalla, Christopher D. Gocke, James R. Eshleman and Ming-Tseh Lin

    Citation: BMC Cancer 2019 19:665

    Content type: Research article

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  8. Studies have consistently indicated that the majority of individuals meeting the US Prevention Services Task Force guidelines for genetic testing have not had genetic counseling or testing. Despite increased a...

    Authors: Nadine Rayes, Deborah J. Bowen, Tara Coffin, Denise Nebgen, Christine Peterson, Mark F. Munsell, Kathleen Gavin, Rebecca Lechner, Jamie Crase, Deborah Polinsky, Iris Romero, Stephanie V. Blank, Douglas A. Levine, Barbara M. Norquist, Elizabeth M. Swisher and Karen H. Lu

    Citation: BMC Cancer 2019 19:648

    Content type: Study protocol

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  9. Zinc-finger E-box binding homeobox 1 (ZEB-1) plays crucial roles in epithelial-to-mesenchymal transition during tumor carcinogenesis. Published studies have examined the potential value of ZEB-1 as a biomarker...

    Authors: Borong Chen, Baisheng Chen, Zhipeng Zhu, Weipeng Ye, Junjie Zeng, Gang Liu, Shengjie Wang, Jin Gao, Guoxing Xu and Zhengjie Huang

    Citation: BMC Cancer 2019 19:635

    Content type: Research article

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  11. Hereditary cancer syndromes have inherited germline mutations which predispose to benign and malignant tumors. Understanding of the molecular causes in hereditary cancer syndromes has advanced cancer treatment...

    Authors: Yanting Jiang, Yue Sun, Jiandong Hu, Nan Yu, Hui Liu, Jiankun Fan, Xuelian Ning, Yilan Li, Baogang Liu, Yihua Sun, Jinwei Zhang, Xiaohong Qiu, Songbin Fu, Chunshui Zhou and Hui Xu

    Citation: BMC Cancer 2019 19:613

    Content type: Research article

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  12. Chemo-resistance is one of the major challenges in the therapy of small cell lung cancer (SCLC). Multiple mechanisms are thought to be involved in chemo-resistance during SCLC treatment, but unfortunately, the...

    Authors: Jinzhi Lai, Hainan Yang, Yanyang Zhu, Mei Ruan, Yayu Huang and Qiuyu Zhang

    Citation: BMC Cancer 2019 19:602

    Content type: Research article

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  13. Pulmonary sarcomatoid carcinoma (SC) consists of both carcinomatous and sarcomatous tumors with high degree of malignancy, rapid progression, and poor prognosis. However, little is known regarding how pulmonar...

    Authors: Jianjun Ge, Bin Yao, Jia Huang, Xue Wu, Hua Bao, Qiuxiang Ou, Yang W. Shao and Jun Chen

    Citation: BMC Cancer 2019 19:592

    Content type: Case report

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  14. Research into Philadelphia-negative chronic myeloproliferative neoplasms is heterogeneous. In addition, no systematization of studies of polycythemia vera (PV), essential thrombocythemia (ET) or primary myelof...

    Authors: Mónica Mejía-Ochoa, Paola Andrea Acevedo Toro and Jaiberth Antonio Cardona-Arias

    Citation: BMC Cancer 2019 19:590

    Content type: Research article

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  16. Detection of circulating tumor DNA (ctDNA) is a promising method for postoperative surveillance of lung cancer. However, relatively low positive rate in early stage patients restricts its application. Aberrant...

    Authors: Guannan Kang, Kezhong Chen, Fan Yang, Shannon Chuai, Heng Zhao, Kai Zhang, Bingsi Li, Zhihong Zhang and Jun Wang

    Citation: BMC Cancer 2019 19:579

    Content type: Study protocol

    Published on:

  17. Triple-negative breast cancer (TNBC) is a type of breast cancer with a high degree of malignancy. Because of the remarkable biological characteristics of high invasion, metastasis and recurrence, TNBC is often...

