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https://www.readbyqxmd.com/read/29149504/mybl1-rearrangements-and-myb-amplification-in-breast-adenoid-cystic-carcinomas-lacking-the-myb-nfib-fusion-gene
#1
Jisun Kim, Felipe C Geyer, Luciano G Martelotto, Charlotte K Y Ng, Raymond S Lim, Pier Selenica, Anqi Li, Fresia Pareja, Nicola Fusco, Marcia Edelweiss, Rahul Kumar, Rodrigo Gularte-Merida, Andre N Forbes, Ekta Khurana, Odette Mariani, Sunil Badve, Anne Vincent-Salomon, Larry Norton, Jorge S Reis-Filho, Britta Weigelt
Breast adenoid cystic carcinoma (AdCC), a rare type of triple-negative breast cancer (TNBC), has been shown to be driven by MYB pathway activation, most often underpinned by the MYB-NFIB fusion gene. Alternative genetic mechanisms, such as MYBL1 rearrangements, have been reported in MYB-NFIB-negative salivary gland AdCCs. Here we report on the molecular characterization by massively parallel sequencing of four breast AdCCs lacking the MYB-NFIB fusion gene. In two cases, we identified MYBL1 rearrangements (MYBL1-ACTN1 and MYBL1-NFIB), which were associated with MYBL1 overexpression...
November 17, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29141020/genomic-analysis-of-atypical-fibroxanthoma
#2
Kevin Lai, Catherine A Harwood, Karin J Purdie, Charlotte M Proby, Irene M Leigh, Namita Ravi, Thaddeus W Mully, Lionel Brooks, Priscilla M Sandoval, Michael D Rosenblum, Sarah T Arron
Atypical fibroxanthoma (AFX), is a rare type of skin cancer affecting older individuals with sun damaged skin. Since there is limited genomic information about AFX, our study seeks to improve the understanding of AFX through whole-exome and RNA sequencing of 8 matched tumor-normal samples. AFX is a highly mutated malignancy with recurrent mutations in a number of genes, including COL11A1, ERBB4, CSMD3, and FAT1. The majority of mutations identified were UV signature (C>T in dipyrimidines). We observed deletion of chromosomal segments on chr9p and chr13q, including tumor suppressor genes such as KANK1 and CDKN2A, but no gene fusions were found...
2017: PloS One
https://www.readbyqxmd.com/read/29137313/rna-seq-reveals-distinctive-rna-profiles-of-small-extracellular-vesicles-from-different-human-liver-cancer-cell-lines
#3
Martina Berardocco, Annalisa Radeghieri, Sara Busatto, Marialucia Gallorini, Chiara Raggi, Clarissa Gissi, Igea D'Agnano, Paolo Bergese, Armando Felsani, Anna C Berardi
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29132146/identification-of-unique-neoantigen-qualities-in-long-term-survivors-of-pancreatic-cancer
#4
Vinod P Balachandran, Marta Łuksza, Julia N Zhao, Vladimir Makarov, John Alec Moral, Romain Remark, Brian Herbst, Gokce Askan, Umesh Bhanot, Yasin Senbabaoglu, Daniel K Wells, Charles Ian Ormsby Cary, Olivera Grbovic-Huezo, Marc Attiyeh, Benjamin Medina, Jennifer Zhang, Jennifer Loo, Joseph Saglimbeni, Mohsen Abu-Akeel, Roberta Zappasodi, Nadeem Riaz, Martin Smoragiewicz, Z Larkin Kelley, Olca Basturk, Mithat Gönen, Arnold J Levine, Peter J Allen, Douglas T Fearon, Miriam Merad, Sacha Gnjatic, Christine A Iacobuzio-Donahue, Jedd D Wolchok, Ronald P DeMatteo, Timothy A Chan, Benjamin D Greenbaum, Taha Merghoub, Steven D Leach
Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8(+) T-cell infiltrates, but neither alone, stratified patients with the longest survival...
November 8, 2017: Nature
https://www.readbyqxmd.com/read/29127096/retention-of-interstitial-genes-between-tmprss2-and-erg-is-associated-with-low-risk-prostate-cancer
#5
Stephen J Murphy, Farhad Kosari, R Jeffrey Karnes, Aqsa Nasir, Sarah H Johnson, Athanasios G Gaitatzes, James B Smadbeck, Laureano J Rangel, George Vasmatzis, John C Cheville
TMPRSS2-ERG gene fusions occur in over 50% of prostate cancers, but their impact on clinical outcomes is not well understood. Retention of interstitial genes between TMPRSS2 and ERG has been reported to influence tumor progression in an animal model. In this study, we analyzed the status of TMPRSS2-ERG fusion genes and interstitial genes in tumors from a large cohort of men treated surgically for prostate cancer, associating alterations with biochemical progression. Through whole-genome mate pair sequencing, we mapped and classified rearrangements driving ETS family gene fusions in 133 cases of very low-, low-, intermediate-, and high-risk prostate cancer from radical prostatectomy specimens...
