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https://www.readbyqxmd.com/read/29471527/the-heterogeneity-between-lynch-associated-and-sporadic-mmr-deficiency-in-colorectal-cancers
#1
Guo-Chen Liu, Ran-Yi Liu, Jun-Ping Yan, Xin An, Wu Jiang, Yi-Hong Ling, Jie-Wei Chen, Jin-Xin Bei, Xiao-Yu Zuo, Mu-Yan Cai, Ze-Xian Liu, Zhi-Xiang Zuo, Ji-Hong Liu, Zhi-Zhong Pan, Pei-Rong Ding
Background: Previous studies demonstrated that prognosis of germline deficiency in mismatch repair protein (dMMR) was different from that of sporadic dMMR. The underlying mechanism has not been studied. Methods: From a prospectively maintained database, we collected dMMR colorectal cancer (CRC) patients identified by postoperative immunohistochemistry screening. According to genetic test, patients were grouped as Lynch-associated or sporadic dMMR. We compared the clinical-pathological features, prognosis, and immunoreactive differences between the two groups...
February 20, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29471325/dual-stain-with-satb2-and-ck20-villin-is-useful-to-distinguish-colorectal-carcinomas-from-other-tumors
#2
Zaibo Li, Jonathan B Rock, Rachel Roth, Amy Lehman, William L Marsh, Adrian Suarez, Wendy L Frankel
Objectives: Small sample size limits the number of immunostains that may be attempted in colorectal carcinoma (CRC) biopsy specimens. We investigated the utility of dual stain with special AT-rich sequence binding protein 2 (SATB2) or caudal-type homeobox 2 (CDX2) and cytokeratin 20 (CK20) or villin in identifying CRC. Methods: Tissue microarrays with 222 CRCs and 375 other carcinomas were built. Dual stain was performed pairing nuclear stains CDX2 or SATB2 with CK20 or villin...
February 17, 2018: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29471113/validation-of-a-customized-bioinformatics-pipeline-for-a-clinical-next-generation-sequencing-test-targeting-solid-tumor-associated-variants
#3
Thomas Schneider, Geoffrey H Smith, Michael R Rossi, Charles E Hill, Linsheng Zhang
Bioinformatic analysis is an integral and critical part of clinical next-generation sequencing. It is especially challenging for some pipelines to consistently identify insertions and deletions. We present the validation of an open source tumor amplicon pipeline (OTA-pipeline) for clinical next-generation sequencing targeting solid tumor-associated variants. Raw data generated from 557 TruSight Tumor 26 samples as well as in silico data were analyzed by the OTA-pipeline and legacy pipeline and compared. Discrepant results were confirmed by orthogonal methods...
February 19, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29470627/value-of-hepatocellular-phase-imaging-after-intravenous-gadoxetate-disodium-for-assessing-hepatic-metastases-from-gastroenteropancreatic-neuroendocrine-tumors-comparison-with-other-mri-pulse-sequences-and-with-extracellular-agent
#4
Sree Harsha Tirumani, Jyothi P Jagannathan, Marta Braschi-Amirfarzan, Lei Qin, Patricia Balthazar, Nikhil H Ramaiya, Atul B Shinagare
OBJECTIVE: To compare hepatocellular phase imaging after intravenous gadoxetate disodium with other MRI pulse sequences and with extracellular agent for assessing hepatic metastases from gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN). MATERIALS AND METHODS: In this IRB-approved, HIPAA-compliant retrospective study, we included 30 patients (15 women, mean age: 58 years, range 44-77 years) with GEP-NEN metastatic to the liver, who underwent MRI with gadoxetate disodium...
