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"next generation sequencing"

Robert H Press, Chao Zhang, Richard J Cassidy, Matthew J Ferris, Jim Zhong, Conor E Steuer, Rathi N Pillai, Taofeek K Owonikoko, Shannon Kahn, Suresh S Ramalingam, Pretesh R Patel, Walter J Curran, Hui-Kuo G Shu, Gabriel L Sica, Kristin A Higgins
BACKGROUND: Treatment for advanced lung adenocarcinoma (AC) has become increasingly personalized based on molecular results. However, for patients with AC brain metastases (BMs), intracranial outcomes based on molecular subtype and the frequency of molecular aberrations are less well defined. This study sought to report targeted next-generation sequencing results and investigate molecularly based outcomes for patients with AC-BMs treated with radiotherapy. METHODS: The records of 132 patients with AC-BMs treated at Emory University from September 2008 to August 2016 with successful next-generation sequencing were reviewed...
August 18, 2018: Cancer
Valérie Malan, Laurence Bussières, Norbert Winer, Jean-Philippe Jais, Amandine Baptiste, Marc Le Lorc'h, Caroline Elie, Neil O'Gorman, Nicolas Fries, Véronique Houfflin-Debarge, Loic Sentilhes, Michel Vekemans, Yves Ville, Laurent J Salomon
Importance: Cell-free DNA (cfDNA) tests are increasingly being offered to women in the first trimester of pregnancies at a high risk of trisomy 21 to decrease the number of required invasive fetal karyotyping procedures and their associated miscarriages. The effect of this strategy has not been evaluated. Objective: To compare the rates of miscarriage following invasive procedures only in the case of positive cfDNA test results vs immediate invasive testing procedures (amniocentesis or chorionic villus sampling) in women with pregnancies at high risk of trisomy 21 as identified by first-trimester combined screening...
August 14, 2018: JAMA: the Journal of the American Medical Association
Shuolin Li, Sida Liu, Weicheng Chen, Yuan Yuan, Ruoyi Gu, Yangliu Song, Jian Li, Yinyin Cao, Yixiang Lin, Jun Xu, Huijun Wang, Duan Ma, Xiaojing Ma, Wei Sheng, Guoying Huang
Heterotaxy syndrome (HTX) is characterized by left-right (LR) asymmetry disturbances associated with severe heart malformations. However, the exact genetic cause of HTX pathogenesis remains unclear. The aim of this study was to investigate the pathogenic mechanism underlying heterotaxy syndrome. Targeted next-generation sequencing (NGS) was performed for twenty-two candidate genes correlated with LR axis development in sixty-six HTX patients from unrelated families. Variants were filtered from databases and predicted in silico using prediction programs...
August 17, 2018: Scientific Reports
Ji Sun Kim, Ah Reum Kim, Jinyoung Youn, Chung Lee, Nam-Soon Kim, Woong-Yang Park, Jong Kyu Park, Nayoung K D Kim, Jin Whan Cho
INTRODUCTION: Recent advances in next generation sequencing technologies have uncovered the genetic background of various diseases. The mutations in the SYNE1 gene was previously identified as a potential cause of pure cerebellar ataxia. Although autosomal recessive ataxias are slightly more frequent than autosomal dominant forms worldwide, autosomal recessive forms are extremely rare in Korea. In this study, we aimed to identify SYNE1-associated ataxia by whole exome sequencing in a Korean sample, and to review the prevalence of SYNE1 in non-French-Canadians...
August 13, 2018: Parkinsonism & related Disorders
Shujuan Zhou, Bo Xu, Liang Qi, Dongqin Zhu, Baorui Liu, Jia Wei
Cell-free DNA (cfDNA) has been a research hotspot in molecular tumor profiling. In advanced gastric cancer patients, malignant pleural effusion (MPE) and ascites provide a wealth of tumor cells that can be investigated. Here we conducted next-generation sequencing (NGS) on matched cfDNA from plasma, MPE and ascites from a stage-IV gastric cancer patient to identify potential therapeutic targets. In all three samples, we detected an amplification in the cellular-mesenchymal to epithelial transition factor (MET) gene, a truncation mutation in SMAD3 (p...
August 17, 2018: Cancer Biology & Therapy
Lina M Valencia, Amely Martins, Edgardo M Ortiz, Anthony Di Fiore
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods...
2018: PloS One
Saiki Imamura, Hiromi Kanezashi, Tomoko Goshima, Atsushi Suto, You Ueki, Naoko Sugawara, Hiroshi Ito, Bizhen Zou, Chizuko Kawasaki, Tsukasa Okada, Masashi Uema, Mamoru Noda, Keiko Akimoto
The contamination of oysters with human norovirus (HuNoV) poses a human health risk, as oysters are often consumed raw. In this study, the effect of high pressure processing (HPP) on a wide variety of HuNoVs naturally present in aqua-cultured Japanese oysters was determined through a polymerase chain reaction-based method with enzymatic pretreatment, to distinguish between infectious HuNoV. Among five batches, genogroup I. genotype 1 (GI.1), GI.2, GI.3, and GI.8 HuNoV were detected from only one oyster not treated with HPP in the fifth batch, while genogroup II...
