Systems biology, post-genomic analysis and emerging technologies
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Tumor cell sensitivity to vemurafenib can be predicted from protein expression in a BRAF-V600E basket trial setting
Genetics-based basket trials have emerged to test targeted therapeutics across multiple cancer types. However, while vemurafenib is FDA-approved for BRAF-V600E melanomas, the non-melanoma basket trial was unsucce...BMC Cancer 2019 19:1025lionessR: single sample network inference in R
In biomedical research, network inference algorithms are typically used to infer complex association patterns between biological entities, such as between genes or proteins, using data from a population. This ...BMC Cancer 2019 19:1003Validation of computational determination of microsatellite status using whole exome sequencing data from colorectal cancer patients
Microsatellite instability (MSI), resulting from a defective mismatch repair system, occurs in approximately 15% of sporadic colorectal cancers (CRC). Since MSI is associated with a poor response to 5-fluorour...BMC Cancer 2019 19:971Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response
Genomic initiatives such as The Cancer Genome Atlas (TCGA) contain data from -omics profiling of thousands of tumor samples, which may be used to decipher cancer signaling, and related alterations. Managing an...BMC Cancer 2019 19:824The design, analysis and application of mouse clinical trials in oncology drug development
Mouse clinical trials (MCTs) are becoming wildly used in pre-clinical oncology drug development, but a statistical framework is yet to be developed. In this study, we establish such as framework and provide ge...BMC Cancer 2019 19:718Absence of an embryonic stem cell DNA methylation signature in human cancer
Differentiated cells that arise from stem cells in early development contain DNA methylation features that provide a memory trace of their fetal cell origin (FCO). The FCO signature was developed to estimate t...BMC Cancer 2019 19:711Best fitting tumor growth models of the von Bertalanffy-PütterType
Longitudinal studies of tumor volume have used certain named mathematical growth models. The Bertalanffy-Pütter differential equation unifies them: It uses five parameters, amongst them two exponents related t...BMC Cancer 2019 19:683Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma
Liver cancer is among top deadly cancers worldwide with a very poor prognosis, and the liver is a vulnerable site for metastases of other cancers. Early diagnosis is crucial for treatment of the predominant li...BMC Cancer 2019 19:663Biological molecular layer classification of muscle-invasive bladder cancer opens new treatment opportunities
Muscle-invasive bladder tumors are associated with a high risk of relapse and metastasis even after neoadjuvant chemotherapy and radical cystectomy. Therefore, further therapeutic options are needed and molecu...BMC Cancer 2019 19:636A subtype of oral, laryngeal, esophageal, and lung, squamous cell carcinoma with high levels of TrkB-T1 neurotrophin receptor mRNA
The NTRK2 genetic locus encodes neurotrophin membrane receptors that play an important role in normal neural tissue plasticity, growth, and survival. One NTRK2-encoded protein is TrkB-FL, which can regulate mu...BMC Cancer 2019 19:607Circulating tumor cell and cell-free RNA capture and expression analysis identify platelet-associated genes in metastatic lung cancer
Circulating tumor cells (CTC) and plasma cell-free RNA (cfRNA) can serve as biomarkers for prognosis and treatment response in lung cancer. One barrier to the selected or routine use of CTCs and plasma cfRNA i...BMC Cancer 2019 19:603Computational analysis of receptor tyrosine kinase inhibitors and cancer metabolism: implications for treatment and discovery of potential therapeutic signatures
Receptor tyrosine kinase (RTK) inhibitors are frequently used to treat cancers and the results have been mixed, some of these small molecule drugs are highly successful while others show a more modest response...BMC Cancer 2019 19:600Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma
Cancer patients with advanced disease routinely exhaust available clinical regimens and lack actionable genomic medicine results, leaving a large patient population without effective treatments options when th...BMC Cancer 2019 19:593Exploring serum and immunoglobulin G N-glycome as diagnostic biomarkers for early detection of breast cancer in Ethiopian women
Alterations in protein glycosylation patterns have potentially been targeted for biomarker discovery in a wide range of diseases including cancer. Although there have been improvements in patient diagnosis and...BMC Cancer 2019 19:588
The value of 3D visualization operative planning system in ultrasound-guided percutaneous microwave ablation for large hepatic hemangiomas: a clinical comparative study
To evaluate the value of a three dimension (3D)visualization operative planning system in ultrasound-guided percutaneous microwave ablation (US-PMWA) for large hepatic hemangiomas (LHHs).BMC Cancer 2019 19:550Impact of body mass index and fat distribution on sex steroid levels in endometrial carcinoma: a retrospective study
Obesity is an important cause of multiple cancer types, amongst which endometrial cancer (EC). The relation between obesity and cancer is complicated and involves alterations in insulin metabolism, response to...BMC Cancer 2019 19:547Stochastic modelling of tyrosine kinase inhibitor rotation therapy in chronic myeloid leukaemia
Resistance towards targeted cancer treatments caused by single nucleotide variations is a major issue in many malignancies. Currently, there are a number of available drugs for chronic myeloid leukaemia (CML),...BMC Cancer 2019 19:508How many samples are needed to infer truly clonal mutations from heterogenous tumours?
