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Cancer Informatics

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https://www.readbyqxmd.com/read/29343938/cindex-a-bioconductor-package-for-analysis-of-chromosome-instability-in-dna-copy-number-data
#1
Lei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan, Yuriy Gusev
The CINdex Bioconductor package addresses an important area of high-throughput genomic analysis. It calculates the chromosome instability (CIN) index, a novel measurement that quantitatively characterizes genome-wide copy number alterations (CNAs) as a measure of CIN. The advantage of this package is an ability to compare CIN index values between several groups for patients (case and control groups), which is a typical use case in translational research. The differentially changed cytobands or chromosomes can then be linked to genes located in the affected genomic regions, as well as pathways...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/29308008/selection-of-x-chromosome-inactivation-model
#2
Jian Wang, Rajesh Talluri, Sanjay Shete
To address the complexity of the X-chromosome inactivation (XCI) process, we previously developed a unified approach for the association test for X-chromosomal single-nucleotide polymorphisms (SNPs) and the disease of interest, accounting for different biological possibilities of XCI: random, skewed, and escaping XCI. In the original study, we focused on the SNP-disease association test but did not provide knowledge regarding the underlying XCI models. One can use the highest likelihood ratio (LLR) to select XCI models (max-LLR approach)...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/29276373/longitudinal-transcriptional-response-of-glycosylation-related-genes-regulators-and-targets-in-cancer-cell-lines-treated-with-11-antitumor-agents
#3
Julia Krushkal, Yingdong Zhao, Curtis Hose, Anne Monks, James H Doroshow, Richard Simon
Cellular glycosylation processes are vital to cell functioning. In malignant cells, they are profoundly altered. We used time-course gene expression data from the NCI-60 cancer cell lines treated with 11 antitumor agents to analyze expression changes of genes involved in glycosylation pathways, genes encoding glycosylation targets or regulators, and members of cancer pathways affected by glycosylation. We also identified glycosylation genes for which pretreatment expression levels or changes after treatment were correlated with drug sensitivity...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/29276372/zdhhc3-as-a-risk-and-mortality-marker-for-breast-cancer-in-african-american-women
#4
Nick Kinney, Robin T Varghese, Ramu Anandakrishnan, Harold R Skip Garner
African American woman are 43% more likely to die from breast cancer than white women and have increased the risk of tumor recurrence despite lower incidence. We investigate variations in microsatellite genomic regions-a type of repetitive DNA-and possible links to the breast cancer mortality gap. We screen 33 854 microsatellites in germline DNA of African American women with and without breast cancer: 4 are statistically significant. These are located in the 3' UTR (untranslated region) of gene ZDHHC3, an intron of transcribed pseudogene INTS4L1, an intron of ribosomal gene RNA5-8S5, and an intergenic region of chromosome 16...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/29162974/nonmonotonic-pathway-gene-expression-analysis-reveals-oncogenic-role-of-p27-kip1-at-intermediate-dose
#5
Hien H Nguyen, Susan C Tilton, Christopher J Kemp, Mingzhou Song
The mechanistic basis by which the level of p27Kip1 expression influences tumor aggressiveness and patient mortality remains unclear. To elucidate the competing tumor-suppressing and oncogenic effects of p27Kip1 on gene expression in tumors, we analyzed the transcriptomes of squamous cell papilloma derived from Cdkn1b nullizygous, heterozygous, and wild-type mice. We developed a novel functional pathway analysis method capable of testing directional and nonmonotonic dose response. This analysis can reveal potential causal relationships that might have been missed by other nondirectional pathway analysis methods...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28932104/gene-set-reduction-for-analysis-of-major-and-minor-gleason-scores-based-on-differential-gene-set-expressions-and-biological-pathways-in-prostate-cancer
#6
Irina Dinu, Surya Poudel, Saumyadipta Pyne
The Gleason score (GS) plays an important role in prostate cancer detection and treatment. It is calculated based on a sum between its major and minor components, each ranging from 1 to 5, assigned after examination of sample cells taken from each side of the prostate gland during biopsy. A total GS of at least 7 is associated with more aggressive prostate cancer. However, it is still unclear how prostate cancer outcomes differ for various distributions of GS between its major and minor components. This article applies Significance Analysis of Microarray for Gene-Set Reduction to a real microarray study of patients with prostate cancer and identifies 13 core genes differentially expressed between patients with a major GS of 3 and a minor GS of 4, or (3,4), vs patients with a combination of (4,3), starting from a less aggressive GS combination of (3,3), and moving toward a more aggressive one of (4,4) via gray areas of (3,4) and (4,3)...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28874883/xsyn-a-software-tool-for-identifying-sophisticated-3-way-interactions-from-cancer-expression-data
#7
Baishali Bandyopadhyay, Veda Chanda, Yupeng Wang