August 17, 2018: Foodborne Pathogens and Disease
Dan Peng, Haixia Li, Zhiyuan Wang, Riga Wu, Hongyu Sun
DRB1*14:54:01:04 has 5 nucleotide differences from DRB1*14:54:01:01 at 10,544 (G>A) and 9068 (TGAG insertion). This article is protected by copyright. All rights reserved.
August 16, 2018: HLA
Xiaoli Mi, Gabriel Griffin, Winston Lee, Sanjay Patel, Robert Ohgami, Chi Young Ok, Sa Wang, Julia T Geyer, Wenbin Xiao, Mikhail Roshal, Jacqueline S Garcia, Lewis B Silverman, Stephen E Sallan, Jon C Aster, Marian H Harris, Olga K Weinberg
The B/T subtype of mixed phenotype acute leukemia (B/T MPAL) is defined by co-expression of antigens of both B- and T-cell lineages on leukemic blasts. Although it has been suggested that multilineage antigen expression portends poor response to chemotherapy, the clinical characteristics and driver mutations that underlie the pathogenesis of this rare subtype of acute leukemia are scarcely known. We identified 9 cases of B/T MPAL from multiple institutions and correlated clinical and immunophenotypic findings with next-generation sequencing data...
August 16, 2018: American Journal of Hematology
Shaheen Alanee, Ahmed El-Zawahry, Danuta Dynda, Ali Dabaja, Kevin McVary, Mallory Karr, Andrea Braundmeier-Fleming
INTRODUCTION: There is accumulating evidence that variations in the human microbiota may promote disease states including cancer. Our goal was to examine the association between urinary and fecal microbial profiles and the diagnosis of prostate cancer (PC) in patients undergoing transrectal biopsy of the prostate. MATERIALS AND METHODS: We extracted total DNA from urine and fecal samples collected before a prostate biopsy performed for elevated prostatic specific antigen in patients suspected of having PC...
August 16, 2018: Prostate
N Haddad, L Horth, B Al-Shagour, N Adjlane, W Loucif-Ayad
RNA viruses are associated with honey bee (Apis mellifera) colony losses in many parts of the world. Their consequences may be exacerbated when the ectoparasite mite Varroa destructor is present in hives. While evidence of pathogenic, viral-induced disease is abundant in western honey bees (Apis mellifera mellifera) from many parts of the world, less information exists regarding the pathogen load of Apis mellifera syriaca and Apis mellifera intermissa, honey bees from the Middle East and North Africa (MENA) that play substantial roles in regional beekeeping...
August 16, 2018: Virus Genes
Atsushi Tsuji, Miyuki Kozawa, Koji Tokuda, Toshiki Enomoto, Takashi Koyanagi
The successful production of sake (Japanese rice wine) is brought about by drastic changes in microbial flora and chemical components during fermentation. In the traditional manufacturing process of sake starter (yamahai-moto), spontaneous growth of lactic acid bacteria suppresses inappropriate microorganisms and prepares the optimum environment for the alcohol fermentative yeast. In this study, we analyzed the changes in bacterial flora and chemical components of yamahai-moto. High-throughput next-generation sequencing (NGS) of the 16S ribosomal RNA gene V4 region revealed that various kinds of bacteria, including nitrate-reducing bacteria, existed in the early fermentation stage; however, Lactobacillus sakei then increased drastically to become dominant in the middle stage...
August 16, 2018: Current Microbiology
Shota Nakade, Keiji Mochida, Atsushi Kunii, Kazuki Nakamae, Tomomi Aida, Kohichi Tanaka, Naoaki Sakamoto, Tetsushi Sakuma, Takashi Yamamoto
Selective genome editing such as gene knock-in has recently been achieved by administration of chemical enhancer or inhibitor of particular DNA double-strand break (DSB) repair pathways, as well as overexpression of pathway-specific genes. In this study, we attempt to enhance the efficiency further to secure robust gene knock-ins, by using the local accumulation of DSB repair molecules (LoAD) system. We identify CtIP as a strong enhancer of microhomology-mediated end-joining (MMEJ) repair by genetic screening, and show the knock-in-enhancing effect of CtIP LoADing...
