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Integrative genomics

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https://www.readbyqxmd.com/read/28351082/future-perspectives-for-uterine-cervical-cancer-treatment-based-on-integrative-genomic-and-molecular-characterizations
#1
Daniel G Tiezzi
No abstract text is available yet for this article.
March 28, 2017: Revista Brasileira de Ginecologia e Obstetrícia
https://www.readbyqxmd.com/read/28350845/abnormal-expression-of-mrna-microrna-alteration-and-aberrant-dna-methylation-patterns-in-rectal-adenocarcinoma
#2
Yang Hua, Xiukun Ma, Xianglong Liu, Xiangfei Yuan, Hai Qin, Xipeng Zhang
AIM: Rectal adenocarcinoma (READ) is a malignancy cancer with the high morbidity and motility worldwide. Our study aimed to explore the potential pathogenesis of READ through integrated analysis of gene expression profiling and DNA methylation data. METHODS: The miRNA, mRNA expression profiling and corresponding DNA methylation data were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed mRNAs/ miRNAs/methylated regions (DEmRNA/DEmiRNAs) were identified in READ...
2017: PloS One
https://www.readbyqxmd.com/read/28350798/research-priorities-for-harnessing-plant-microbiomes-in-sustainable-agriculture
#3
Posy E Busby, Chinmay Soman, Maggie R Wagner, Maren L Friesen, James Kremer, Alison Bennett, Mustafa Morsy, Jonathan A Eisen, Jan E Leach, Jeffery L Dangl
Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28346895/wheat-genomics-comes-of-age
#4
REVIEW
Cristobal Uauy
Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs...
March 24, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28346467/characterization-and-interstrain-transfer-of-prophage-pp3-of-pseudomonas-aeruginosa
#5
Gang Li, Shuguang Lu, Mengyu Shen, Shuai Le, Wei Shen, Yinling Tan, Jing Wang, Xia Zhao, Yan Zhao, Yali Gong, Yuhui Yang, Hongbin Zhu, Fuquan Hu, Ming Li
Prophages are major contributors to horizontal gene transfer and drive the evolution and diversification of bacteria. Here, we describe the characterization of a prophage element designated pp3 in the clinical Pseudomonas aeruginosa isolate PA1. pp3 spontaneously excises from the PA1 genome and circularizes at a very high frequency of 25%. pp3 is likely to be a defective prophage due to its inability to form plaques on P. aeruginosa indicator strains, and no phage particles could be detected in PA1 supernatants...
2017: PloS One
https://www.readbyqxmd.com/read/28346442/identification-of-12-new-susceptibility-loci-for-different-histotypes-of-epithelial-ovarian-cancer
#6
Catherine M Phelan, Karoline B Kuchenbaecker, Jonathan P Tyrer, Siddhartha P Kar, Kate Lawrenson, Stacey J Winham, Joe Dennis, Ailith Pirie, Marjorie J Riggan, Ganna Chornokur, Madalene A Earp, Paulo C Lyra, Janet M Lee, Simon Coetzee, Jonathan Beesley, Lesley McGuffog, Penny Soucy, Ed Dicks, Andrew Lee, Daniel Barrowdale, Julie Lecarpentier, Goska Leslie, Cora M Aalfs, Katja K H Aben, Marcia Adams, Julian Adlard, Irene L Andrulis, Hoda Anton-Culver, Natalia Antonenkova, Gerasimos Aravantinos, Norbert Arnold, Banu K Arun, Brita Arver, Jacopo Azzollini, Judith Balmaña, Susana N Banerjee, Laure Barjhoux, Rosa B Barkardottir, Yukie Bean, Matthias W Beckmann, Alicia Beeghly-Fadiel, Javier Benitez, Marina Bermisheva, Marcus Q Bernardini, Michael J Birrer, Line Bjorge, Amanda Black, Kenneth Blankstein, Marinus J Blok, Clara