BACKGROUND: Constructing gene co-expression networks from cancer expression data is important for investigating the genetic mechanisms underlying cancer. However, correlation coefficients or linear regression models are not able to model sophisticated relationships among gene expression profiles. Here, we address the 3-way interaction that 2 genes' expression levels are clustered in different space locations under the control of a third gene's expression levels. RESULTS: We present xSyn, a software tool for identifying such 3-way interactions from cancer gene expression data based on an optimization procedure involving the usage of UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and synergy...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28835735/adaptive-multiview-nonnegative-matrix-factorization-algorithm-for-integration-of-multimodal-biomedical-data
#8
Bisakha Ray, Wenke Liu, David Fenyö
The amounts and types of available multimodal tumor data are rapidly increasing, and their integration is critical for fully understanding the underlying cancer biology and personalizing treatment. However, the development of methods for effectively integrating multimodal data in a principled manner is lagging behind our ability to generate the data. In this article, we introduce an extension to a multiview nonnegative matrix factorization algorithm (NNMF) for dimensionality reduction and integration of heterogeneous data types and compare the predictive modeling performance of the method on unimodal and multimodal data...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28804242/immuno-oncology-integrative-networks-elucidating-the-influences-of-osteosarcoma-phenotypes
#9
REVIEW
Ankush Sharma, Enrico Capobianco
In vivo and in vitro functional phenotyping characterization was recently obtained with reference to an experimental pan-cancer study of 22 osteosarcoma (OS) cell lines. Here, differentially expressed gene (DEG) profiles were recomputed from the publicly available data to conduct network inference on the immune system regulatory activity across the characterized OS phenotypes. Based on such DEG profiles, and for each phenotype that was analyzed, we obtained coexpression networks and bio-annotations for them...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28747816/prediction-with-dimension-reduction-of-multiple-molecular-data-sources-for-patient-survival
#10
Adam Kaplan, Eric F Lock
Predictive modeling from high-dimensional genomic data is often preceded by a dimension reduction step, such as principal component analysis (PCA). However, the application of PCA is not straightforward for multisource data, wherein multiple sources of 'omics data measure different but related biological components. In this article, we use recent advances in the dimension reduction of multisource data for predictive modeling. In particular, we apply exploratory results from Joint and Individual Variation Explained (JIVE), an extension of PCA for multisource data, for prediction of differing response types...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28690395/an-assessment-of-database-validated-microrna-target-genes-in-normal-colonic-mucosa-implications-for-pathway-analysis
#11
Martha L Slattery, Jennifer S Herrick, John R Stevens, Roger K Wolff, Lila E Mullany
BACKGROUND: Determination of functional pathways regulated by microRNAs (miRNAs), while an essential step in developing therapeutics, is challenging. Some miRNAs have been studied extensively; others have limited information. In this study, we focus on 254 miRNAs previously identified as being associated with colorectal cancer and their database-identified validated target genes. METHODS: We use RNA-Seq data to evaluate messenger RNA (mRNA) expression for 157 subjects who also had miRNA expression data...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28690394/a-software-application-for-mining-and-presenting-relevant-cancer-clinical-trials-per-cancer-mutation
#12
Lisa M Gandy, Jordan Gumm, Amanda L Blackford, Elana J Fertig, Luis A Diaz
ClinicalTrials.org is a popular portal which physicians use to find clinical trials for their patients. However, the current setup of ClinicalTrials.org makes it difficult for oncologists to locate clinical trials for patients based on mutational status. We present CTMine, a system that mines ClinicalTrials.org for clinical trials per cancer mutation and displays the trials in a user-friendly Web application. The system currently lists clinical trials for 6 common genes (ALK, BRAF, ERBB2, EGFR, KIT, and KRAS)...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28659712/the-model-based-study-of-the-effectiveness-of-reporting-lists-of-small-feature-sets-using-rna-seq-data
#13
Eunji Kim, Ivan Ivanov, Jianping Hua, Johanna W Lampe, Meredith Aj Hullar, Robert S Chapkin, Edward R Dougherty
Ranking feature sets for phenotype classification based on gene expression is a challenging issue in cancer bioinformatics. When the number of samples is small, all feature selection algorithms are known to be unreliable, producing significant error, and error estimators suffer from different degrees of imprecision. The problem is compounded by the fact that the accuracy of classification depends on the manner in which the phenomena are transformed into data by the measurement technology. Because next-generation sequencing technologies amount to a nonlinear transformation of the actual gene or RNA concentrations, they can potentially produce less discriminative data relative to the actual gene expression levels...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28634423/tumor-ras-gene-expression-levels-are-influenced-by-the-mutational-status-of-ras-genes-and-both-upstream-and-downstream-ras-pathway-genes
