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copy number variation AND cancer

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https://www.readbyqxmd.com/read/28327601/bcip-a-gene-centered-platform-for-identifying-potential-regulatory-genes-in-breast-cancer
#1
Jiaqi Wu, Shuofeng Hu, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, Xiaomin Ying
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320758/tumor-cell-free-dna-copy-number-instability-predicts-therapeutic-response-to-immunotherapy
#2
Glen J Weiss, Julia Beck, Donald P Braun, Kristen Bornemann-Kolatzki, Heather Barilla, Rhiannon Cubello, Walter Quan, Ashish Sangal, Vivek Khemka, Jordan Waypa, William M Mitchell, Howard Urnovitz, Ekkehard Schütz
PURPOSE: Chromosomal instability is a fundamental property of cancer, which can be quantified by Next Generation Sequencing (NGS) from plasma/serum derived cell-free DNA (cfDNA). We hypothesized that cfDNA could be used as a real time surrogate for imaging analysis of disease status as a function of response to immunotherapy and as a more reliable tool than tumor biomarkers. EXPERIMENTAL DESIGN: Plasma cfDNA sequences from 56 patients with diverse advanced cancers, were prospectively collected and analyzed in a single-blinded study for copy number variations, expressed as a quantitative chromosomal number instability (CNI) score versus 126 non-cancer controls in a training set of 23 and a blinded validation set of 33...
March 20, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28318489/deletion-of-the-mad2l1-spindle-assembly-checkpoint-gene-is-tolerated-in-mouse-models-of-acute-t-cell-lymphoma-and-hepatocellular-carcinoma
#3
Floris Foijer, Lee A Albacker, Bjorn Bakker, Diana C Spierings, Ying Yue, Stephanie Z Xie, Stephanie H Davis, Annegret Lutum-Jehle, Darin Takemoto, Brian Hare, Brinley Furey, Roderick T Bronson, Peter M Lansdorp, Allan Bradley, Peter K Sorger
Chromosome instability (CIN) is deleterious to normal cells because of the burden of aneuploidy. However, most human solid tumors have an abnormal karyotype implying that gain and loss of chromosomes by cancer cells confers a selective advantage. CIN can be induced in the mouse by inactivating the spindle assembly checkpoint. This is lethal in the germline but we show here that adult T cells and hepatocytes can survive conditional inactivation of the Mad2l1 SAC gene and resulting CIN. This causes rapid onset of acute lymphoblastic leukemia (T-ALL) and progressive development of hepatocellular carcinoma (HCC), both lethal diseases...
March 20, 2017: ELife
https://www.readbyqxmd.com/read/28315434/identifying-the-clonal-relationship-model-of-multifocal-papillary-thyroid-carcinoma-by-whole-genome-sequencing
#4
Mao Xia, Hengyu Li, Qian Ma, Dong Yu, Jing Li, Yi Zhang, Yuan Sheng, Yingjun Guo
PURPOSE: To evaluate the application of whole genome sequencing (WGS) in determining the inter-foci clonal relationship of multifocal papillary thyroid carcinoma (mPTC). METHODS: After reviewing PTC patient profiles, 8 cancer foci and germline control samples from 3 mPTC patients were analyzed by WGS. Single nucleotide variations (SNVs), copy number variation (CNV), structural variation and mutational signature were examined. RESULTS: The multifocality rate of PTC was 35...
March 14, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28298214/climat-het-detecting-subclonal-copy-number-alterations-and-loss-of-heterozygosity-in-heterogeneous-tumor-samples-from-whole-genome-sequencing-data
#5
Zhenhua Yu, Ao Li, Minghui Wang
BACKGROUND: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28279470/novel-targeted-therapies-for-esophagogastric-cancer
#6
REVIEW
Steven B Maron, Daniel V T Catenacci
Gastroesophageal cancer (GEC) remains a major cause of cancer-related mortality worldwide. Although the incidence of distal gastric adenocarcinoma (GC) is declining in the United States, proximal esophagogastric junction adenocarcinoma (EGJ) is increasing in incidence. GEC, including GC and EGJ, is treated uniformly in the metastatic setting. Overall survival in the metastatic setting remains poor. Molecular characterization of GEC has identified mutations and copy number variations, along with other oncogenes, biomarkers, and immuno-oncologic checkpoints that may serve as actionable therapeutic targets...