Bodelon, Natalia Bogdanova, Anders Bojesen, Bernardo Bonanni, Åke Borg, Angela R Bradbury, James D Brenton, Carole Brewer, Louise Brinton, Per Broberg, Angela Brooks-Wilson, Fiona Bruinsma, Joan Brunet, Bruno Buecher, Ralf Butzow, Saundra S Buys, Trinidad Caldes, Maria A Caligo, Ian Campbell, Rikki Cannioto, Michael E Carney, Terence Cescon, Salina B Chan, Jenny Chang-Claude, Stephen Chanock, Xiao Qing Chen, Yoke-Eng Chiew, Jocelyne Chiquette, Wendy K Chung, Kathleen B M Claes, Thomas Conner, Linda S Cook, Jackie Cook, Daniel W Cramer, Julie M Cunningham, Aimee A D'Aloisio, Mary B Daly, Francesca Damiola, Sakaeva Dina Damirovna, Agnieszka Dansonka-Mieszkowska, Fanny Dao, Rosemarie Davidson, Anna DeFazio, Capucine Delnatte, Kimberly F Doheny, Orland Diez, Yuan Chun Ding, Jennifer Anne Doherty, Susan M Domchek, Cecilia M Dorfling, Thilo Dörk, Laure Dossus, Mercedes Duran, Matthias Dürst, Bernd Dworniczak, Diana Eccles, Todd Edwards, Ros Eeles, Ursula Eilber, Bent Ejlertsen, Arif B Ekici, Steve Ellis, Mingajeva Elvira, Kevin H Eng, Christoph Engel, D Gareth Evans, Peter A Fasching, Sarah Ferguson, Sandra Fert Ferrer, James M Flanagan, Zachary C Fogarty, Renée T Fortner, Florentia Fostira, William D Foulkes, George Fountzilas, Brooke L Fridley, Tara M Friebel, Eitan Friedman, Debra Frost, Patricia A Ganz, Judy Garber, María J García, Vanesa Garcia-Barberan, Andrea Gehrig, Aleksandra Gentry-Maharaj, Anne-Marie Gerdes, Graham G Giles, Rosalind Glasspool, Gord Glendon, Andrew K Godwin, David E Goldgar, Teodora Goranova, Martin Gore, Mark H Greene, Jacek Gronwald, Stephen Gruber, Eric Hahnen, Christopher A Haiman, Niclas Håkansson, Ute Hamann, Thomas V O Hansen, Patricia A Harrington, Holly R Harris, Jan Hauke, Alexander Hein, Alex Henderson, Michelle A T Hildebrandt, Peter Hillemanns, Shirley Hodgson, Claus K Høgdall, Estrid Høgdall, Frans B L Hogervorst, Helene Holland, Maartje J Hooning, Karen Hosking, Ruea-Yea Huang, Peter J Hulick, Jillian Hung, David J Hunter, David G Huntsman, Tomasz Huzarski, Evgeny N Imyanitov, Claudine Isaacs, Edwin S Iversen, Louise Izatt, Angel Izquierdo, Anna Jakubowska, Paul James, Ramunas Janavicius, Mats Jernetz, Allan Jensen, Uffe Birk Jensen, Esther M John, Sharon Johnatty, Michael E Jones, Päivi Kannisto, Beth Y Karlan, Anthony Karnezis, Karin Kast, Catherine J Kennedy, Elza Khusnutdinova, Lambertus A Kiemeney, Johanna I Kiiski, Sung-Won Kim, Susanne K Kjaer, Martin Köbel, Reidun K Kopperud, Torben A Kruse, Jolanta Kupryjanczyk, Ava Kwong, Yael Laitman, Diether Lambrechts, Nerea Larrañaga, Melissa C Larson, Conxi Lazaro, Nhu D Le, Loic Le Marchand, Jong Won Lee, Shashikant B Lele, Arto Leminen, Dominique Leroux, Jenny Lester, Fabienne Lesueur, Douglas A Levine, Dong Liang, Clemens Liebrich, Jenna Lilyquist, Loren Lipworth, Jolanta Lissowska, Karen H Lu, Jan Lubinński, Craig Luccarini, Lene Lundvall, Phuong L Mai, Gustavo Mendoza-Fandiño, Siranoush Manoukian, Leon F A G Massuger, Taymaa May, Sylvie Mazoyer, Jessica N McAlpine, Valerie McGuire, John R McLaughlin, Iain McNeish, Hanne Meijers-Heijboer, Alfons Meindl, Usha Menon, Arjen R Mensenkamp, Melissa A Merritt, Roger L Milne, Gillian Mitchell, Francesmary Modugno, Joanna Moes-Sosnowska, Melissa Moffitt, Marco Montagna, Kirsten B Moysich, Anna Marie Mulligan, Jacob Musinsky, Katherine L Nathanson, Lotte Nedergaard, Roberta B Ness, Susan L Neuhausen, Heli Nevanlinna, Dieter