November 10, 2017: Cancer Research
https://www.readbyqxmd.com/read/29125853/whole-genome-dna-methylation-characteristics-in-pediatric-precursor-b-cell-acute-lymphoblastic-leukemia-bcp-all
#6
Radosław Chaber, Artur Gurgul, Grażyna Wróbel, Olga Haus, Anna Tomoń, Jerzy Kowalczyk, Tomasz Szmatoła, Igor Jasielczuk, Blanka Rybka, Renata Ryczan-Krawczyk, Ewa Duszeńko, Sylwia Stąpor, Krzysztof Ciebiera, Sylwia Paszek, Natalia Potocka, Christopher J Arthur, Izabela Zawlik
In addition to genetic alterations, epigenetic abnormalities have been shown to underlie the pathogenesis of acute lymphoblastic leukemia (ALL)-the most common pediatric cancer. The purpose of this study was to characterize the whole genome DNA methylation profile in children with precursor B-cell ALL (BCP ALL) and to compare this profile with methylation observed in normal bone marrow samples. Additional efforts were made to correlate the observed methylation patterns with selected clinical features. We assessed DNA methylation from bone marrow samples obtained from 38 children with BCP ALL at the time of diagnosis along with 4 samples of normal bone marrow cells as controls using Infinium MethylationEPIC BeadChip Array...
2017: PloS One
https://www.readbyqxmd.com/read/29123100/dna-methylation-at-enhancers-identifies-distinct-breast-cancer-lineages
#7
Thomas Fleischer, Xavier Tekpli, Anthony Mathelier, Shixiong Wang, Daniel Nebdal, Hari P Dhakal, Kristine Kleivi Sahlberg, Ellen Schlichting, Anne-Lise Børresen-Dale, Elin Borgen, Bjørn Naume, Ragnhild Eskeland, Arnoldo Frigessi, Jörg Tost, Antoni Hurtado, Vessela N Kristensen
Breast cancers exhibit genome-wide aberrant DNA methylation patterns. To investigate how these affect the transcriptome and which changes are linked to transformation or progression, we apply genome-wide expression-methylation quantitative trait loci (emQTL) analysis between DNA methylation and gene expression. On a whole genome scale, in cis and in trans, DNA methylation and gene expression have remarkably and reproducibly conserved patterns of association in three breast cancer cohorts (n = 104, n = 253 and n = 277)...
November 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/29117265/genomic-sequencing-identifies-a-few-mutations-driving-the-independent-origin-of-primary-liver-tumors-in-a-chronic-hepatitis-murine-model
#8
Zuyu Yang, Mingming Jia, Guojing Liu, Huaining Hao, Li Chen, Guanghao Li, Sixue Liu, Yawei Li, Chung-I Wu, Xuemei Lu, Shengdian Wang
With the development of high-throughput genomic analysis, sequencing a mouse primary cancer model provides a new opportunity to understand fundamental mechanisms of tumorigenesis and progression. Here, we characterized the genomic variations in a hepatitis-related primary hepatocellular carcinoma (HCC) mouse model. A total of 12 tumor sections and four adjacent non-tumor tissues from four mice were used for whole exome and/or whole genome sequencing and validation of genotyping. The functions of the mutated genes in tumorigenesis were studied by analyzing their mutation frequency and expression in clinical HCC samples...
2017: PloS One
https://www.readbyqxmd.com/read/29113995/time-for-change-a-new-training-programme-for-morpho-molecular-pathologists
#9
REVIEW
David A Moore, Caroline A Young, Hayley T Morris, Karin A Oien, Jessica L Lee, J Louise Jones, Manuel Salto-Tellez
The evolution of cellular pathology as a specialty has always been driven by technological developments and the clinical relevance of incorporating novel investigations into diagnostic practice. In recent years, the molecular characterisation of cancer has become of crucial relevance in patient treatment both for predictive testing and subclassification of certain tumours. Much of this has become possible due to the availability of next-generation sequencing technologies and the whole-genome sequencing of tumours is now being rolled out into clinical practice in England via the 100 000 Genome Project...