April 2017: Surgical Oncology Clinics of North America
https://www.readbyqxmd.com/read/28266251/an-integrated-analysis-of-cancer-genes-in-clear-cell-renal-cell-carcinoma
#7
Jin Li, Liping Guo, Zisheng Ai
AIM: This study was performed to detect driver genes and implement integrated analyses on these drivers in clear cell renal cell carcinoma (ccRCC). METHODS: Driver genes and pathways were predicted by OncodriveFM and Dendrix using 39,636 somatic mutations from The Cancer Genome Atlas, followed by DNA methylation, copy number variation, differential expression and survival analyses. RESULTS: Overall, 342 driver genes and 106 pathways were determined by OncodriveFM, two driver genes by Dendrix...
April 2017: Future Oncology
https://www.readbyqxmd.com/read/28260349/somatic-structural-variations-in-pediatric-brain-tumors-an-update
#8
Zhengwei Li, Qingzeng Sun, Yingchun Shi
Pediatrics brain tumours are the second most frequent malignancy in children, and the most common cause of cancer-related deaths in both the 0-14-year and the 15-24-year age group. Although, pediatrics high-grade glioma (pHGG) is a histologically similar tumour to that arising in adults, these are distinct biological diseases, differing in copy number profiles and driver genetic alterations. Recent sequencing initiatives have conclusively shown the existence of subgroups of HGG marked by distinct driver mutations, which are significantly enriched in young children (H3F3A K27M), teenagers and young adults (H3F3A G34R/V), and middle- aged adults (IDH1/2)...
March 3, 2017: Minerva Pediatrica
https://www.readbyqxmd.com/read/28257835/stratifying-melanoma-and-breast-cancer-tcga-datasets-on-the-basis-of-the-cnv-of-transcription-factor-binding-sites-common-to-proliferation-and-apoptosis-effector-genes
#9
James A Mauro, John M Yavorski, George Blanck
Transcription factors that activate both proliferation- and apoptosis-effector genes, along with a number of related observations, have led to a proposal for a feed forward mechanism of activating the two gene classes, whereby a certain concentration of a transcription factor activates the proliferation-effector genes and a higher concentration of the transcription factor activates the apoptosis-effector genes. We reasoned that this paradigm of regulation could lead to, in the cancer setting, a selection for relatively reduced copy numbers of apoptosis-effector gene, transcription factor binding sites (TFBS)...
February 28, 2017: Gene
https://www.readbyqxmd.com/read/28249643/chromosome-instability-in-tumor-resection-margins-of-primary-oscc-is-a-predictor-of-local-recurrence
#10
Damiana D C G Pierssens, Maarten C Borgemeester, Stijn J H van der Heijden, Carine J Peutz-Kootstra, Andrea M Ruland, Annick M Haesevoets, Peter A W H Kessler, Bernd Kremer, Ernst-Jan M Speel
BACKGROUND: The local recurrence rate in oral squamous cell cancer (OSCC) hardly decreases. This is partly due to the presence of (pre)malignant cells in the remaining tissue after resection, that may lead to the development of a new tumor in time. Detection of histologically (pre)malignant cells in the tumor resection margins should predict these patients at risk for recurrence, however this appears to be difficult in routine practice. Purpose of this study was to apply easy-to-use molecular tests for more accurate detection of (pre)malignant cells in histopathologically tumor-free margins, to improve diagnosis of patients at risk...