    Authors: Cheng Wang, Cheng Xu, Ruijie Niu, Guangfu Hu, Zhangyuan Gu and Zhigang Zhuang

    Citation: BMC Cancer 2019 19:577

    Content type: Research article

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  18. Using a pathway-focused approach, we aimed to provide a subgroup-specific basis for finding novel therapeutic strategies and further refinement of the risk stratification in pediatric medulloblastoma.

    Authors: Ae Kyung Park, Ji Yeoun Lee, Heesun Cheong, Vijay Ramaswamy, Sung-Hye Park, Marcel Kool, Ji Hoon Phi, Seung Ah Choi, Florence Cavalli, Michael D. Taylor and Seung-Ki Kim

    Citation: BMC Cancer 2019 19:571

    Content type: Research article

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  19. Published genetic risk scores for breast cancer (BC) so far have been based on a relatively small number of markers and are not necessarily using the full potential of large-scale Genome-Wide Association Studi...

    Authors: Kristi Läll, Maarja Lepamets, Marili Palover, Tõnu Esko, Andres Metspalu, Neeme Tõnisson, Peeter Padrik, Reedik Mägi and Krista Fischer

    Citation: BMC Cancer 2019 19:557

    Content type: Research article

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  20. Liver function is routinely assessed in clinical practice as liver function tests provide sensitive indicators of hepatocellular injury. However, the prognostic value of enzymes that indicate hepatic injury ha...

    Authors: Ting-Xun Lu, Shuang Wu, Dong-Yan Cai, Ting-Ting Hong, Ying Zhang, Hua-Qiang Gao, Hai-Ying Hua and Xiao-Hong Wu

    Citation: BMC Cancer 2019 19:553

    Content type: Research article

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  21. Mutated BRCA1/2 genes are associated with hereditary breast and ovarian cancer (HBOC). So far most of the identified BRCA1/2 pathogenic variants are single nucleotide variants (SNVs) or insertions/deletions (Inde...

    Authors: Wen-Ming Cao, Ya-Bing Zheng, Yun Gao, Xiao-Wen Ding, Yan Sun, Yuan Huang, Cai-Jin Lou, Zhi-Wen Pan, Guang Peng and Xiao-Jia Wang

    Citation: BMC Cancer 2019 19:551

    Content type: Research article

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  22. Breast cancer is a leading cause of cancer-related death in women worldwide. Despite extensive studies in all areas of basic, clinical and applied research, accurate prognosis remains elusive, thus leading to ...

    Authors: Mariana Bustamante Eduardo, Vlad Popovici, Sara Imboden, Stefan Aebi, Nadja Ballabio, Hans Jörg Altermatt, Andreas Günthert and Rolf Jaggi

    Citation: BMC Cancer 2019 19:549

    Content type: Research article

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  23. The understanding of the molecular biology of pediatric neuronal and mixed neuronal-glial brain tumors is still insufficient due to low frequency and heterogeneity of those lesions which comprise several subty...

    Authors: Magdalena Zakrzewska, Renata Gruszka, Konrad Stawiski, Wojciech Fendler, Joanna Kordacka, Wiesława Grajkowska, Paweł Daszkiewicz, Paweł P. Liberski and Krzysztof Zakrzewski

    Citation: BMC Cancer 2019 19:544

    Content type: Research article

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  24. Hereditary cancer predisposition syndromes are responsible for approximately 5–10% of all diagnosed cancer cases. In the past, single-gene analysis of specific high risk genes was used for the determination of...

    Authors: Georgios N. Tsaousis, Eirini Papadopoulou, Angela Apessos, Konstantinos Agiannitopoulos, Georgia Pepe, Stavroula Kampouri, Nikolaos Diamantopoulos, Theofanis Floros, Rodoniki Iosifidou, Ourania Katopodi, Anna Koumarianou, Christos Markopoulos, Konstantinos Papazisis, Vasileios Venizelos, Ioannis Xanthakis, Grigorios Xepapadakis…

    Citation: BMC Cancer 2019 19:535

    Content type: Research article

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  25. C-C chemokine receptor 5 (CCR5) has attracted wide concern for its critical role in the progression of human immunodeficiency virus type 1 (HIV-1) infection. Several studies have demonstrated that CCR5 affects...

