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whole genome sequencing AND cancer

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https://www.readbyqxmd.com/read/29453410/molecular-characterization-of-colorectal-adenomas-with-and-without-malignancy-reveals-distinguishing-genome-transcriptome-and-methylome-alterations
#1
Brooke R Druliner, Panwen Wang, Taejeong Bae, Saurabh Baheti, Seth Slettedahl, Douglas Mahoney, Nikolaos Vasmatzis, Hang Xu, Minsoo Kim, Matthew Bockol, Daniel O'Brien, Diane Grill, Nathaniel Warner, Miguel Munoz-Gomez, Kimberlee Kossick, Ruth Johnson, Mohamad Mouchli, Donna Felmlee-Devine, Jill Washechek-Aletto, Thomas Smyrk, Ann Oberg, Junwen Wang, Nicholas Chia, Alexej Abyzov, David Ahlquist, Lisa A Boardman
The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. The molecular determinants that distinguish benign from malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Cancer Free Polyp (CFP) patients. CAPs had tissues from the residual polyp of origin and contiguous cancer; CFPs had polyp tissues matched to CAPs based on polyp size, histology and dysplasia. To determine whether molecular features distinguish CAPs and CFPs, we conducted Whole Genome Sequencing, RNA-seq, and RRBS on over 90 tissues from 31 patients...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449679/tert-promoter-mutation-in-adult-granulosa-cell-tumor-of-the-ovary
#2
Jessica A Pilsworth, Dawn R Cochrane, Zhouchunyang Xia, Geraldine Aubert, Anniina E M Färkkilä, Hugo M Horlings, Satoshi Yanagida, Winnie Yang, Jamie L P Lim, Yi Kan Wang, Ali Bashashati, Jacqueline Keul, Adele Wong, Kevin Norris, Sara Y Brucker, Florin-Andrei Taran, Bernhard Krämer, Annette Staebler, Esther Oliva, Sohrab P Shah, Stefan Kommoss, Friedrich Kommoss, C Blake Gilks, Duncan M Baird, David G Huntsman
The telomerase reverse transcriptase (TERT) gene is highly expressed in stem cells and silenced upon differentiation. Cancer cells can attain immortality by activating TERT to maintain telomere length and telomerase activity, which is a crucial step of tumorigenesis. Two somatic mutations in the TERT promoter (C228T; C250T) have been identified as gain-of-function mutations that promote transcriptional activation of TERT in multiple cancers, such as melanoma and glioblastoma. A recent study investigating TERT promoter mutations in ovarian carcinomas found C228T and C250T mutations in 15...
February 15, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29445421/evidence-for-a-pre-malignant-cell-line-in-a-skin-biopsy-from-a-patient-with-nijmegen-breakage-syndrome
#3
Raneem Habib, Heidemarie Neitzel, Aurelie Ernst, John K L Wong, Bozenna Goryluk-Kozakiewicz, Antje Gerlach, Ilja Demuth, Karl Sperling, Krystyna Chrzanowska
Background: Nijmegen breakage syndrome is an autosomal recessive disorder characterized by microcephaly, immunodeficiency, hypersensitivity to X-irradiation, and a high predisposition to cancer. Nibrin, the product of the NBN gene, is part of the MRE11/RAD50 (MRN) complex that is involved in the repair of DNA double strand breaks (DSBs), and plays a critical role in the processing of DSBs in immune gene rearrangements, telomere maintenance, and meiotic recombination. NBS skin fibroblasts grow slowly in culture and enter early into senescence...
2018: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29440180/resistance-promoting-effects-of-ependymoma-treatment-revealed-through-genomic-analysis-of-multiple-recurrences-in-a-single-patient
#4
Christopher A Miller, Sonika Dahiya, Tiandao Li, Robert Fulton, Matthew D Smyth, Gavin P Dunn, Joshua B Rubin, Elaine R Mardis
BACKGROUND: As in other brain tumors, multiple recurrences after complete resection and irradiation of supratentorial ependymoma are common and frequently result in patient death. This standard-of-care treatment was established in the pre-genomic era without the ability to evaluate the effect that mutagenic therapies may exert on tumor evolution and in promoting resistance, recurrence, and death. We seized a rare opportunity to characterize treatment effects and the evolution of a single patient's ependymoma across four recurrences after different therapies...