November 7, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29113982/nanopore-sequencing-of-complex-genomic-rearrangements-in-yeast-reveals-mechanisms-of-repeat-mediated-double-strand-break-repair
#10
Ryan J McGinty, Rachel G Rubinstein, Alexander J Neil, Margaret Dominska, Denis Kiktev, Thomas D Petes, Sergei M Mirkin
Improper DNA double-strand break (DSB) repair results in complex genomic rearrangements (CGRs) in many cancers and various congenital disorders in humans. Trinucleotide repeat sequences, such as (GAA)n repeats in Friedreich's ataxia, (CTG)n repeats in myotonic dystrophy and (CGG)n repeats in fragile X syndrome, are also subject to double strand breaks within the repetitive tract followed by DNA repair. Mapping the outcomes of CGRs is important for understanding their causes and potential phenotypic effects...
November 7, 2017: Genome Research
https://www.readbyqxmd.com/read/29112974/impact-of-extensive-antibiotic-treatment-on-faecal-carriage-of-antibiotic-resistant-enterobacteria-in-children-in-a-low-resistance-prevalence-setting
#11
Per Kristian Knudsen, Petter Brandtzaeg, E Arne Høiby, Jon Bohlin, Ørjan Samuelsen, Martin Steinbakk, Tore G Abrahamsen, Fredrik Müller, Karianne Wiger Gammelsrud
We prospectively studied the consequences of extensive antibiotic treatment on faecal carriage of antibiotic-resistant enterobacteria in a cohort of children with cystic fibrosis (CF) and a cohort of children with cancer compared to healthy children with no or low antibiotic exposure. The study was conducted in Norway in a low resistance prevalence setting. Sixty longitudinally collected faecal samples from children with CF (n = 32), 88 samples from children with cancer (n = 45) and 127 samples from healthy children (n = 70) were examined...
2017: PloS One
https://www.readbyqxmd.com/read/29112732/identifying-structural-variants-using-linked-read-sequencing-data
#12
Rebecca Elyanow, Hsin-Ta Wu, Benjamin J Raphael
Motivation: Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing...
November 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29111877/dna-methylation-alterations-induced-by-transient-exposure-of-mcf-7-cells-to-maghemite-nanoparticles
#13
Raphael S Bonadio, Ana Carolina Arcanjo, Emilia Cd Lima, Alline T Vasconcelos, Renata C Silva, Frederico H Horst, Ricardo B Azevedo, Marcio José Poças-Fonseca, João Paulo F Longo
AIM: To evaluate the DNA methylation profile of MCF-7 cells during and after the treatment with maghemite nanoparticles (MNP-CIT). MATERIALS & METHODS: Noncytotoxic MNP-CIT concentrations and cell morphology were evaluated by standard methods. DNA methylation was assessed by whole genome bisulfite sequencing. DNA methyltransferase (DNMT) genes expression was analyzed by qRT-PCR. RESULTS: A total of 30 and 60 µgFeml(-1) MNP-CIT accumulated in cytoplasm but did not present cytotoxic effects...
November 7, 2017: Nanomedicine
https://www.readbyqxmd.com/read/29111481/draft-genome-sequence-of-broad-spectrum-antibiotic-sparsomycin-producing-streptomyces-sparsogenes-atcc-25498-from-the-american-type-culture-collection
#14
Hongyu Zhang, Qiuling Zhou, Tingting Lou, Suying Wang, Haihua Ruan
OBJECTIVES: Sparsomycin, which exhibits rare broad-spectrum antibiotic and antitumour activity against bacteria, Archaea, Eucarya and various cancer cell lines, has been widely used as a powerful tool to study protein synthesis. Here we report the draft genome sequence of Streptomyces sparsogenes ATCC 25498 from the American Type Culture Collection (ATCC), which has become an organism of interest owing to its ability to produce sparsomycin. METHODS: The whole-genome sequence of S...