February 22, 2018: Abdominal Radiology
https://www.readbyqxmd.com/read/29470101/ebselen-reversibly-inhibits-human-glutamate-dehydrogenase-at-the-catalytic-site
#5
Yanhong Jin, Di Li, Shiying Lu, Han Zhao, Zhao Chen, Wei Hou, Benfang Helen Ruan
Human glutamate dehydrogenase (GDH) plays an important role in neurological diseases, tumor metabolism, and hyperinsulinism-hyperammonemia syndrome (HHS). However, there are very few inhibitors known for human GDH. Recently, Ebselen was reported to crosslink with Escherichia coli GDH at the active site cysteine residue (Cys321), but the sequence alignment showed that the corresponding residue is Ala329 in human GDH. To investigate whether Ebselen could be an inhibitor for human GDH, we cloned and expressed an N-terminal His-tagged human GDH in E...
February 22, 2018: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/29469200/mutiple-dicer1-related-lesions-associated-with-a-germline-deep-intronic-mutation
#6
Florian Verrier, Catherine Dubois d'Enghien, Marion Gauthier-Villars, Valérie Bonadona, Cécile Faure-Conter, Frédérique Dijoud, Dominique Stoppa-Lyonnet, Claude Houdayer, Lisa Golmard
Germline DICER1 pathogenic variants predispose to numerous benign and malignant tumors. In this report, we describe DICER1 gene analysis in an adolescent diagnosed with multinodular goiter, ovarian Sertoli-Leydig cell tumor, and lung cyst. DICER1 mutational screening at the DNA level failed to detect any pathogenic variant. Subsequent messenger RNA (mRNA) analysis revealed a 132 nucleotide intronic sequence exonization. This truncating event was caused by a deep intronic mutation generating a de novo acceptor splice site...
February 22, 2018: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/29469071/microsatellite-instability-in-chronic-myeloid-leukemia-using-d17s261-and-d3s643-markers-a-pilot-study-in-gujarat-population
#7
T N Patel, M Chakraborty, P Bhattacharya
CONTEXT: Tumor progresses through a series of genetic alterations that involve proto-oncogenes and tumor suppressor genes - the gatekeeper, caretakers, and landscaper genes. Microsatellites are short tandem repeat sequences, present over the span of human genome and are known to be variable at multiple loci due to errors in DNA Mismatch Repair machinery. AIM: The present study was aimed to evaluate the association between Microsatellite Instability (MSI) and evolution of Chronic Myeloid Leukemia (CML) - genetically a rare event but profound in this pilot study...
April 2017: Indian Journal of Cancer
https://www.readbyqxmd.com/read/29468972/investigating-hiv-human-interaction-networks-to-unravel-pathogenic-mechanism-for-drug-discovery-a-systems-biology-approach
#8
Cheng-Wei Li, Bor-Sen Chen
BACKGROUND: Two big issues in the study of pathogens are determining how pathogens infect hosts and how the host defends itself against infection. Therefore, investigating host-pathogen interactions is important for understanding pathogenicity and host defensive mechanisms and treating infections. METHODS: In this study, we used omics data, including time-course data from high throughput sequencing, real-time polymerase chain reaction, and human microRNA (miRNA) and protein-protein interaction to construct an interspecies protein-protein and miRNA interaction (PPMI) network of human CD4+ T cells during HIV-1 infection through system modeling and identification...
February 19, 2018: Current HIV Research
https://www.readbyqxmd.com/read/29468660/spatiotemporal-homogeneity-and-distinctness-of-the-t-cell-receptor-%C3%AE-chain-repertoires-in-epstein-barr-virus-associated-primary-and-metastatic-nasopharyngeal-carcinomas
#9
Yih-Lin Chung, Mei-Ling Wu
Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated lymphoepithelioma. The aim of the present study was to characterize the homogeneity and distinctness of the T-cell repertoires within and between primary and metastatic NPCs. We used ultra-deep sequencing of the hypervariably rearranged antigen-binding CDR3 regions of T-cell receptor beta (TCRbeta ) to comprehensively profile the T-cell repertoires in NPC patients receiving definitive chemoradiotherapy with long-term follow-up. We observed not only various spatially heterogeneous patient-specific TCRbeta clone compositions that changed with time but also several commonly enriched TCRbeta subclones that were constantly shared between primary NPCs in the head and neck regions, locally recurrent tumors after treatment, and later-developed distant metastatic tumors in the liver, lung and bone...
