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https://www.readbyqxmd.com/read/29227476/the-molecular-landscape-of-pediatric-acute-myeloid-leukemia-reveals-recurrent-structural-alterations-and-age-specific-mutational-interactions
#1
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, Todd A Alonzo, Yussanne Ma, Richard Moore, Andrew J Mungall, Marco A Marra, Jinghui Zhang, Xiaotu Ma, Yu Liu, Yanling Liu, Jaime M Guidry Auvil, Tanja M Davidsen, Patee Gesuwan, Leandro C Hermida, Bodour Salhia, Stephen Capone, Giridharan Ramsingh, Christian Michel Zwaan, Sanne Noort, Stephen R Piccolo, E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG-National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults...
December 11, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29225701/cytotoxic-escherichia-coli-strains-encoding-colibactin-and-cytotoxic-necrotizing-factor-cnf-colonize-laboratory-macaques
#2
Yan Feng, Anthony Mannion, Carolyn M Madden, Alton G Swennes, Catherine Townes, Charles Byrd, Robert P Marini, James G Fox
Background: Many Escherichia coli strains are considered to be a component of the normal flora found in the human and animal intestinal tracts. While most E. coli strains are commensal, some strains encode virulence factors that enable the bacteria to cause intestinal and extra-intestinal clinically-relevant infections. Colibactin, encoded by a genomic island (pks island), and cytotoxic necrotizing factor (CNF), encoded by the cnf gene, are genotoxic and can modulate cellular differentiation, apoptosis and proliferation...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/29224155/targeted-bisulfite-sequencing-using-the-seqcap-epi-enrichment-system
#3
Jennifer Wendt, Heidi Rosenbaum, Todd A Richmond, Jeffrey A Jeddeloh, Daniel L Burgess
Cytosine methylation has been shown to have a role in a host of biological processes. In mammalian biology these include stem cell differentiation, embryonic development, genomic imprinting, inflammation, and silencing of transposable elements. Given the central importance of these processes, it is not surprising to find aberrant cytosine methylation patterns associated with many disorders in humans, including cancer, cardiovascular disease, and neurological disease. While whole genome shotgun bisulfite sequencing (WGBS) has recently become feasible, generating high sequence coverage data for the entire genome is expensive, both in terms of money and analysis time, when generally only a small subset of the genome is of interest to most researchers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29221171/proteogenomic-analysis-prioritises-functional-single-nucleotide-variants-in-cancer-samples
#4
Shiyong Ma, Ranjeeta Menon, Rebecca C Poulos, Jason W H Wong
Massively parallel DNA sequencing enables the detection of thousands of germline and somatic single nucleotide variants (SNVs) in cancer samples. The functional analysis of these mutations is often carried out through in silico predictions, with further downstream experimental validation rarely performed. Here, we examine the potential of using mass spectrometry-based proteomics data to further annotate the function of SNVs in cancer samples. RNA-seq and whole genome sequencing (WGS) data from Jurkat cells were used to construct a custom database of single amino acid variant (SAAV) containing peptides and identified over 1,000 such peptides in two Jurkat proteomics datasets...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29216271/genomic-and-phenotypic-characteristics-of-swedish-c-jejuni-water-isolates
#5
Anna Nilsson, Cecilia Johansson, Astrid Skarp, René Kaden, Lars Engstrand, Hilpi Rautelin
Campylobacter jejuni is the most common cause of bacterial gastroenteritis. Major reservoirs are warm-blooded animals, poultry in particular, but Campylobacter can also be transmitted via water. In this paper, we have taken a closer look at the biology and potential virulence of C. jejuni water isolates. Seven C. jejuni isolates from incoming surface water at water plants in Sweden were characterized with whole genome sequencing and phenotypical testing. Multi locus sequence typing analysis revealed that these isolates belonged to groups known to include both common (ST48CC) and uncommon (ST1275CC, ST683, ST793 and ST8853) human pathogens...