Niederacher, Robert L Nussbaum, Kunle Odunsi, Edith Olah, Olufunmilayo I Olopade, Håkan Olsson, Curtis Olswold, David M O'Malley, Kai-Ren Ong, N Charlotte Onland-Moret, Nicholas Orr, Sandra Orsulic, Ana Osorio, Domenico Palli, Laura Papi, Tjoung-Won Park-Simon, James Paul, Celeste L Pearce, Inge Søkilde Pedersen, Petra H M Peeters, Bernard Peissel, Ana Peixoto, Tanja Pejovic, Liisa M Pelttari, Jennifer B Permuth, Paolo Peterlongo, Lidia Pezzani, Georg Pfeiler, Kelly-Anne Phillips, Marion Piedmonte, Malcolm C Pike, Anna M Piskorz, Samantha R Poblete, Timea Pocza, Elizabeth M Poole, Bruce Poppe, Mary E Porteous, Fabienne Prieur, Darya Prokofyeva, Elizabeth Pugh, Miquel Angel Pujana, Pascal Pujol, Paolo Radice, Johanna Rantala, Christine Rappaport-Fuerhauser, Gad Rennert, Kerstin Rhiem, Patricia Rice, Andrea Richardson, Mark Robson, Gustavo C Rodriguez, Cristina Rodríguez-Antona, Jane Romm, Matti A Rookus, Mary Anne Rossing, Joseph H Rothstein, Anja Rudolph, Ingo B Runnebaum, Helga B Salvesen, Dale P Sandler, Minouk J Schoemaker, Leigha Senter, V Wendy Setiawan, Gianluca Severi, Priyanka Sharma, Tameka Shelford, Nadeem Siddiqui, Lucy E Side, Weiva Sieh, Christian F Singer, Hagay Sobol, Honglin Song, Melissa C Southey, Amanda B Spurdle, Zsofia Stadler, Doris Steinemann, Dominique Stoppa-Lyonnet, Lara E Sucheston-Campbell, Grzegorz Sukiennicki, Rebecca Sutphen, Christian Sutter, Anthony J Swerdlow, Csilla I Szabo, Lukasz Szafron, Yen Y Tan, Jack A Taylor, Muy-Kheng Tea, Manuel R Teixeira, Soo-Hwang Teo, Kathryn L Terry, Pamela J Thompson, Liv Cecilie Vestrheim Thomsen, Darcy L Thull, Laima Tihomirova, Anna V Tinker, Marc Tischkowitz, Silvia Tognazzo, Amanda Ewart Toland, Alicia Tone, Britton Trabert, Ruth C Travis, Antonia Trichopoulou, Nadine Tung, Shelley S Tworoger, Anne M van Altena, David Van Den Berg, Annemarie H van der Hout, Rob B van der Luijt, Mattias Van Heetvelde, Els Van Nieuwenhuysen, Elizabeth J van Rensburg, Adriaan Vanderstichele, Raymonda Varon-Mateeva, Ana Vega, Digna Velez Edwards, Ignace Vergote, Robert A Vierkant, Joseph Vijai, Athanassios Vratimos, Lisa Walker, Christine Walsh, Dorothea Wand, Shan Wang-Gohrke, Barbara Wappenschmidt, Penelope M Webb, Clarice R Weinberg, Jeffrey N Weitzel, Nicolas Wentzensen, Alice S Whittemore, Juul T Wijnen, Lynne R Wilkens, Alicja Wolk, Michelle Woo, Xifeng Wu, Anna H Wu, Hannah Yang, Drakoulis Yannoukakos, Argyrios Ziogas, Kristin K Zorn, Steven A Narod, Douglas F Easton, Christopher I Amos, Joellen M Schildkraut, Susan J Ramus, Laura Ottini, Marc T Goodman, Sue K Park, Linda E Kelemen, Harvey A Risch, Mads Thomassen, Kenneth Offit, Jacques Simard, Rita Katharina Schmutzler, Dennis Hazelett, Alvaro N Monteiro, Fergus J Couch, Andrew Berchuck, Georgia Chenevix-Trench, Ellen L Goode, Thomas A Sellers, Simon A Gayther, Antonis C Antoniou, Paul D P Pharoah
To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28345654/the-soybean-gmsnap18-gene-underlies-two-types-of-resistance-to-soybean-cyst-nematode
#7
Shiming Liu, Pramod K Kandoth, Naoufal Lakhssassi, Jingwen Kang, Vincent Colantonio, Robert Heinz, Greg Yeckel, Zhou Zhou, Sadia Bekal, Johannes Dapprich, Bjorn Rotter, Silvia Cianzio, Melissa G Mitchum, Khalid Meksem