February 13, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29436261/an-epigenomic-approach-to-identifying-differential-overlapping-and-cis-acting-lncrnas-in-cisplatin-resistant-cancer-cells
#5
Olga Vera, Carlos Rodriguez-Antolin, Javier de Castro, Florian A Karreth, Thomas A Sellers, Inmaculada Ibañez de Caceres
Long noncoding RNAs (lncRNAs) are critical regulators of cell biology whose alteration can lead to the development of diseases such as cancer. The potential role of lncRNAs and their epigenetic regulation in response to platinum treatment are largely unknown. We analyzed four paired cisplatin-sensitive/resistant non-small cell lung cancer and ovarian cancer cell lines. The epigenetic landscape of overlapping and cis-acting lncRNAs was determined by combining human microarray data on 30,586 lncRNAs and 20,109 protein coding mRNAs with whole-genome bisulfite sequencing...
February 13, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29433971/large-scale-sequencing-of-testicular-germ-cell-tumour-tgct-cases-excludes-major-tgct-predisposition-gene
#6
Kevin Litchfield, Chey Loveday, Max Levy, Darshna Dudakia, Elizabeth Rapley, Jeremie Nsengimana, D Tim Bishop, Alison Reid, Robert Huddart, Peter Broderick, Richard S Houlston, Clare Turnbull
Testicular germ cell tumour (TGCT), the most common cancer in young men, has a significant heritable basis that has long raised questions as to the existence of underlying major high-penetrance susceptibility gene(s). To determine the contribution of rare gene mutations to the inherited risk of TGCT, we analysed germline whole-exome data for 919 TGCT cases and 1609 cancer-free controls. We compared frequencies between TGCT cases and controls of rare (<1%) and low-frequency (1-5%) coding variants (1) individually and (2) collapsed at the gene level via burden testing (T1, disruptive; T2, all deleterious; and T3, all nonsynonymous) using Fisher's exact test with Bonferroni correction of significance thresholds...
February 9, 2018: European Urology
https://www.readbyqxmd.com/read/29432426/single-cell-on-chip-whole-genome-amplification-via-micropillar-arrays-for-reduced-amplification-bias
#7
Harvey C Tian, Jaime J Benitez, Harold G Craighead
Single cell whole genome amplification is susceptible to amplification biases that impact the accuracy of single cell sequencing data. To address this, we have developed a microfluidic device for the isolation and purification of genomic DNA from individual cells. The device uses a micropillar array to physically capture single cells and its chromosomal DNA upon extraction. The extracted DNA is immobilized within the micropillar array in a way that allows isothermal amplification. In this system, whole genome amplification of the single cell is carried out under a continual fluid flow within the microfluidic channel...
2018: PloS One
https://www.readbyqxmd.com/read/29431110/the-personal-genome-project-canada-findings-from-whole-genome-sequences-of-the-inaugural-56-participants
#8
Miriam S Reuter, Susan Walker, Bhooma Thiruvahindrapuram, Joe Whitney, Iris Cohn, Neal Sondheimer, Ryan K C Yuen, Brett Trost, Tara A Paton, Sergio L Pereira, Jo-Anne Herbrick, Richard F Wintle, Daniele Merico, Jennifer Howe, Jeffrey R MacDonald, Chao Lu, Thomas Nalpathamkalam, Wilson W L Sung, Zhuozhi Wang, Rohan V Patel, Giovanna Pellecchia, John Wei, Lisa J Strug, Sherilyn Bell, Barbara Kellam, Melanie M Mahtani, Anne S Bassett, Yvonne Bombard, Rosanna Weksberg, Cheryl Shuman, Ronald D Cohn, Dimitri J Stavropoulos, Sarah Bowdin, Matthew R Hildebrandt, Wei Wei, Asli Romm, Peter Pasceri, James Ellis, Peter Ray, M Stephen Meyn, Nasim Monfared, S Mohsen Hosseini, Ann M Joseph-George, Fred W Keeley, Ryan A Cook, Marc Fiume, Hin C Lee, Christian R Marshall, Jill Davies, Allison Hazell, Janet A Buchanan, Michael J Szego, Stephen W Scherer
BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant...