    Authors: Shuyuan Liu, Jun Chen, Zhiling Yan, Shuying Dai, Chuanyin Li, Yufeng Yao and Li Shi

    Citation: BMC Cancer 2019 19:525

    Content type: Research article

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  26. Patients with lymph node metastasis-negative (pN0) invasive breast cancer have favorable outcomes following initial treatment. However, false negatives which occur during routine histologic examination of lymp...

    Authors: Ryoko Kikuchi-Koike, Kazunori Nagasaka, Hitoshi Tsuda, Yasuyuki Ishii, Masaru Sakamoto, Yoshihiro Kikuchi, Shiho Fukui, Yuko Miyagawa, Haruko Hiraike, Takayuki Kobayashi, Takayuki Kinoshita, Yae Kanai, Tatsuhiro Shibata, Issei Imoto, Johji Inazawa, Osamu Matsubara…

    Citation: BMC Cancer 2019 19:521

    Content type: Research article

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  27. Chronic Lymphocytic Leukemia (CLL) is the most frequent lymphoproliferative disorder in western countries and is characterized by a remarkable clinical heterogeneity. During the last decade, multiple genomic s...

    Authors: Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, José Ángel Díaz Arias, Nicolás Díaz Varela, Manuel Mateo Pérez Encinas, Catarina Allegue Toscano, Elena María Goiricelaya Seco, Ángel Carracedo Álvarez and José Luis Bello López

    Citation: BMC Cancer 2019 19:515

    Content type: Research article

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  28. Deletion of the CDKN2A locus is centrally involved in the development of several malignancies. In malignant pleural mesothelioma (MPM), it is one of the most frequently reported genomic alteration. MPM is strongl...

    Authors: Eeva Kettunen, Sauli Savukoski, Kaisa Salmenkivi, Tom Böhling, Esa Vanhala, Eeva Kuosma, Sisko Anttila and Henrik Wolff

    Citation: BMC Cancer 2019 19:507

    Content type: Research article

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  29. Breast cancer ranks first in women, and is the second cause of death in this gender. In addition to genetics, the environment contributes to the development of the disease, although the factors involved are no...

    Authors: Julio Plaza-Díaz, Ana I. Álvarez-Mercado, Carmen M Ruiz-Marín, Iris Reina-Pérez, Alejandro J. Pérez-Alonso, María Belén Sánchez-Andujar, Pablo Torné, Tania Gallart-Aragón, María Teresa Sánchez-Barrón, Saturnino Reyes Lartategui, Federico García, Natalia Chueca, Ana Moreno-Delgado, Katia Torres-Martínez, María José Sáez-Lara, Cándido Robles-Sánchez…

    Citation: BMC Cancer 2019 19:495

    Content type: Study protocol

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  30. Telomere genetics has recently been emerged as an important field in molecular oncology. Various genome-wide association studies in different population groups have revealed that polymorphisms in Telomere main...

    Authors: Gh. Rasool Bhat, Amrita Bhat, Sonali Verma, Itty Sethi, Ruchi Shah, Varun Sharma, Khursheed A. Dar, Deepak Abrol, Subiya Kaneez, Sandeep Kaul, Ramesh Ganju and Rakesh Kumar

    Citation: BMC Cancer 2019 19:493

    Content type: Research article

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  31. The relationship between polymorphisms in vascular endothelial growth factor (VEGF) and gastric cancer is still inconclusive. We investigated whether there is an association between VEGF genetic polymorphisms ...

    Authors: Yeon-Ji Kim, Woo Chul/ Chung, Kyong-Hwa Jun and Hyung-Min Chin

    Citation: BMC Cancer 2019 19:483

    Content type: Research article

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  32. Recent studies have extensively investigated the role of miRNAs in colorectal cancer (CRC), and several associations have been reported. In addition, single nucleotide polymorphisms (SNPs) in promoter regions ...