February 22, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29468546/detection-of-ccnd1-locus-amplification-by-fluorescence-in-situ-hybridization
#10
Margit Balázs, Viktória Koroknai, István Szász, Szilvia Ecsedi
It is well known that chromosomal aberrations of tumors are associated with the initiation and progression of malignancy. Fluorescence in situ hybridization (FISH) is a powerful, rapid method to detect chromosome copy number and structural alterations in tissue sections, chromosome, or interphase cellular preparations via hybridization of complementary probe sequences. The technique is based on the complementary nature of DNA double strands, which allows fluorescently labeled DNA probes to be used as probes to label the complementary sequences of target cells, chromosomes, and tissues...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29468485/characterization-of-a-novel-breast-cancer-cell-line-derived-from-a-metastatic-bone-lesion-of-a-breast-cancer-patient
#11
Julie Johnson, Darrell C Bessette, Jodi M Saunus, Chanel E Smart, Sarah Song, Rebecca L Johnston, Sibylle Cocciardi, Esdy N Rozali, Cameron N Johnstone, Ana Christina Vargas, Stephen H Kazakoff, Victorian Cancer BioBank, Kum Kum Khanna, Sunil R Lakhani, Georgia Chenevix-Trench, Peter T Simpson, Katia Nones, Nicola Waddell, Fares Al-Ejeh
PURPOSE: We aimed to generate and characterize a novel cell line from a breast cancer bone metastasis to better study the progression of the disease. METHODS: The cell line, P7731, was derived from a metastatic bone lesion of a breast cancer patient and assessed for marker expression. P7731 was analyzed for DNA copy number variation, somatic mutations, and gene expression and was compared with the primary tumor. RESULTS: P7731 cells are negative for estrogen receptor alpha (ERα), progesterone receptor (PR), and HER2 (triple-negative); strongly express vimentin (100% of cells positive) and also express cytokeratins 8/18 and 19 but at lower frequencies...
February 21, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29467591/whole-exome-sequencing-reveals-novel-somatic-alterations-in-neuroblastoma-patients-with-chemotherapy
#12
Chao Duan, Han Wang, Ying Chen, Ping Chu, Tianyu Xing, Chao Gao, Zhixia Yue, Jie Zheng, Mei Jin, Weiyue Gu, Xiaoli Ma
Background: We ought to explore the acquired somatic alterations, shedding light on genetic basis of somatic alterations in NB patients with chemotherapy. Methods: Marrow blood samples from NB patients were collected before treatment, after the 2nd and 4th chemotherapy for baseline research and continuous monitoring by whole exome sequencing. Plasma cell free DNA (cfDNA) was prepared for baseline research. Finger nail cells were extracted as self control. The clinical data was analyzed...
2018: Cancer Cell International
https://www.readbyqxmd.com/read/29467494/alternative-transcription-of-a-shorter-non-anti-angiogenic-thrombospondin-2-variant-in-cancer-associated-blood-vessels
#13
Filip Roudnicky, Sun Young Yoon, Susanna Poghosyan, Simon Schwager, Cedric Poyet, Giorgia Vella, Samia B Bachmann, Sinem Karaman, Jay W Shin, Vivianne I Otto, Michael Detmar
Thrombospondin-2 (TSP2) is an anti-angiogenic matricellular protein that inhibits tumor growth and angiogenesis. Tumor-associated blood vascular endothelial cells (BECs) were isolated from human invasive bladder cancers and from matched normal bladder tissue by immuno-laser capture microdissection. Exon expression profiling analyses revealed a particularly high expression of a short TSP2 transcript containing only the last 9 (3') exons of the full-length TSP2 transcript. Using 5' and 3' RACE (rapid amplification of cDNA ends) and Sanger sequencing, we confirmed the existence of the shorter transcript of TSP2 (sTSP2) and determined its sequence which completely lacked the anti-angiogenic thrombospondin type 1 repeats domain...