Two types of resistant soybean (Glycine max (L.) Merr.) sources are widely used against soybean cyst nematode (SCN, Heterodera glycines Ichinohe). These include Peking-type soybean, whose resistance requires both the rhg1-a and Rhg4 alleles, and PI 88788-type soybean, whose resistance requires only the rhg1-b allele. Multiple copy number of PI 88788-type GmSNAP18, GmAAT, and GmWI12 in one genomic segment simultaneously contribute to rhg1-b resistance. Using an integrated set of genetic and genomic approaches, we demonstrate that the rhg1-a Peking-type GmSNAP18 is sufficient for resistance to SCN in combination with Rhg4...
March 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28345074/single-cell-rna-seq-and-computational-analysis-using-temporal-mixture-modelling-resolves-th1-tfh-fate-bifurcation-in-malaria
#8
Tapio Lönnberg, Valentine Svensson, Kylie R James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S F Soon, Lily G Fogg, Arya Sheela Nair, Urijah Liligeto, Michael J T Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T Bunn, Christian R Engwerda, William R Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, Sarah A Teichmann
Differentiation of naïve CD4(+) T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice...
March 3, 2017: Science Immunology
https://www.readbyqxmd.com/read/28345042/human-genetic-and-metabolite-variation-reveals-that-methylthioadenosine-is-a-prognostic-biomarker-and-an-inflammatory-regulator-in-sepsis
#9
Liuyang Wang, Emily R Ko, James J Gilchrist, Kelly J Pittman, Anna Rautanen, Matti Pirinen, J Will Thompson, Laura G Dubois, Raymond J Langley, Sarah L Jaslow, Raul E Salinas, D Clayburn Rouse, M Arthur Moseley, Salim Mwarumba, Patricia Njuguna, Neema Mturi, Thomas N Williams, J Anthony G Scott, Adrian V S Hill, Christopher W Woods, Geoffrey S Ginsburg, Ephraim L Tsalik, Dennis C Ko
Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mouse model demonstrate that the methionine salvage pathway is a regulator of sepsis that can accurately predict prognosis in patients. Pathway-based genome-wide association analysis of nontyphoidal Salmonella bacteremia showed a strong enrichment for single-nucleotide polymorphisms near the components of the methionine salvage pathway...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28345004/homology-directed-recombination-for-enhanced-engineering-of-chimeric-antigen-receptor-t-cells
#10
Malika Hale, Baeckseung Lee, Yuchi Honaker, Wai-Hang Leung, Alexandra E Grier, Holly M Jacobs, Karen Sommer, Jaya Sahni, Shaun W Jackson, Andrew M Scharenberg, Alexander Astrakhan, David J Rawlings
Gene editing by homology-directed recombination (HDR) can be used to couple delivery of a therapeutic gene cassette with targeted genomic modifications to generate engineered human T cells with clinically useful profiles. Here, we explore the functionality of therapeutic cassettes delivered by these means and test the flexibility of this approach to clinically relevant alleles. Because CCR5-negative T cells are resistant to HIV-1 infection, CCR5-negative anti-CD19 chimeric antigen receptor (CAR) T cells could be used to treat patients with HIV-associated B cell malignancies...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344997/simple-derivation-of-spinal-motor-neurons-from-escs-ipscs-using-sendai-virus-vectors
#11
Kazuya Goto, Keiko Imamura, Kenichi Komatsu, Kohnosuke Mitani, Kazuhiro Aiba, Norio Nakatsuji, Makoto Inoue, Akihiro Kawata, Hirofumi Yamashita, Ryosuke Takahashi, Haruhisa Inoue