March 2017: Oral Oncology
https://www.readbyqxmd.com/read/28245287/study-of-association-and-molecular-analysis-of-human-papillomavirus-in-breast-cancer-of-indian-patients-clinical-and-prognostic-implication
#11
Saimul Islam, Hemantika Dasgupta, Anirban Roychowdhury, Rittwika Bhattacharya, Nupur Mukherjee, Anup Roy, Gautam Kumar Mandal, Neyaz Alam, Jaydip Biswas, Shyamsundar Mandal, Susanta Roychoudhury, Chinmay Kumar Panda
OBJECTIVES: Human papillomavirus (HPV) causes tumors primarily Cervical cancer. Recently, inconsistent reports came up in Breast cancer (BC) too. In India, despite treatment 70,218 BC patients die each year. So, we explored the association of HPV, if any, with BC prognosis in Indian pre-therapeutic (PT) and Neo-adjuvant chemotherapy (NACT) patients with subsequent analysis of HPV profile. METHODS: HPV prevalence was checked and analysis of physical status, copy number, genome variation, promoter methylation and expression (mRNA and protein) of the prevalent subtype was done...
2017: PloS One
https://www.readbyqxmd.com/read/28235418/baalchip-bayesian-analysis-of-allele-specific-transcription-factor-binding-in-cancer-genomes
#12
Ines de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A J Ponder, Kerstin B Meyer, Florian Markowetz
Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods of detecting an allelic imbalance assume diploid genomes. This assumption severely limits their applicability to cancer samples with frequent DNA copy-number changes. Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of background allele frequency on the observed ChIP-seq read counts...
February 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/28231327/functionally-focused-algorithmic-analysis-of-high-resolution-microarray-cgh-genomic-landscapes-demonstrates-comparable-genomic-copy-number-aberrations-in-msi-and-mss-sporadic-colorectal-cancer
#13
Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers...
2017: PloS One
https://www.readbyqxmd.com/read/28223454/dynamic-expansion-and-contraction-of-caga-copy-number-in-helicobacter-pylori-impact-development-of-gastric-disease
#14
Sungil Jang, Hanfu Su, Faith C Blum, Sarang Bae, Yun Hui Choi, Aeryun Kim, Youngmin A Hong, Jinmoon Kim, Ji-Hye Kim, Niluka Gunawardhana, Yeong-Eui Jeon, Yun-Jung Yoo, D Scott Merrell, Linhu Ge, Jeong-Heon Cha
Infection with Helicobacter pylori is a major risk factor for development of gastric disease, including gastric cancer. Patients infected with H. pylori strains that express CagA are at even greater risk of gastric carcinoma. Given the importance of CagA, this report describes a new molecular mechanism by which the cagA copy number dynamically expands and contracts in H. pylori Analysis of strain PMSS1 revealed a heterogeneous population in terms of numbers of cagA copies; strains carried from zero to four copies of cagA that were arranged as direct repeats within the chromosome...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28194035/recurrently-deregulated-lncrnas-in-hepatocellular-carcinoma
#15
Yang Yang, Lei Chen, Jin Gu, Hanshuo Zhang, Jiapei Yuan, Qiuyu Lian, Guishuai Lv, Siqi Wang, Yang Wu, Yu-Cheng T Yang, Dongfang Wang, Yang Liu, Jing Tang, Guijuan Luo, Yang Li, Long Hu, Xinbao Sun, Dong Wang, Mingzhou Guo, Qiaoran Xi, Jianzhong Xi, Hongyang Wang, Michael Q Zhang, Zhi John Lu
Hepatocellular carcinoma (HCC) cells often invade the portal venous system and subsequently develop into portal vein tumour thrombosis (PVTT). Long noncoding RNAs (lncRNAs) have been associated with HCC, but a comprehensive analysis of their specific association with HCC metastasis has not been conducted. Here, by analysing 60 clinical samples' RNA-seq data from 20 HCC patients, we have identified and characterized 8,603 candidate lncRNAs. The expression patterns of 917 recurrently deregulated lncRNAs are correlated with clinical data in a TCGA cohort and published liver cancer data...