2017: PloS One
https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#6
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29215633/measuring-mutation-accumulation-in-single-human-adult-stem-cells-by-whole-genome-sequencing-of-organoid-cultures
#7
Myrthe Jager, Francis Blokzijl, Valentina Sasselli, Sander Boymans, Roel Janssen, Nicolle Besselink, Hans Clevers, Ruben van Boxtel, Edwin Cuppen
Characterization of mutational processes in adult stem cells (ASCs) will improve our understanding of aging-related diseases, such as cancer and organ failure, and may ultimately help prevent the development of these diseases. Here, we present a method for cataloging mutations in individual human ASCs without the necessity of using error-prone whole-genome amplification. Single ASCs are expanded in vitro into clonal organoid cultures to generate sufficient DNA for accurate whole-genome sequencing (WGS) analysis...
January 2018: Nature Protocols
https://www.readbyqxmd.com/read/29215049/str-profiling-and-copy-number-variation-analysis-on-single-preserved-cells-using-current-whole-genome-amplification-methods
#8
Ann-Sophie Vander Plaetsen, Lieselot Deleye, Senne Cornelis, Laurentijn Tilleman, Filip Van Nieuwerburgh, Dieter Deforce
The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29205775/donor-derived-metastatic-urothelial-cancer-after-kidney-transplantation-associated-with-a-potentially-oncogenic-bk-polyomavirus
#9
David C Müller, Maarit Rämö, Klaudia Naegele, Sebastian Ribi, Christian Wetterauer, Valeria Perrina, Luca Quagliata, Tatjana Vlajnic, Christian Ruiz, Beate Balitzki, Rainer Grobholz, Rainer Gosert, Elvis T Ajuh, Hans H Hirsch, Lukas Bubendorf, Cyrill A Rentsch
BK polyomavirus has been linked to urothelial carcinoma in immunosuppressed patients. Here, we performed comprehensive genomic analysis of a BK polyomavirus -associated, metachronous, multifocal and metastatic micropapillary urothelial cancer in a kidney transplant recipient. Dissecting cancer heterogeneity by sorting technologies prior to array-comparative genomic hybridization followed by short tandem repeat analysis revealed that the metastatic urothelial cancer was of donor-origin (4 year-old male). The top 50 cancer-associated genes displayed no key driver mutations as assessed by next generation sequencing...
December 4, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29204651/whole-exome-sequencing-in-adults-with-chronic-kidney-disease-a-pilot-study
#10
Sneh Lata, Maddalena Marasa, Yifu Li, David A Fasel, Emily Groopman, Vaidehi Jobanputra, Hila Rasouly, Adele Mitrotti, Rik Westland, Miguel Verbitsky, Jordan Nestor, Lindsey M Slater, Vivette D'Agati, Marcin Zaniew, Anna Materna-Kiryluk, Francesca Lugani, Gianluca Caridi, Luca Rampoldi, Aditya Mattoo, Chad A Newton, Maya K Rao, Jai Radhakrishnan, Wooin Ahn, Pietro A Canetta, Andrew S Bomback, Gerald B Appel, Corinne Antignac, Glen S Markowitz, Christine K Garcia, Krzysztof Kiryluk, Simone Sanna-Cherchi, Ali G Gharavi
Background: The utility of whole-exome sequencing (WES) for the diagnosis and management of adult-onset constitutional disorders has not been adequately studied. Genetic diagnostics may be advantageous in adults with chronic kidney disease (CKD), in whom the cause of kidney failure often remains unknown. Objective: To study the diagnostic utility of WES in a selected referral population of adults with CKD. Design: Observational cohort. Setting: A major academic medical center...