February 5, 2018: CMAJ: Canadian Medical Association Journal, Journal de L'Association Medicale Canadienne
https://www.readbyqxmd.com/read/29425284/chromosomal-instability-in-women-with-primary-ovarian-insufficiency
#9
Sunita Katari, Mahmoud Aarabi, Angela Kintigh, Susan Mann, Svetlana A Yatsenko, Joseph S Sanfilippo, Anthony J Zeleznik, Aleksandar Rajkovic
STUDY QUESTION: What is the prevalence of somatic chromosomal instability among women with idiopathic primary ovarian insufficiency (POI)? SUMMARY ANSWER: A subset of women with idiopathic POI may have functional impairment in DNA repair leading to chromosomal instability in their soma. WHAT IS KNOWN ALREADY: The formation and repair of DNA double-strand breaks during meiotic recombination are fundamental processes of gametogenesis. Oocytes with compromised DNA integrity are susceptible to apoptosis which could trigger premature ovarian aging and accelerated wastage of the human follicle reserve...
February 7, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29423790/identification-of-disease-susceptibility-alleles-in-the-next-generation-sequencing-era
#10
Johanna K DiStefano, Christopher B Kingsley
The development of next generation sequencing (NGS) technologies has transformed the study of human genetic variation. In less than a decade, NGS has facilitated the discovery of causal mutations in both rare, monogenic diseases and common, heterogeneous disorders, leading to unprecedented improvements in disease diagnosis and treatment strategies. Given the rapid evolution of NGS platforms, it is now possible to analyze whole genomes and exomes quickly and affordably. Further, emerging NGS applications, such as single-cell sequencing, have the power to address specific issues like somatic variation, which is yielding new insights into the role of somatic mutations in cancer and late-onset diseases...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29414918/high-whole-genome-sequence-diversity-of-human-papillomavirus-type-18-isolates
#11
Pascal van der Weele, Chris J L M Meijer, Audrey J King
BACKGROUND: The most commonly found human papillomavirus (HPV) types in cervical cancer are HPV16 and HPV18. Genome variants of these types have been associated with differential carcinogenic potential. To date, only a handful of studies have described HPV18 whole genome sequencing results. Here we describe HPV18 variant diversity and conservation of persistent infections in a longitudinal retrospective cohort study. METHODS: Cervical self-samples were obtained annually over four years and genotyped on the SPF10-DEIA-LiPA25 platform...
February 7, 2018: Viruses
https://www.readbyqxmd.com/read/29413762/the-epithelial-sodium-channel-%C3%AE-enac-is-a-downstream-therapeutic-target-of-ascl1-in-pulmonary-neuroendocrine-tumors
#12
Min He, Shanshan Liu, Sachith Gallolu Kankanamalage, Mark D Borromeo, Luc Girard, Adi F Gazdar, John D Minna, Jane E Johnson, Melanie H Cobb
Small cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma, designated as a recalcitrant cancer by the National Cancer Institute, in urgent need of new rational therapeutic targets. Previous studies have determined that the basic helix-loop-helix transcription factor achaete-scute homolog 1 (ASCL1) is essential for the survival and progression of a fraction of pulmonary neuroendocrine cancer cells, which include both SCLC and a subset of non-SCLC. Previously, to understand how ASCL1 initiates tumorigenesis in pulmonary neuroendocrine cancer and identify the transcriptional targets of ASCL1, whole-genome RNA-sequencing analysis combined with chromatin immunoprecipitation-sequencing was performed with a series of lung cancer cell lines...