February 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28191267/single-cell-digital-polymerase-chain-reaction-on-self-priming-compartmentalization-chip
#16
Qiangyuan Zhu, Lin Qiu, Yanan Xu, Guang Li, Ying Mu
Single cell analysis provides a new framework for understanding biology and disease, however, an absolute quantification of single cell gene expression still faces many challenges. Microfluidic digital polymerase chain reaction (PCR) provides a unique method to absolutely quantify the single cell gene expression, but only limited devices are developed to analyze a single cell with detection variation. This paper describes a self-priming compartmentalization (SPC) microfluidic digital polymerase chain reaction chip being capable of performing single molecule amplification from single cell...
January 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28184012/chromosome-20q-amplification-defines-a-subtype-of-microsatellite-stable-left-sided-colon-cancers-with-wild-type-ras-raf-and-better-overall-survival
#17
Ryan N Ptashkin, Carlos Pagan, Rona Yaeger, Sumit Middha, Jinru Shia, Kevin P O'Rourke, Michael F Berger, Lu Wang, Robert Cimera, Jiajing Wang, David S Klimstra, Leonard Saltz, Marc Ladanyi, Ahmet Zehir, Jaclyn F Hechtman
Here comprehensive analysis was performed on the molecular and clinical features of colorectal carcinoma (CRC) harboring chromosome 20q amplification. Tumor and normal DNA from patients with advanced CRC underwent next generation sequencing (NGS) via MSK-IMPACT and a subset of case samples were subjected to high resolution microarray (Oncoscan). Relationships between genomic copy number and transcript expression were assessed with The Cancer Genome Atlas (TCGA) CRC data. Of the CRC patients sequenced (n=401) with MSK-IMPACT, 148 (37%) had 20q gain, and 30 (7%) had 20q amplification...
February 9, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28165479/whole-genome-single-cell-copy-number-profiling-from-formalin-fixed-paraffin-embedded-samples
#18
Luciano G Martelotto, Timour Baslan, Jude Kendall, Felipe C Geyer, Kathleen A Burke, Lee Spraggon, Salvatore Piscuoglio, Kalyani Chadalavada, Gouri Nanjangud, Charlotte K Y Ng, Pamela Moody, Sean D'Italia, Linda Rodgers, Hilary Cox, Arnaud da Cruz Paula, Asya Stepansky, Michail Schizas, Hannah Y Wen, Tari A King, Larry Norton, Britta Weigelt, James B Hicks, Jorge S Reis-Filho
A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens...
March 2017: Nature Medicine
https://www.readbyqxmd.com/read/28161563/single-center-experience-with-a-targeted-next-generation-sequencing-assay-for-assessment-of-relevant-somatic-alterations-in-solid-tumors
#19
Aino Paasinen-Sohns, Viktor H Koelzer, Angela Frank, Julian Schafroth, Aline Gisler, Melanie Sachs, Anne Graber, Sacha I Rothschild, Andreas Wicki, Gieri Cathomas, Kirsten D Mertz
Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material...
February 2, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28147217/ccg-an-integrative-resource-of-cancer-protein-coding-genes-and-long-noncoding-rnas
#20
Mengrong Liu, Yu-Cheng T Yang, Gang Xu, Chang Tan, Zhi John Lu
The identification of cancer genes remains a main aim of cancer research. With the advances of high-throughput sequencing technologies, thousands of novel cancer genes were identified through recurrent mutation analyses and differential expression analyses between normal tissues and tumors in large populations. Many databases were developed to document the cancer genes. However, no public database providing both cancer protein-coding genes and cancer lncRNAs is available presently. Here, we present the Catalogue of Cancer Genes (CCG) database (http://ccg...
December 2016: Discovery Medicine
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