#14
Robert M Stephens, Ming Yi, Bailey Kessing, Dwight V Nissley, Frank McCormick
The 3 human RAS genes play pivotal roles regulating proliferation, differentiation, and survival in normal cells and become mutated in 15% to 20% of all human tumors and amplified in many others. In this report, we examined data from The Cancer Genome Atlas to investigate the relationship between RAS gene mutational status and messenger RNA expression. We show that all 3 RAS genes exhibit increased expression when they are mutated in a context-dependent manner. In the case of KRAS, this increase is manifested by a larger proportional increase in KRAS4A than KRAS4B, although both increase significantly...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28615920/immune-checkpoint-inhibition-and-the-prevalence-of-autoimmune-disorders-among-patients-with-lung-and-renal-cancer
#15
Sherif M El-Refai, Joshua D Brown, Esther P Black, Jeffery C Talbert
PURPOSE: Immune checkpoint inhibition reactivates the immune response against cancer cells in multiple tissue types and has been shown to induce durable responses. However, for patients with autoimmune disorders, their conditions can worsen with this reactivation. We sought to identify, among patients with lung and renal cancer, how many harbor a comorbid autoimmune condition and may be at risk of worsening their condition while on immune checkpoint inhibitors such as nivolumab and pembrolizumab...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28615919/sequence-analysis-and-phylogenetic-studies-of-hypoxia-inducible-factor-1%C3%AE
#16
Jagadeesha Poyya, Chandrashekhar G Joshi, D Jagadeesha Kumar, H G Nagendra
Hypoxia-inducible factors (HIF) belong to the basic helix loop helix-PER ARNT SIM (bHLH-PAS) family of transcription factors that induce metabolic reprogramming under hypoxic condition. The phylogenetic studies of hypoxia-inducible factor-1α (HIF-1α) sequences across different organisms/species may leave a clue on the evolutionary relationships and its probable correlation to tumorigenesis and adaptation to low oxygen environments. In this study, we have aimed at the evolutionary investigation of the protein HIF-1α across different species to decipher their sequence variations/mutations and look into the probable causes and abnormal behaviour of this molecule under exotic conditions...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28615918/lung-cancer-pathological-image-analysis-using-a-hidden-potts-model
#17
Qianyun Li, Faliu Yi, Tao Wang, Guanghua Xiao, Faming Liang
Nowadays, many biological data are acquired via images. In this article, we study the pathological images scanned from 205 patients with lung cancer with the goal to find out the relationship between the survival time and the spatial distribution of different types of cells, including lymphocyte, stroma, and tumor cells. Toward this goal, we model the spatial distribution of different types of cells using a modified Potts model for which the parameters represent interactions between different types of cells and estimate the parameters of the Potts model using the double Metropolis-Hastings algorithm...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28579741/time-based-switching-control-of-genetic-regulatory-networks-toward-sequential-drug-intake-for-cancer-therapy
#18
Wasiu Opeyemi Oduola, Xiangfang Li, Chang Duan, Lijun Qian, Fen Wu, Edward R Dougherty
As cancer growth and development typically involves multiple genes and pathways, combination therapy has been touted as the standard of care in the treatment of cancer. However, drug toxicity becomes a major concern whenever a patient takes 2 or more drugs simultaneously at the maximum tolerable dosage. A potential solution would be administering the drugs in a sequential or alternating manner rather than concurrently. This study therefore examines the feasibility of such an approach from a switched system control perspective...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28579740/applying-multivariate-adaptive-splines-to-identify-genes-with-expressions-varying-after-diagnosis-in-microarray-experiments
#19
REVIEW
Fenghai Duan, Ye Xu
PURPOSE: To analyze a microarray experiment to identify the genes with expressions varying after the diagnosis of breast cancer. METHODS: A total of 44 928 probe sets in an Affymetrix microarray data publicly available on Gene Expression Omnibus from 249 patients with breast cancer were analyzed by the nonparametric multivariate adaptive splines. Then, the identified genes with turning points were grouped by K-means clustering, and their network relationship was subsequently analyzed by the Ingenuity Pathway Analysis...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28579739/quantitative-study-of-thermal-disturbances-due-to-nonuniformly-perfused-tumors-in-peripheral-regions-of-women-s-breast
#20
Akshara Makrariya, Neeru Adlakha
BACKGROUND: Mathematical modeling of biothermal processes is widely used to enhance the quantitative understanding of thermoregulation system of human body organs. This quantitative knowledge of thermal information of various human body organs can be used for developing clinical applications. In the past, investigators have studied thermal distribution in hemisphere-shaped human breast in the presence of sphere-shaped tumor. The shape and size of the breast as well as tumor may also affect thermal distribution which can have serious implications in thermography...
2017: Cancer Informatics
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