    Authors: Eun-Gyo Kim, Jung Oh Kim, Han Sung Park, Chang Soo Ryu, Jisu Oh, Hak Hoon Jun, Jong Woo Kim and Nam Keun Kim

    Citation: BMC Cancer 2019 19:480

    Content type: Research article

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  33. Gene variants are dependable and sensitive biomarkers for target-specific therapies in breast cancer (BC). However, detection of mutations within tissues has many limitations. Plasma circulating free DNA (cfDN...

    Authors: Xin Yang, Kuo Zhang, Caiji Zhang, Rongxue Peng and Chengming Sun

    Citation: BMC Cancer 2019 19:465

    Content type: Research article

    Published on:

  35. Helicobacter pylori infection is recognized as the main risk factor for gastric cancer (GC), the fifth most common neoplasia worldwide. H. pylori interacts with the immune system, disrupting the cytokine network ...

    Authors: Cecilia Martínez-Campos, Kirvis Torres-Poveda, Margarita Camorlinga-Ponce, Lourdes Flores-Luna, Carmen Maldonado-Bernal, Vicente Madrid-Marina and Javier Torres

    Citation: BMC Cancer 2019 19:453

    Content type: Research article

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  36. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies and is not a clinically homogeneous disease, but subsets of patients with distinct prognosis and response to therapy can be identi...

    Authors: Maria Cristina Curia, Fabiana Fantini, Rossano Lattanzio, Francesca Tavano, Francesco Di Mola, Mauro Piantelli, Pasquale Battista, Pierluigi Di Sebastiano and Alessandro Cama

    Citation: BMC Cancer 2019 19:452

    Content type: Research article

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  37. TIMP-2 gene plays an important role in the development of breast cancer. The present study was conducted to evaluate whether TIMP-2 gene polymorphisms are associated with breast cancer risk in a Han Chinese cohor...

    Authors: Kai Wang, Guanying Wang, Shangke Huang, Anqi Luo, Xin Jing, Gang Li, Yi Zhou and Xinhan Zhao

    Citation: BMC Cancer 2019 19:446

    Content type: Research article

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  38. The progress of treatments of childhood acute lymphoblastic leukemia (ALL) has made it possible to reach a survival rate superior to 80%. However, the treatments lead to several long-term adverse effects, incl...

    Authors: Maxime Caru, Kateryna Petrykey, Simon Drouin, Patrick Beaulieu, Pascal St-Onge, Valérie Lemay, Laurence Bertout, Caroline Laverdiere, Gregor Andelfinger, Maja Krajinovic, Daniel Sinnett and Daniel Curnier

    Citation: BMC Cancer 2019 19:443

    Content type: Research article

    Published on:

  39. Several subunits of the SWI/SNF chromatin remodeling complex are implicated in both cancer and neurodevelopmental disorders (NDD). Though there is no clinical evidence for an increased tumor risk in individual...

    Authors: Bernt Popp, Abbas Agaimy, Cornelia Kraus, Karl X. Knaup, Arif B. Ekici, Steffen Uebe, André Reis, Michael Wiesener and Christiane Zweier

    Citation: BMC Cancer 2019 19:435

    Content type: Research article

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  41. Wilms’ tumor is also called nephroblastoma and is the most common pediatric renal cancer. Several genetic and epigenetic factors have been found to account for the development of Wilms’ tumor. MiRNAs play impo...

    Authors: Zhuo Liu, Feng He, Shengrong OuYang, Yuanyuan Li, Feifei Ma, Huibo Chang, Dingding Cao and Jianxin Wu

    Citation: BMC Cancer 2019 19:405

    Content type: Research article

    Published on:

  42. With the introduction of Olaparib treatment for BRCA-deficient recurrent ovarian cancer, testing for somatic and/or germline mutations in BRCA1/2 genes in tumor tissues became essential for treatment decisions. I...