August 16, 2018: Nature Communications
Ya-Ling Hsu, Yi-Jen Chen, Wei-An Chang, Shu-Fang Jian, Hsiao-Li Fan, Jaw-Yuan Wang, Po-Lin Kuo
Crosstalk of a tumor with its microenvironment is a critical factor contributing to cancer development. This study investigates the soluble factors released by tumor-associated dendritic cells (TADCs) responsible for increasing cancer stem cell (CSC) properties, cell mobility, and epithelial-to-mesenchymal transition (EMT). Dendritic cells (DCs) of colon cancer patients were collected for phenotype and CXCL1 expression by flow cytometry and Luminex assays. The transcriptome of CXCL1-treated cancer cells was established by next generation sequencing...
August 16, 2018: International Journal of Molecular Sciences
Jiji T Kurup, Benjamin L Kidder
RNA has been shown to interact with various proteins to regulate chromatin dynamics and gene expression. However, it is unknown whether RNAs associate with epigenetic marks such as post-translational modifications of histones, including histone 4 lysine 20 trimethylation (H4K20me3) or trimethylated histone 3 lysine 4 (H3K4me3), to regulate chromatin and gene expression. Here, we used chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) to survey RNAs associated with H4K20me3 and H3K4me3-marked chromatin on a global-scale in embryonic stem (ES) cells...
August 16, 2018: Journal of Biological Chemistry
Ming-Ju Tsai, Wei-An Chang, Shu-Fang Jian, Kuo-Feng Chang, Chau-Chyun Sheu, Po-Lin Kuo
PURPOSE: Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory airway disease characterized by persistent airflow limitation. Apoptosis of pulmonary structural cells contributes to pulmonary destruction and dysfunction. This study aimed to explore the possible mechanisms underlying decreased cell proliferation and increased apoptosis of bronchial epithelial cells of COPD. MATERIALS AND METHODS: The expression profiles of mRNAs and microRNAs in bronchial epithelial cells from a COPD patient and a normal subject were identified using next-generation sequencing (NGS) and analyzed using bioinformatic tools...
August 7, 2018: Pathology, Research and Practice
Josephine Zimudzi, Jacquie E van der Waals, Teresa A Coutinho, Don A Cowan, Angel Valverde
Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated...
September 2018: Fungal Biology
Tomoya Yokota, Masakuni Serizawa, Ayumu Hosokawa, Kimihide Kusafuka, Keita Mori, Toshiro Sugiyama, Yasuhiro Tsubosa, Yasuhiro Koh
BACKGROUND: Practical and reliable genotyping procedures with a considerable number of samples are required not only for risk-adapted therapeutic strategies, but also for stratifying patients into future clinical trials for molecular-targeting drugs. Recent advances in mutation testing, including next-generation sequencing, have led to the increased use of formalin-fixed paraffin-embedded tissue. We evaluated gene alteration profiles of cancer-related genes in esophageal cancer patients and correlated them with clinicopathological features, such as smoking status and survival outcomes...
August 16, 2018: BMC Cancer
Cecily P Vaughn, José Luis Costa, Harriet E Feilotter, Rosella Petraroli, Varun Bagai, Anna Maria Rachiglio, Federica Zito Marino, Bastiaan Tops, Henriette M Kurth, Kazuko Sakai, Andrea Mafficini, Roy R L Bastien, Anne Reiman, Delphine Le Corre, Alexander Boag, Susan Crocker, Michel Bihl, Astrid Hirschmann, Aldo Scarpa, José Carlos Machado, Hélène Blons, Orla Sheils, Kelli Bramlett, Marjolijn J L Ligtenberg, Ian A Cree, Nicola Normanno, Kazuto Nishio, Pierre Laurent-Puig
BACKGROUND: Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. METHODS: We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples...
August 16, 2018: BMC Cancer
Gaël Nicolas, Rocio Acuna-Hidalgo, Michael J Keogh, Olivier Quenez, Marloes Steehouwer, Stefan Lelieveld, Stéphane Rousseau, Anne-Claire Richard, Manon S Oud, Florent Marguet, Annie Laquerrière, Chris M Morris, Johannes Attems, Colin Smith, Olaf Ansorge, Safa Al Sarraj, Thierry Frebourg, Dominique Campion, Didier Hannequin, David Wallon, Christian Gilissen, Patrick F Chinnery, Joris A Veltman, Alexander Hoischen
INTRODUCTION: A minority of patients with sporadic early-onset Alzheimer's disease (AD) exhibit de novo germ line mutations in the autosomal dominant genes such as APP, PSEN1, or PSEN2. We hypothesized that negatively screened patients may harbor somatic variants in these genes. METHODS: We applied an ultrasensitive approach based on single-molecule molecular inversion probes followed by deep next generation sequencing of 11 genes to 100 brain and 355 blood samples from 445 sporadic patients with AD (>80% exhibited an early onset, <66 years)...
August 13, 2018: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
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