February 22, 2018: Oncogene
https://www.readbyqxmd.com/read/29467487/loss-of-heterozygosity-as-a-marker-of-homologous-repair-deficiency-in-multiple-myeloma-a-role-for-parp-inhibition
#14
Charlotte Pawlyn, Andrea Loehr, Cody Ashby, Ruslana Tytarenko, Shayu Deshpande, James Sun, Kyle Fedorchak, Tariq Mughal, Faith E Davies, Brian A Walker, Gareth J Morgan
PARP inhibitors can induce synthetic lethality in tumors characterized by homologous recombination deficiency (HRD), which can be detected by evaluating genome-wide loss of heterozygosity (LOH). Multiple myeloma (MM) is a genetically unstable tumor and we hypothesized that HRD-related LOH (HRD-LOH) could be detected in patient samples, supporting a potential role for PARP inhibition in MM. Using results from targeted next-generation sequencing studies (FoundationOne® Heme), we analyzed HRD-LOH in patients at all disease stages (MGUS (n = 7), smoldering MM (SMM, n = 30), newly diagnosed MM (NDMM, n = 71), treated MM (TRMM, n = 64), and relapsed MM (RLMM, n = 234)) using an algorithm to identify HRD-LOH segments...
February 2, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29467463/bifunctional-immune-checkpoint-targeted-antibody-ligand-traps-that-simultaneously-disable-tgf%C3%AE-enhance-the-efficacy-of-cancer-immunotherapy
#15
Rajani Ravi, Kimberly A Noonan, Vui Pham, Rishi Bedi, Alex Zhavoronkov, Ivan V Ozerov, Eugene Makarev, Artem V Artemov, Piotr T Wysocki, Ranee Mehra, Sridhar Nimmagadda, Luigi Marchionni, David Sidransky, Ivan M Borrello, Evgeny Izumchenko, Atul Bedi
A majority of cancers fail to respond to immunotherapy with antibodies targeting immune checkpoints, such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) or programmed death-1 (PD-1)/PD-1 ligand (PD-L1). Cancers frequently express transforming growth factor-β (TGFβ), which drives immune dysfunction in the tumor microenvironment by inducing regulatory T cells (Tregs) and inhibiting CD8+ and TH 1 cells. To address this therapeutic challenge, we invent bifunctional antibody-ligand traps (Y-traps) comprising an antibody targeting CTLA-4 or PD-L1 fused to a TGFβ receptor II ectodomain sequence that simultaneously disables autocrine/paracrine TGFβ in the target cell microenvironment (a-CTLA4-TGFβRIIecd and a-PDL1-TGFβRIIecd)...
February 21, 2018: Nature Communications
https://www.readbyqxmd.com/read/29467336/frameshift-events-predict-anti-pd-1-l1-response-in-head-and-neck-cancer
#16
Glenn J Hanna, Patrick Lizotte, Megan Cavanaugh, Frank C Kuo, Priyanka Shivdasani, Alexander Frieden, Nicole G Chau, Jonathan D Schoenfeld, Jochen H Lorch, Ravindra Uppaluri, Laura E MacConaill, Robert I Haddad
Programmed cell death protein 1 (PD-1) inhibitors have efficacy in treating squamous cell carcinoma of the head and neck (SCCHN), but objective response rates are low. PD-1 ligand (PD-L1) expression alone is not considered a robust predictor of response and additional biomarkers are needed. This 3-year observational cohort followed 126 SCCHN patients treated with anti-PD-1/L1 therapy. Prior to treatment, 81 (64%) had targeted massively parallel tumor sequencing. Of these, 42 (52%) underwent fluorescence-activated cell sorting and PD-L1 immunohistochemistry for tumor immunoprofiling...