December 5, 2017: Annals of Internal Medicine
https://www.readbyqxmd.com/read/29197744/transcriptional-landscape-of-a-retc634y-mutated-ipsc-and-its-crispr-corrected-isogenic-control-reveals-the-putative-role-of-egr1-transcriptional-program-in-the-development-of-multiple-endocrine-neoplasia-type-2a-associated-cancers
#11
Julien Hadoux, Christophe Desterke, Olivier Féraud, Mathieu Guibert, Roberta Francesca De Rose, Paule Opolon, Dominique Divers, Emilie Gobbo, Frank Griscelli, Martin Schlumberger, Annelise Bennaceur-Griscelli, Ali G Turhan
MEN2A is a hereditary cancer-predisposing syndrome that affects patients with germline RET mutations. The effects of this oncogenic tyrosine kinase in the context of primitive stem cells are not known. In order to study these events, we generated a MEN2A induced Pluripotent Stem Cell (iPSC) line from a patient with RET mutation and an isogenic counterpart by CRISPR-Cas9 correction of the mutation. Whole exome sequencing of iPSC before and after CRISPR-Cas9 genome edition revealed no major exonic off target effect of the CRISPR correction...
November 23, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29196356/the-rise-of-the-genome-and-personalised-medicine
#12
Helen K Brittain, Richard Scott, Ellen Thomas
Virtually all medical specialties are impacted by genetic disease. Enhanced understanding of the role of genetics in human disease, coupled with rapid advancement in sequencing technology, is transforming the speed of diagnosis for patients and providing increasing opportunities to tailor management. As set out in the Annual report of the Chief Medical Officer 2016: Generation Genome1 and the recent NHS England board paper Creating a genomic medicine service to lay the foundations to deliver personalised interventions and treatments,2 the increasing 'mainstreaming' of genetic testing into routine practice and plans to embed whole genome sequencing in the NHS mean that the profile and importance of genomics is on the rise for many clinicians...
December 2017: Clinical Medicine: Journal of the Royal College of Physicians of London
https://www.readbyqxmd.com/read/29190660/actionable-mutations-in-canine-hemangiosarcoma
#13
Guannan Wang, Ming Wu, Martha A Maloneyhuss, John Wojcik, Amy C Durham, Nicola J Mason, David B Roth
BACKGROUND: Angiosarcomas (AS) are rare in humans, but they are a deadly subtype of soft tissue sarcoma. Discovery sequencing in AS, especially the visceral form, is hampered by the rarity of cases. Most diagnostic material exists as archival formalin fixed, paraffin embedded tissue which serves as a poor source of high quality DNA for genome-wide sequencing. We approached this problem through comparative genomics. We hypothesized that exome sequencing a histologically similar tumor, hemangiosarcoma (HSA), that occurs in approximately 50,000 dogs per year, may lead to the identification of potential oncogenic drivers and druggable targets that could also occur in angiosarcoma...
2017: PloS One
https://www.readbyqxmd.com/read/29187174/intra-tumor-heterogeneity-in-breast-cancer-has-limited-impact-on-transcriptomic-based-molecular-profiling
#14
Govindasamy-Muralidharan Karthik, Mattias Rantalainen, Gustav Stålhammar, John Lövrot, Ikram Ullah, Amjad Alkodsi, Ran Ma, Lena Wedlund, Johan Lindberg, Jan Frisell, Jonas Bergh, Johan Hartman
BACKGROUND: Transcriptomic profiling of breast tumors provides opportunity for subtyping and molecular-based patient stratification. In diagnostic applications the specimen profiled should be representative of the expression profile of the whole tumor and ideally capture properties of the most aggressive part of the tumor. However, breast cancers commonly exhibit intra-tumor heterogeneity at molecular, genomic and in phenotypic level, which can arise during tumor evolution. Currently it is not established to what extent a random sampling approach may influence molecular breast cancer diagnostics...