February 1, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29413684/human-epidermal-receptor-family-inhibitors-in-patients-with-erbb3-mutated-cancers-entering-the-back-door
#13
Loic Verlingue, Antoine Hollebecque, Ludovic Lacroix, Sophie Postel-Vinay, Andrea Varga, Yolla El Dakdouki, Capucine Baldini, Rastilav Balheda, Anas Gazzah, Jean-Marie Michot, Aurélien Marabelle, Olivier Mir, Monica Arnedos, Etienne Rouleau, Eric Solary, Thierry De Baere, Eric Angevin, Jean-Pierre Armand, Stefan Michiels, Fabrice André, Eric Deutsch, Jean-Yves Scoazec, Jean-Charles Soria, Christophe Massard
INTRODUCTION: Therapeutic inhibition of the human epidermal receptor 3 (ERBB3, HER3) has been challenged by the low frequency of ERBB3 somatic alterations across cancer types. We have evaluated the clinical utility to use available inhibitors of the HER family in the context of ERBB3 mutations. PATIENTS AND METHODS: In this study, we have selected patients with somatic ERBB3 alterations detected in their tumours from the molecular screening programs running at our institution...
January 27, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29410677/development-of-a-method-to-implement-whole-genome-bisulfite-sequencing-of-cfdna-from-cancer-patients-and-a-mouse-tumor-model
#14
Elaine C Maggi, Silvia Gravina, Haiying Cheng, Bilal Piperdi, Ziqiang Yuan, Xiao Dong, Steven K Libutti, Jan Vijg, Cristina Montagna
The goal of this study was to develop a method for whole genome cell-free DNA (cfDNA) methylation analysis in humans and mice with the ultimate goal to facilitate the identification of tumor derived DNA methylation changes in the blood. Plasma or serum from patients with pancreatic neuroendocrine tumors or lung cancer, and plasma from a murine model of pancreatic adenocarcinoma was used to develop a protocol for cfDNA isolation, library preparation and whole-genome bisulfite sequencing of ultra low quantities of cfDNA, including tumor-specific DNA...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29408647/whole-exome-mutational-and-transcriptional-landscapes-of-combined-hepatocellular-cholangiocarcinoma-and-intrahepatic-cholangiocarcinoma-reveal-molecular-diversity
#15
Zhen-Hao Liu, Bao-Feng Lian, Qiong-Zhu Dong, Han Sun, Jin-Wang Wei, Yuan-Yuan Sheng, Wei Li, Yixue Li, Lu Xie, Lei Liu, Lun-Xiu Qin
BACKGROUND: Primary liver cancer (PLC) is the third largest contributor to cancer mortality in the world. PLC is a heterogeneous disease that encompasses several biologically distinct subtypes including hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). CHC is a distinct, albeit rare, subtype of PLC and is comprised of cells with histopathological features of both HCC and ICC. Several studies have focused on the mutation and expression landscapes of HCC and ICC...
January 31, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29405996/familial-esophageal-squamous-cell-carcinoma-with-damaging-rare-germline-mutations-in-kcnj12-kcnj18-and-gprin2-genes
#16
Narjes Khalilipour, Ancha Baranova, Amir Jebelli, Alireza Heravi-Moussavi, Sergey Bruskin, Mohammad Reza Abbaszadegan
In Iran, esophageal cancer is the fourth common cancers in women and sixth common cancers in men. Here we evaluated the importance of familial risk factors and the role of genetic predisposition in Esophageal Squamous Cell Carcinoma (ESCC) using Whole-Exome Sequencing (WES). Germline damaging mutations were identified in WES data from 9 probands of 9 unrelated ESCC pedigrees. Mutations were confirmed with Sanger sequencing and evaluated amplification-refractory mutation system-Polymerase Chain Reaction (ARMS-PCR) in 50 non-related ethnically matched samples and in complete genomics database...