October 27, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29110840/immunohistochemical-and-genetic-characteristics-of-lung-cancer-mimicking-organizing-pneumonia
#15
Tomohiro Ichikawa, Koichi Saruwatari, Sachiyo Mimaki, Masato Sugano, Keiju Aokage, Motohiro Kojima, Tomoyuki Hishida, Satoshi Fujii, Junji Yoshida, Takeshi Kuwata, Atsushi Ochiai, Kenji Suzuki, Masahiro Tsuboi, Koichi Goto, Katsuya Tsuchihara, Genichiro Ishii
INTRODUCTION: Lung cancer mimicking organizing pneumonia (LCOP) is a novel radiological entity of lung adenocarcinoma that could be misdiagnosed as inflammatory lesions. However, the characteristic biological and genetic features of LCOP are not fully clarified. MATERIALS AND METHODS: We used thin-section CT images to select cases of (LCOP) among surgically resected lung adenocarcinoma patients. We compared the clinicopathological characteristics and the immunophenotypes of LCOP (n=44) and other lepidic-predominant adenocarcinomas (non-LCOP, n=56)...
November 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29109480/detection-of-subclonal-l1-transductions-in-colorectal-cancer-by-long-distance-inverse-pcr-and-nanopore-sequencing
#16
Barun Pradhan, Tatiana Cajuso, Riku Katainen, Päivi Sulo, Tomas Tanskanen, Outi Kilpivaara, Esa Pitkänen, Lauri A Aaltonen, Liisa Kauppi, Kimmo Palin
Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29109393/scalable-whole-exome-sequencing-of-cell-free-dna-reveals-high-concordance-with-metastatic-tumors
#17
Viktor A Adalsteinsson, Gavin Ha, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush, Sarah C Reed, Denisse Rotem, Justin Rhoades, Denis Loginov, Dimitri Livitz, Daniel Rosebrock, Ignaty Leshchiner, Jaegil Kim, Chip Stewart, Mara Rosenberg, Joshua M Francis, Cheng-Zhong Zhang, Ofir Cohen, Coyin Oh, Huiming Ding, Paz Polak, Max Lloyd, Sairah Mahmud, Karla Helvie, Margaret S Merrill, Rebecca A Santiago, Edward P O'Connor, Seong H Jeong, Rachel Leeson, Rachel M Barry, Joseph F Kramkowski, Zhenwei Zhang, Laura Polacek, Jens G Lohr, Molly Schleicher, Emily Lipscomb, Andrea Saltzman, Nelly M Oliver, Lori Marini, Adrienne G Waks, Lauren C Harshman, Sara M Tolaney, Eliezer M Van Allen, Eric P Winer, Nancy U Lin, Mari Nakabayashi, Mary-Ellen Taplin, Cory M Johannessen, Levi A Garraway, Todd R Golub, Jesse S Boehm, Nikhil Wagle, Gad Getz, J Christopher Love, Matthew Meyerson
Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing...
November 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/29107929/viral-sequences-in-human-cancer
#18
Paul G Cantalupo, Joshua P Katz, James M Pipas
We have developed a virus detection and discovery computational pipeline, Pickaxe, and applied it to NGS databases provided by The Cancer Genome Atlas (TCGA). We analyzed a collection of whole genome (WGS), exome (WXS), and RNA (RNA-Seq) sequencing libraries from 3052 participants across 22 different cancers. NGS data from nearly all tumor and normal tissues examined contained contaminating viral sequences. Intensive computational and manual efforts are required to remove these artifacts. We found that several different types of cancers harbored Herpesviruses including EBV, CMV, HHV1, HHV2, HHV6 and HHV7...
November 3, 2017: Virology
https://www.readbyqxmd.com/read/29106441/orchid-a-novel-management-annotation-and-machine-learning-framework-for-analyzing-cancer-mutations
#19
Clinton L Cario, John S Witte
Motivation: As whole-genome tumor sequence and biological annotation datasets grow in size, number, and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments, and machine learning algorithms, there is also a need for the integration of functionality across frameworks. Results: We present orchid, a python based software package for the management, annotation, and machine learning of cancer mutations...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29105159/a-6-bp-deletion-variant-in-a-novel-canine-glutathione-s-transferase-gene-gstt5-leads-to-loss-of-enzyme-function
#20
S Craft, J Ekena, J Sacco, K Luethcke, L Trepanier
OBJECTIVES: Glutathione-S-transferases (GSTs) detoxify reactive xenobiotics, and defective GST gene polymorphisms increase cancer risk in humans. A low activity GST-theta variant was previously found in research beagles. The purpose of our study was to determine the molecular basis for this phenotype and its allele frequency in pet dogs. METHODS: Banked livers from 45 dogs of various breeds were screened for low GST-theta activity by the substrate 1,2-dichloro-4-nitrobenzene (DCNB), and were genotyped for variants in a novel canine GST gene, GSTT5...
November 3, 2017: Journal of Veterinary Internal Medicine
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