    Authors: Falk Zakrzewski, Laura Gieldon, Andreas Rump, Michael Seifert, Konrad Grützmann, Alexander Krüger, Sina Loos, Silke Zeugner, Karl Hackmann, Joseph Porrmann, Johannes Wagner, Karin Kast, Pauline Wimberger, Gustavo Baretton, Evelin Schröck, Daniela Aust…

    Citation: BMC Cancer 2019 19:396

    Content type: Technical advance

    Published on:

  43. The impact of Tet oncogene family member 2 (TET2) mutations on the prognosis of acute myeloid leukemia (AML) is still controversial. A meta analysis is needed in order to assess the prognostic significance of TET...

    Authors: Ruiqi Wang, Xiaoning Gao and Li Yu

    Citation: BMC Cancer 2019 19:389

    Content type: Research article

    Published on:

  44. Gene expression profiling provides key information for prognosis of breast cancer to establish treatment strategy. However, the genetic assessment should be available before induction of treatment to be useful...

    Authors: Jeeyeon Lee, Eun Hye Lee, Ho Yong Park, Wan Wook Kim, Ryu Kyung Lee, Yee Soo Chae, Soo Jung Lee, Jee-Eun Kim, Byeong-il Kang, Jee Young Park, Ji-Young Park and Jin Hyang Jung

    Citation: BMC Cancer 2019 19:388

    Content type: Research article

    Published on:

  45. Intratumoral epidermal growth factor receptor (EGFR) mutational heterogeneity is yet controversial in non-small cell lung cancer (NSCLC) patients. Single-cell analysis provides the genetic profile of single cance...

    Authors: Longhua Guo, Zhihong Chen, Chongrui Xu, Xuchao Zhang, Honghong Yan, Jian Su, Jinji Yang, Zhi Xie, Weibang Guo, Feng Li, Yilong Wu and Qing Zhou

    Citation: BMC Cancer 2019 19:369

    Content type: Research article

    Published on:

  47. Osteosarcoma is the most common malignant bone tumor in children. Survival remains poor among histologically poor responders, and there is a need to identify them at diagnosis to avoid delivering ineffective t...

    Authors: Krithika Bhuvaneshwar, Michael Harris, Yuriy Gusev, Subha Madhavan, Ramaswamy Iyer, Thierry Vilboux, John Deeken, Elizabeth Yang and Sadhna Shankar

    Citation: BMC Cancer 2019 19:357

    Content type: Research article

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  48. High risk human papillomaviruses (HPV) plays important roles in the development of cervical cancer, a number of other anogenital cancer and they are increasingly found in oropharyngeal squamous cell carcinoma ...

    Authors: Ge Gao, Jintu Wang, Jan L. Kasperbauer, Nicole M. Tombers, Fei Teng, Honglan Gou, Yonggang Zhao, Zhenhong Bao and David I. Smith

    Citation: BMC Cancer 2019 19:352

    Content type: Research article

    Published on:

  49. Visceral organ metastasis is associated with poor survival outcomes in terms of metastasis free- and overall survival in breast carcinomas. Identification of a gene expression profile in tumours that selects a...

    Authors: C. D. Savci-Heijink, H. Halfwerk, J. Koster, H. M. Horlings and M. J. van de Vijver

    Citation: BMC Cancer 2019 19:333

    Content type: Research article

    Published on:

  50. Non-muscular invasive bladder cancer (NMIBC) has a high risk of recurrence. As androgen receptor (AR) reportedly affects bladder cancer, we assessed the correlation between NMIBC recurrence and tumor AR expressio...

    Authors: Masato Yasui, Takashi Kawahara, Koji Izumi, Masahiro Yao, Yukari Ishiguro, Hitoshi Ishiguro, Hiroji Uemura and Yasuhide Miyoshi

    Citation: BMC Cancer 2019 19:331

    Content type: Research article

    Published on:

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