February 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29402903/loss-of-function-uorf-mutations-in-human-malignancies
#17
Julia Schulz, Nancy Mah, Martin Neuenschwander, Tabea Kischka, Richard Ratei, Peter M Schlag, Esmeralda Castaños-Vélez, Iduna Fichtner, Per-Ulf Tunn, Carsten Denkert, Oliver Klaas, Wolfgang E Berdel, Jens P von Kries, Wojciech Makalowski, Miguel A Andrade-Navarro, Achim Leutz, Klaus Wethmar
Ribosome profiling revealed widespread translational activity at upstream open reading frames (uORFs) and validated uORF-mediated translational control as a commonly repressive mechanism of gene expression. Translational activation of proto-oncogenes through loss-of-uORF mutations has been demonstrated, yet a systematic search for cancer-associated genetic alterations in uORFs is lacking. Here, we applied a PCR-based, multiplex identifier-tagged deep sequencing approach to screen 404 uORF translation initiation sites of 83 human tyrosine kinases and 49 other proto-oncogenes in 308 human malignancies...
February 5, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29397622/-current-situation-and-prospect-of-breast-cancer-liquid-biopsy
#18
B Zhou, L Xin, L Xu, J M Ye, Y H Liu
Liquid biopsy is a diagnostic approach by analyzing body fluid samples. Peripheral blood is the most common sample. Urine, saliva, pleural effusion and ascites are also used. Now liquid biopsy is mainly used in the area of neoplasm diagnosis and treatment. Compared with traditional tissue biopsy, liquid biopsy is minimally invasive, convenient to sample and easy to repeat. Liquid biopsy mainly includes circulating tumor cells and circulating tumor DNA (ctDNA) detection. Detection of ctDNA requires sensitive and accurate methods...
February 1, 2018: Zhonghua Wai Ke za Zhi [Chinese Journal of Surgery]
https://www.readbyqxmd.com/read/29396858/recapitulating-the-clinical-scenario-of-brca-associated-pancreatic-cancer-in-pre-clinical-models
#19
Talia Golan, Chani Stossel, Dikla Atias, Ella Buzhor, Sharon Halperin, Keren Cohen, Maria Raitses-Gurevich, Yulia Glick, Stephen Raskin, Daniel Yehuda, Anna Feldman, Michael Schvimer, Eitan Friedman, Rotem Karni, Julie M Wilson, Robert E Denroche, Ilinca Lungu, John M S Bartlett, Faridah Mbabaali, Steven Gallinger, Raanan Berger
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies. BRCA-associated PDAC comprises a clinically relevant subtype. A portion of these patients are highly susceptible to DNA damaging therapeutics, however, responses are heterogeneous and clinical resistance evolves. We have developed unique patient-derived xenograft (PDX) models from metastatic lesions of germline BRCA-mutated patients obtained at distinct time points; before treatment and at progression. Thus, closely mimicking clinical scenarios, to further investigate treatment naïve and resistant patients...
February 3, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29392687/whole-genome-sequencing-based-discovery-of-structural-variants-in-glioblastoma
#20
Kazimierz O Wrzeszczynski, Vanessa Felice, Minita Shah, Sadia Rahman, Anne-Katrin Emde, Vaidehi Jobanputra, Mayu O Frank, Robert B Darnell
Next-generation DNA sequencing (NGS) technologies are currently being applied in both research and clinical settings for the understanding and management of disease. The goal is to use high-throughput sequencing to identify specific variants that drive tumorigenesis within each individual's tumor genomic profile. The significance of copy number and structural variants in glioblastoma makes it essential to broaden the search beyond oncogenic single nucleotide variants toward whole genome profiles of genetic aberrations that may contribute to disease progression...
2018: Methods in Molecular Biology
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