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal degenerative disorder of motor neurons (MNs). Embryonic stem cells (ESCs)/induced pluripotent stem cells (iPSCs) now help us to understand the pathomechanisms of ALS via disease modeling. Various methods to differentiate ESCs/iPSCs into MNs by the addition of signaling molecules have been reported. However, classical methods require multiple steps, and newer simple methods using the transduction of transcription factors run the risk of genomic integration of the vector genes...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344990/inspiired-a-pipeline-for-quantitative-analysis-of-sites-of-new-dna-integration-in-cellular-genomes
#12
Eric Sherman, Christopher Nobles, Charles C Berry, Emmanuelle Six, Yinghua Wu, Anatoly Dryga, Nirav Malani, Frances Male, Shantan Reddy, Aubrey Bailey, Kyle Bittinger, John K Everett, Laure Caccavelli, Mary J Drake, Paul Bates, Salima Hacein-Bey-Abina, Marina Cavazzana, Frederic D Bushman
Integration of new DNA into cellular genomes mediates replication of retroviruses and transposons; integration reactions have also been adapted for use in human gene therapy. Tracking the distributions of integration sites is important to characterize populations of transduced cells and to monitor potential outgrow of pathogenic cell clones. Here, we describe a pipeline for quantitative analysis of integration site distributions named INSPIIRED (integration site pipeline for paired-end reads). We describe optimized biochemical steps for site isolation using Illumina paired-end sequencing, including new technology for suppressing recovery of unwanted contaminants, then software for alignment, quality control, and management of integration site sequences...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344988/inspiired-quantification-and-visualization-tools-for-analyzing-integration-site-distributions
#13
Charles C Berry, Christopher Nobles, Emmanuelle Six, Yinghua Wu, Nirav Malani, Eric Sherman, Anatoly Dryga, John K Everett, Frances Male, Aubrey Bailey, Kyle Bittinger, Mary J Drake, Laure Caccavelli, Paul Bates, Salima Hacein-Bey-Abina, Marina Cavazzana, Frederic D Bushman
Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to genomic features and that support numerous user-defined statistical tests...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344933/precision-medicine-the-golden-gate-for-detection-treatment-and-prevention-of-alzheimer-s-disease
#14
H Hampel, S E O'Bryant, J I Castrillo, C Ritchie, K Rojkova, K Broich, N Benda, R Nisticò, R A Frank, B Dubois, V Escott-Price, S Lista
During this decade, breakthrough conceptual shifts have commenced to emerge in the field of Alzheimer's disease (AD) recognizing risk factors and the non-linear dynamic continuum of complex pathophysiologies amongst a wide dimensional spectrum of multi-factorial brain proteinopathies/neurodegenerative diseases. As is the case in most fields of medicine, substantial advancements in detecting, treating and preventing AD will likely evolve from the generation and implementation of a systematic precision medicine strategy...
December 2016: Journal of Prevention of Alzheimer's Disease
https://www.readbyqxmd.com/read/28344905/evolution-of-the-patellar-sesamoid-bone-in-mammals
#15
Mark E Samuels, Sophie Regnault, John R Hutchinson
The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here, we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella...