Modern cancer treatment strategies aim to target tumour specific genetic (or epigenetic) alterations. Treatment response improves if these alterations are clonal, i.e. present in all cancer cells within tumour...BMC Cancer 2019 19:403Protein interaction disruption in cancer
Most methods that integrate network and mutation data to study cancer focus on the effects of genes/proteins, quantifying the effect of mutations or differential expression of a gene and its neighbors, or iden...BMC Cancer 2019 19:370Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow
Worldwide, breast cancer is the main cause of cancer mortality in women. Most cases originate in mammary ductal cells that produce the nipple aspirate fluid (NAF). In cancer patients, this secretome contains p...BMC Cancer 2019 19:365A novel microfluidic device capable of maintaining functional thyroid carcinoma specimens ex vivo provides a new drug screening platform
Though the management of malignancies has improved vastly in recent years, many treatment options lack the desired efficacy and fail to adequately augment patient morbidity and mortality. It is increasingly cl...BMC Cancer 2019 19:259Molecular tumor analysis and liquid biopsy: a feasibility investigation analyzing circulating tumor DNA in patients with central nervous system lymphomas
Central nervous system lymphomas (CNSL) is a devastating disease. Currently, a confirmatory biopsy is required prior to treatment.BMC Cancer 2019 19:192Different next-generation sequencing pipelines based detection of tumor DNA in cerebrospinal fluid of lung adenocarcinoma cancer patients with leptomeningeal metastases
The nucleic acid mutation status in intracranial metastasis is markedly significant clinically. The goal of the current study was to explore whether the tumor-associated mutations can be detected by different ...BMC Cancer 2019 19:143Development of a miRNA-seq based prognostic signature in lung adenocarcinoma
We utilized miRNAs expression and clinical data to develop a prognostic signature for patients with lung adenocarcinoma, with respect to their overall survival, to identify high-risk subjects based on their mi...BMC Cancer 2019 19:34OMCD: OncomiR Cancer Database
microRNAs (miRNAs) are crucially important in the development of cancer. Their dysregulation, commonly observed in various types of cancer, is largely cancer-dependent. Thus, to understand the tumor biology an...BMC Cancer 2018 18:1223Factors associated with high-risk HPV infection and cervical cancer screening methods among rural Uyghur women aged > 30 years in Xinjiang
Cervical cancer is the most common genital malignant tumor in women worldwide. However, the reliability of different detection methods may vary according to populations and epidemics. This study analyzed facto...BMC Cancer 2018 18:1162The predictive powers of plasma trefoil factor 3 or its related micro RNAs for patients with hepatocellular carcinoma
Earlier diagnosis is beneficial for the prognosis of hepatocellular carcinoma (HCC). Alpha fetoprotein (AFP) is the most widely used biomarker for HCC, but its sensitivity and specificity are only 60 and 90%, ...BMC Cancer 2018 18:1110Inflammation marker ESR is effective in predicting outcome of diffuse large B-cell lymphoma
Systemic inflammation has been implicated in cancer development and progression. This study examined the best cutoff value of erythrocyte sedimentation rate (ESR) in diffuse large B-cell lymphoma (DLBCL) patie...BMC Cancer 2018 18:997The plasma glutamate concentration as a complementary tool to differentiate benign PET-positive lung lesions from lung cancer
Pulmonary imaging often identifies suspicious abnormalities resulting in supplementary diagnostic procedures. This study aims to investigate whether the metabolic fingerprint of plasma allows to discriminate b...BMC Cancer 2018 18:868An in-silico study examining the induction of apoptosis by Cryptotanshinone in metastatic melanoma cell lines
Metastatic melanoma is an aggressive form of skin cancer that evades various anti-cancer treatments including surgery, radio-,immuno- and chemo-therapy. TRAIL-induced apoptosis is a desirable method to treat m...BMC Cancer 2018 18:855Early detection of colorectal adenocarcinoma: a clinical decision support tool based on plasma porphyrin accumulation and risk factors
An increase in naturally-occurring porphyrins has been described in the blood of subjects bearing different kinds of tumors, including colorectal, and this is probably related to a systemic alteration of heme ...BMC Cancer 2018 18:841AKT isoform-specific expression and activation across cancer lineages
Aberrant AKT activation is prevalent across human cancer lineages, providing an important therapeutic target. AKT comprises three isoforms that mediate critical non-redundant, even opposing functions in cancer...BMC Cancer 2018 18:742A first-in-human study investigating biodistribution, safety and recommended dose of a new radiolabeled MAb targeting FZD10 in metastatic synovial sarcoma patients
Synovial Sarcomas (SS) are rare tumors occurring predominantly in adolescent and young adults with a dismal prognosis in advanced phases. We report a first-in-human phase I of monoclonal antibody (OTSA-101) ta...BMC Cancer 2018 18:646An implementation of normal distribution based segmentation and entropy controlled features selection for skin lesion detection and classification