November 29, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29186904/the-roles-of-micrornas-in-regulating-the-expression-of-pd-1-pd-l1-immune-checkpoint
#15
REVIEW
Qingshui Wang, Wei Lin, Xiaoqiong Tang, Suhuan Li, Libin Guo, Yao Lin, Hang Fai Kwok
Engagement of programmed death-ligand 1 (PD-L1) with its receptor programmed death 1 (PD-1) on T cells has been speculated to play a major role in suppressing the immune system, which helps tumor cells evade anti-tumor immunity. With the development of whole genome sequencing technologies, microRNAs have gained more attention as an important new layer of molecular regulation. Recent studies have revealed that altered expression of microRNAs play a pivotal role in immune checkpoint and various cellular processes in cancer...
November 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29186506/identification-of-large-rearrangements-in-cancer-genomes-with-barcode-linked-reads
#16
Li C Xia, John M Bell, Christina Wood-Bouwens, Jiamin J Chen, Nancy R Zhang, Hanlee P Ji
Large genomic rearrangements involve inversions, deletions and other structural changes that span Megabase segments of the human genome. This category of genetic aberration is the cause of many hereditary genetic disorders and contributes to pathogenesis of diseases like cancer. We developed a new algorithm called ZoomX for analysing barcode-linked sequence reads-these sequences can be traced to individual high molecular weight DNA molecules (>50 kb). To generate barcode linked sequence reads, we employ a library preparation technology (10X Genomics) that uses droplets to partition and barcode DNA molecules...
November 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29185122/genomic-variations-in-the-counterpart-normal-controls-of-lung-squamous-cell-carcinomas
#17
Liwei Qu, Bo Zhou, Guizhen Wang, Guangbiao Zhou
Lung squamous cell carcinoma (LUSC) causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas...
November 28, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/29184442/exome-and-transcriptome-sequencing-identifies-loss-of-pdlim2-in-metastatic-colorectal-cancers
#18
Bo Young Oh, Jeonghee Cho, Hye Kyung Hong, Joon Seol Bae, Woong-Yang Park, Je-Gun Joung, Yong Beom Cho
Background: Understanding the genomic determinants associated with metastasis in colorectal cancers (CRCs) provides crucial clues for improving patient care. Patients and methods: In this study, we performed whole-exome sequencing as well as RNA sequencing analyses on five pairs of primary and liver metastasized samples from CRC patients together with blood/normal control samples for each pair. Results: We identified genomic deletions in the region of 8p21-23 (q value <0...
2017: Cancer Management and Research
https://www.readbyqxmd.com/read/29172773/an-update-on-liquid-biopsy-analysis-for-diagnostic-and-monitoring-applications-in-non-small-cell-lung-cancer
#19
Clara Mayo-de-Las-Casas, Mónica Garzón Ibáñez, Núria Jordana-Ariza, Beatriz García-Peláez, Ariadna Balada-Bel, Sergio Villatoro, Umberto Malapelle, Niki Karachaliou, Giancarlo Troncone, Rafael Rosell, Miguel Angel Molina-Vila
Collection of tumor samples is not always feasible in non-small cell lung cancer (NSCLC) patients, and circulating free DNA (cfDNA) extracted from blood represents a viable alternative. Different sensitive platforms have been developed for genetic cfDNA testing, some of which are already in clinical use. However, several difficulties remain, particularly the lack of standardization of these methodologies. Areas covered: Here, the authors present a review of the literature to update the applicability of cfDNA for diagnosis and monitoring of NSCLC patients...
November 26, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/29172275/interleukin-6-genetic-variation-and-susceptibility-to-gastric-cancer-in-an-iranian-population
#20
Marzieh Attar, Maryam Mansoori, Majid Shahbazi
Background: Despite recent decrease in the incidence of gastric cancer, it is still a common type of cancer in the north of Iran. Many evaluations have shown that polymorphisms of cytokine genes like that for interleukin 6 (IL-6), which play important roles in regulation of the immune response, can increase the risk of gastric cancer. This study examined the role of the IL-6-174 gene polymorphism in susceptibility in an Iranian population. Method: Genomic DNA was extracted from peripheral whole blood of 100 patients and 361 healthy controls...
November 26, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
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