2017: PeerJ
https://www.readbyqxmd.com/read/28344893/integrated-analysis-of-somatic-mutations-and-immune-microenvironment-in-malignant-pleural-mesothelioma
#16
Kazuma Kiyotani, Jae-Hyun Park, Hiroyuki Inoue, Aliya Husain, Sope Olugbile, Makda Zewde, Yusuke Nakamura, Wickii T Vigneswaran
To investigate the link between the genomic landscape of cancer cells and immune microenvironment in tumor tissues, we characterized somatic mutations and tumor-infiltrating lymphocytes (TILs) in malignant pleural mesothelioma (MPM), including mutation/neoantigen load, spatial heterogeneity of somatic mutations of cancer cells and TILs (T-cell receptor β (TCRβ) repertoire), and expression profiles of immune-related genes using specimens of three different tumor sites (anterior, posterior, and diaphragm) obtained from six MPM patients...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28344865/identification-of-genetic-determinants-of-breast-cancer-immune-phenotypes-by-integrative-genome-scale-analysis
#17
Wouter Hendrickx, Ines Simeone, Samreen Anjum, Younes Mokrab, François Bertucci, Pascal Finetti, Giuseppe Curigliano, Barbara Seliger, Luigi Cerulo, Sara Tomei, Lucia Gemma Delogu, Cristina Maccalli, Ena Wang, Lance D Miller, Francesco M Marincola, Michele Ceccarelli, Davide Bedognetti
Cancer immunotherapy is revolutionizing the clinical management of several tumors, but has demonstrated limited activity in breast cancer. The development of more effective treatments is hindered by incomplete knowledge of the genetic determinant of immune responsiveness. To fill this gap, we mined copy number alteration, somatic mutation, and expression data from The Cancer Genome Atlas (TCGA). By using RNA-sequencing data from 1,004 breast cancers, we defined distinct immune phenotypes characterized by progressive expression of transcripts previously associated with immune-mediated rejection...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28344744/automation-of-pacbio-smrtbell-ngs-library-preparation-for-bacterial-genome-sequencing
#18
Nguyet Kong, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin, Bart C Weimer
BACKGROUND: The PacBio RS II provides for single molecule, real-time DNA technology to sequence genomes and detect DNA modifications. The starting point for high-quality sequence production is high molecular weight genomic DNA. To automate the library preparation process, there must be high-throughput methods in place to assess the genomic DNA, to ensure the size and amounts of the sheared DNA fragments and final library. FINDINGS: The library construction automation was accomplished using the Agilent NGS workstation with Bravo accessories for heating, shaking, cooling, and magnetic bead manipulations for template purification...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28343982/single-cell-5-formylcytosine-landscapes-of-mammalian-early-embryos-and-escs-at-single-base-resolution
#19
Chenxu Zhu, Yun Gao, Hongshan Guo, Bo Xia, Jinghui Song, Xinglong Wu, Hu Zeng, Kehkooi Kee, Fuchou Tang, Chengqi Yi
Active DNA demethylation in mammals involves ten-eleven translocation (TET) family protein-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC) (an oxidized derivative of 5mC) at the single-cell level remain unexplored. Here, we present "CLEVER-seq" (chemical-labeling-enabled C-to-T conversion sequencing), which is a single-cell, single-base resolution 5fC-sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing...
March 15, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28342986/oncogenic-roles-of-dna-hypomethylation-through-the-activation-of-cancer-germline-genes
#20
Aurélie Van Tongelen, Axelle Loriot, Charles De Smet
Global loss of DNA methylation is frequently observed in the genome of human tumors. Although this epigenetic alteration is clearly associated with cancer progression, the way it exerts its pro-tumoral effect remains incompletely understood. A remarkable consequence of DNA hypomethylation in tumors is the aberrant activation of "cancer-germline" genes (also known as "cancer-testis" genes), which comprise a diverse group of germline-specific genes that use DNA methylation as a primary mechanism for repression in normal somatic tissues...
March 22, 2017: Cancer Letters
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