Melanoma is the deadliest type of skin cancer with highest mortality rate. However, the annihilation in its early stage implies a high survival rate therefore, it demands early diagnosis. The accustomed diagno...BMC Cancer 2018 18:638Quantitative nuclear histomorphometry predicts oncotype DX risk categories for early stage ER+ breast cancer
Gene-expression companion diagnostic tests, such as the Oncotype DX test, assess the risk of early stage Estrogen receptor (ER) positive (+) breast cancers, and guide clinicians in the decision of whether or n...BMC Cancer 2018 18:610Gene expression profiling of 1200 pancreatic ductal adenocarcinoma reveals novel subtypes
Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer related death in the world with a five-year survival rate of less than 5%. Not all PDAC are the same, because there exist intra-tum...BMC Cancer 2018 18:603The clinical implications of G1-G6 transcriptomic signature and 5-gene score in Korean patients with hepatocellular carcinoma
Efforts have been made to classify Hepatocellular Carcinoma (HCC) at surgically curable stages because molecular classification, which is prognostically informative, can accurately identify patients in need of...BMC Cancer 2018 18:571A computational study of hedgehog signalling involved in basal cell carcinoma reveals the potential and limitation of combination therapy
The smoothened (SMO) receptor is an essential component of the Sonic hedgehog (SHH) signalling, which is associated with the development of skin basal cell carcinoma (BCC). SMO inhibitors are indicated for BCC...BMC Cancer 2018 18:569Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy
Single Nucleotide Polymorphisms (SNPs) can influence patient outcome such as drug response and toxicity after drug intervention. The purpose of this study is to develop a systematic pathway approach to accurat...BMC Cancer 2018 18:555PDXliver: a database of liver cancer patient derived xenograft mouse models
Liver cancer is the second leading cause of cancer-related deaths and characterized by heterogeneity and drug resistance. Patient-derived xenograft (PDX) models have been widely used in cancer research because...BMC Cancer 2018 18:550Pancreatic ductal adenocarcinoma can be detected by analysis of volatile organic compounds (VOCs) in alveolar air
In the last decade many studies showed that the exhaled breath of subjects suffering from several pathological conditions has a peculiar volatile organic compound (VOC) profile. The objective of the present wo...BMC Cancer 2018 18:529Update on the types and usage of liquid biopsies in the clinical setting: a systematic review
This systematic review aimed to gather evidence from research on the current state of liquid biopsy in medical practice, specifically focusing on mutation detection and monitoring.BMC Cancer 2018 18:527Development of a computational promoter with highly efficient expression in tumors
Gene therapy is a potent method to increase the therapeutic efficacy against cancer. However, a gene that is specifically expressed in the tumor area has not been identified. In addition, nonspecific expressio...BMC Cancer 2018 18:480In silico cancer research towards 3R
Improving our understanding of cancer and other complex diseases requires integrating diverse data sets and algorithms. Intertwining in vivo and in vitro data and in silico models are paramount to overcome intrin...BMC Cancer 2018 18:408Serum leucine-rich alpha-2-glycoprotein-1 with fucosylated triantennary N-glycan: a novel colorectal cancer marker
Carcinoembryonic antigen (CEA) and carbohydrate antigen (CA)19–9 are used in clinical practice as tumor markers to diagnose or monitor colorectal cancer (CRC) patients, However, their specificities and sensiti...BMC Cancer 2018 18:406Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups
Molecular data of histologically classified oligodendrogliomas are available offering the possibility to stratify these human brain tumors into clinically relevant molecular subtypes.BMC Cancer 2018 18:399Genomics of NSCLC patients both affirm PD-L1 expression and predict their clinical responses to anti-PD-1 immunotherapy
Programmed Death Ligand 1 (PD-L1) is a co-stimulatory and immune checkpoint protein. PD-L1 expression in non-small cell lung cancers (NSCLC) is a hallmark of adaptive resistance and its expression is often use...BMC Cancer 2018 18:225The Correction to this article has been published in BMC Cancer 2018 18:413Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer
NRF2 is the key regulator of oxidative stress in normal cells and aberrant expression of the NRF2 pathway due to genetic alterations in the KEAP1 (Kelch-like ECH-associated protein 1)-NRF2 (nuclear factor eryt...BMC Cancer 2018 18:46A novel lncRNA-focus expression signature for survival prediction in endometrial carcinoma
Endometrial cancer (UCEC) is a complex malignant tumor characterized by both genetic level and clinical trial. Patients with UCEC exhibit the similar clinical features, however, they have distinct outcomes due...BMC Cancer 2018 18:39The exploration of contrasting pathways in Triple Negative Breast Cancer (TNBC)
Triple Negative Breast Cancers (TNBCs) lack the appropriate targets for currently used breast cancer therapies, conferring an aggressive phenotype, more frequent relapse and poorer survival rates. The biologic...BMC Cancer 2018 18:22
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