February 22, 2018: JCI Insight
https://www.readbyqxmd.com/read/29467311/epstein-barr-virus-nuclear-antigen-leader-protein-co-activates-ep300
#17
Chong Wang, Hufeng Zhou, Yong Xue, Jun Liang, Yohei Narita, Catherine Gerdt, Amy Y Zheng, Runsheng Jiang, Stephen Trudeau, Chih-Wen Peng, Benjamin Gewurz, Bo Zhao
Epstein-Barr virus nuclear antigen (EBNA) leader protein (EBNALP) is one of the first viral genes expressed upon B-cell infection. EBNALP is essential for EBV-mediated B cell immortalization. EBNALP is thought to function primarily by co-activaing EBNA2-mediated transcription. Chromatin immune precipitation followed by deep-sequencing (ChIP-seq) studies highlight that EBNALP frequently co-occupies DNA sites with host cell transcription factors (TFs), in particular EP300, implicating a broader role in transcription regulation...
February 21, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29467240/identification-isolation-and-characterization-of-human-lgr5-positive-colon-adenoma-cells
#18
Michael K Dame, Durga Attili, Shannon D McClintock, Priya H Dedhia, Peter Ouillette, Olaf Hardt, Alana M Chin, Xiang Xue, Julie Laliberte, Erica L Katz, Gina M Newsome, David R Hill, Alyssa J Miller, Yu-Hwai Tsai, David Agorku, Christopher H Altheim, Andreas Bosio, Becky Simon, Linda C Samuelson, Jay A Stoerker, Henry D Appelman, James Varani, Max S Wicha, Dean E Brenner, Yatrik M Shah, Jason R Spence, Justin A Colacino
The intestine is maintained by stem cells located at the base of crypts and distinguished by the expression of LGR5. Genetically engineered mouse models have provided a wealth of information about intestinal stem cells, while less is known about human intestinal stem cells due to difficulty detecting and isolating these cells. We established an organoid repository from patient-derived adenomas, adenocarcinomas, and normal colon, which we analyzed for variants in 71 colorectal cancer (CRC) associated genes. Normal and neoplastic colon tissue organoids were analyzed by immunohistochemistry and fluorescent-activated cell sorting for LGR5...
February 21, 2018: Development
https://www.readbyqxmd.com/read/29467239/frequency-and-consequence-of-the-recurrent-yy1-p-t372r-mutation-in-sporadic-insulinomas
#19
Vaishali I Parekh, Sita D Modali, James Welch, William Simonds, Lee Scott Weinstein, Electron Kebebew, Sunita K Agarwal
Extract: Pancreatic neuroendocrine tumors (PNETs/pNETs/p-NETs/PanNETs) are rare endocrine neoplasms that can be either functioning tumors that secrete hormones characteristic of their endocrine cell of origin, or nonfunctioning tumors. The most common functioning PNETs are the insulin-secreting b-cell tumors (insulinomas) that are mainly sporadic, but may also occur in 10% of patients with the hereditary tumor syndrome multiple endocrine neoplasia type 1 (MEN1) (OMIM ID: 131100). Patients with the MEN1 syndrome carry a heterozygous germline inactivating mutation in the MEN1 tumor suppressor gene and specific somatic loss of the normal MEN1 allele, leading to endocrine tumors mainly of the parathyroids, pituitary and pancreas (PNETs)...
February 21, 2018: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29466950/hpv-positive-wild-type-tp53-and-p16-overexpression-correlate-with-the-absence-of-residual-tumors-after-chemoradiotherapy-in-anal-squamous-cell-carcinoma
#20
Paulo C Soares, Eliana S Abdelhay, Luiz Claudio S Thuler, Bruno Moreira Soares, Samia Demachki, Gessica Valéria Rocha Ferro, Paulo P Assumpção, Leticia Martins Lamarão, Luis Felipe Ribeiro Pinto, Rommel Mario Rodríguez Burbano
BACKGROUND: Anal residual tumors are consensually identified within six months of chemoradiotherapy and represent a persistent lesion that may have prognostic value for overall survival. The aim of this study was to evaluate the association of HPV and HIV status, p16 expression level and TP53 mutations with the absence of residual tumors (local response) in Squamous Cell Carcinoma (SCC) of the anal canal after chemoradiotherapy. METHODS: We performed a study on 78 patients with SCC of the anal canal who submitted to chemoradiotherapy and were followed for a six-month period to identify the absence or presence of residual tumors...
February 21, 2018: BMC Gastroenterology
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